diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 760d9136e47..89a74294bcf 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -646,6 +646,8 @@ jobs:
- name: Install nf-test
uses: nf-core/setup-nf-test@v1
+ with:
+ version: ${{ env.NFTEST_VER }}
- name: Setup apptainer
if: matrix.profile == 'singularity'
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 16c937f2a0b..ae3d4a2c778 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -23,7 +23,7 @@ repos:
- id: renovate-config-validator
# use ruff for python files
- repo: https://github.com/astral-sh/ruff-pre-commit
- rev: v0.6.1
+ rev: v0.6.2
hooks:
- id: ruff
files: \.py$
diff --git a/modules/nf-core/bandage/image/tests/main.nf.test b/modules/nf-core/bandage/image/tests/main.nf.test
new file mode 100644
index 00000000000..160281f9b83
--- /dev/null
+++ b/modules/nf-core/bandage/image/tests/main.nf.test
@@ -0,0 +1,40 @@
+
+nextflow_process {
+
+ name "Test Process BANDAGE_IMAGE"
+ script "../main.nf"
+ process "BANDAGE_IMAGE"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "bandage"
+ tag "bandage/image"
+
+ test("test-bandage-image") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'B-3106' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ file(process.out.png[0][1]).name,
+ file(process.out.svg[0][1]).readLines()[3..7],
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/bandage/image/tests/main.nf.test.snap b/modules/nf-core/bandage/image/tests/main.nf.test.snap
new file mode 100644
index 00000000000..1f260eca921
--- /dev/null
+++ b/modules/nf-core/bandage/image/tests/main.nf.test.snap
@@ -0,0 +1,22 @@
+{
+ "test-bandage-image": {
+ "content": [
+ "B-3106.png",
+ [
+ " xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" version=\"1.2\" baseProfile=\"tiny\">",
+ "
Qt SVG Document",
+ "Generated with Qt",
+ "",
+ ""
+ ],
+ [
+ "versions.yml:md5,443fd5f11eb36f013a1863e66d0eea21"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T15:18:46.613049"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bbmap/bbnorm/meta.yml b/modules/nf-core/bbmap/bbnorm/meta.yml
index 6c8426f88f1..052c5b534d6 100644
--- a/modules/nf-core/bbmap/bbnorm/meta.yml
+++ b/modules/nf-core/bbmap/bbnorm/meta.yml
@@ -10,7 +10,7 @@ tools:
homepage: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/"
documentation: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/"
tool_dev_url: "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbnorm-guide/"
- licence: "BBMap - Bushnell B. - sourceforge.net/projects/bbmap/"
+ licence: ["BBMap - Bushnell B. - sourceforge.net/projects/bbmap/"]
input:
- meta:
type: map
diff --git a/modules/nf-core/bbmap/bbnorm/tests/main.nf.test b/modules/nf-core/bbmap/bbnorm/tests/main.nf.test
new file mode 100644
index 00000000000..fc17dc1c8fa
--- /dev/null
+++ b/modules/nf-core/bbmap/bbnorm/tests/main.nf.test
@@ -0,0 +1,128 @@
+
+nextflow_process {
+
+ name "Test Process BBMAP_BBNORM"
+ script "../main.nf"
+ process "BBMAP_BBNORM"
+ config "./nextflow.config"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "bbmap"
+ tag "bbmap/bbnorm"
+
+ test("test-bbmap-bbnorm-se") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:true ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.fastq[0][1]).linesGzip,
+ file(process.out.log[0][1]).name,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-bbmap-bbnorm-pe") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+ ]
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ process.out.fastq[0][1].collect { path(it).linesGzip[0..1] },
+ file(process.out.log[0][1]).name,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-bbmap-bbnorm-interleaved") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:true ],
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ]
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.fastq[0][1]).linesGzip[3..7],
+ file(process.out.log[0][1]).name,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-bbmap-bbnorm-multiple-input") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [id:'test', single_end:true ],
+ [
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+ ]
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.fastq[0][1]).linesGzip[3..7],
+ file(process.out.log[0][1]).name,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/bbmap/bbnorm/tests/main.nf.test.snap b/modules/nf-core/bbmap/bbnorm/tests/main.nf.test.snap
new file mode 100644
index 00000000000..1d7b2438abd
--- /dev/null
+++ b/modules/nf-core/bbmap/bbnorm/tests/main.nf.test.snap
@@ -0,0 +1,81 @@
+{
+ "test-bbmap-bbnorm-interleaved": {
+ "content": [
+ [
+ "A/AA//EEAEA/E/AEEEE6EE/EEEA/6AEEEEEEEEE6EEEAEAEE//A/EEEEEE//E/E/A//E/E/<
+ all_files << file
+ }
+
+ def all_file_names = all_files.collect { it.name }.toSorted()
+
+ def stable_file_names = [
+ 'chr1_index_k13_c15_b1.block'
+ ]
+
+ def stable_files = all_files.findAll { it.name in stable_file_names }.toSorted()
+
+ assert snapshot(
+ all_file_names,
+ stable_files,
+ process.out.versions[0]
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/bbmap/index/tests/main.nf.test.snap b/modules/nf-core/bbmap/index/tests/main.nf.test.snap
new file mode 100644
index 00000000000..9e691dd41ec
--- /dev/null
+++ b/modules/nf-core/bbmap/index/tests/main.nf.test.snap
@@ -0,0 +1,23 @@
+{
+ "test-bbmap-index": {
+ "content": [
+ [
+ "chr1.chrom.gz",
+ "chr1_index_k13_c15_b1.block",
+ "chr1_index_k13_c15_b1.block2.gz",
+ "info.txt",
+ "scaffolds.txt.gz",
+ "summary.txt"
+ ],
+ [
+ "chr1_index_k13_c15_b1.block:md5,9f0d9a7413c1d2c16cc24555b2381163"
+ ],
+ "versions.yml:md5,00db75f2ebfcae6002a29c49a476dda1"
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T14:41:14.388643"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bbmap/pileup/tests/main.nf.test b/modules/nf-core/bbmap/pileup/tests/main.nf.test
new file mode 100644
index 00000000000..583f407f770
--- /dev/null
+++ b/modules/nf-core/bbmap/pileup/tests/main.nf.test
@@ -0,0 +1,35 @@
+
+nextflow_process {
+
+ name "Test Process BBMAP_PILEUP"
+ script "../main.nf"
+ process "BBMAP_PILEUP"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "bbmap"
+ tag "bbmap/pileup"
+
+ test("test-bbmap-pileup") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/bbmap/pileup/tests/main.nf.test.snap b/modules/nf-core/bbmap/pileup/tests/main.nf.test.snap
new file mode 100644
index 00000000000..f5e7e720d02
--- /dev/null
+++ b/modules/nf-core/bbmap/pileup/tests/main.nf.test.snap
@@ -0,0 +1,55 @@
+{
+ "test-bbmap-pileup": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.coverage.stats.txt:md5,c3fc9d0681589b69e3301ca3cb27b7a4"
+ ]
+ ],
+ "1": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.coverage.hist.txt:md5,96915920ef42ddc9483457dd4585a088"
+ ]
+ ],
+ "2": [
+ "versions.yml:md5,e293e3ed6387ce89f3443050f36fb079"
+ ],
+ "covstats": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.coverage.stats.txt:md5,c3fc9d0681589b69e3301ca3cb27b7a4"
+ ]
+ ],
+ "hist": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.coverage.hist.txt:md5,96915920ef42ddc9483457dd4585a088"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,e293e3ed6387ce89f3443050f36fb079"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T14:33:48.464105"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf
index f73111bb789..c3b8b19652c 100644
--- a/modules/nf-core/bcftools/annotate/main.nf
+++ b/modules/nf-core/bcftools/annotate/main.nf
@@ -8,9 +8,7 @@ process BCFTOOLS_ANNOTATE {
'biocontainers/bcftools:1.20--h8b25389_0' }"
input:
- tuple val(meta), path(input), path(index)
- path(annotations)
- path(annotations_index)
+ tuple val(meta), path(input), path(index), path(annotations), path(annotations_index)
path(header_lines)
output:
diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test b/modules/nf-core/bcftools/annotate/tests/main.nf.test
index fa499de763d..3a5c493314f 100644
--- a/modules/nf-core/bcftools/annotate/tests/main.nf.test
+++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test
@@ -9,20 +9,21 @@ nextflow_process {
tag "bcftools"
tag "bcftools/annotate"
- test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_output") {
+ test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_output") {
config "./vcf.config"
when {
process {
"""
- input[0] = [ [ id:'test', single_end:false ], // meta map
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
- file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)]
-
- input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true)
- input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
- input[3] = []
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+ ]
+ input[1] = []
"""
}
}
@@ -39,20 +40,21 @@ nextflow_process {
}
- test("sarscov2 - [vcf, []] annotation, annotation_tbi, [] - vcf_output") {
+ test("sarscov2 - [vcf, [], annotation, annotation_tbi], [] - vcf_output") {
config "./vcf.config"
when {
process {
"""
- input[0] = [ [ id:'test', single_end:false ], // meta map
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
- []]
-
- input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true)
- input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
- input[3] = []
+ [],
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+ ]
+ input[1] = []
"""
}
}
@@ -68,20 +70,21 @@ nextflow_process {
}
}
- test("sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index") {
+ test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index") {
config "./vcf_gz_index.config"
when {
process {
"""
- input[0] = [ [ id:'test', single_end:false ], // meta map
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
- file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)]
-
- input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true)
- input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
- input[3] = []
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+ ]
+ input[1] = []
"""
}
}
@@ -101,20 +104,21 @@ nextflow_process {
}
- test("sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index_csi") {
+ test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi") {
config "./vcf_gz_index_csi.config"
when {
process {
"""
- input[0] = [ [ id:'test', single_end:false ], // meta map
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
- file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)]
-
- input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true)
- input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
- input[3] = []
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+ ]
+ input[1] = []
"""
}
}
@@ -134,20 +138,21 @@ nextflow_process {
}
- test("sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index_tbi") {
+ test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi") {
config "./vcf_gz_index_tbi.config"
when {
process {
"""
- input[0] = [ [ id:'test', single_end:false ], // meta map
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
- file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)]
-
- input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true)
- input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
- input[3] = []
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+ ]
+ input[1] = []
"""
}
}
@@ -166,20 +171,21 @@ nextflow_process {
}
}
- test("sarscov2 - [vcf, []], annotation, annotation_tbi, header - bcf_output") {
+ test("sarscov2 - [vcf, [], annotation, annotation_tbi], header - bcf_output") {
config "./bcf.config"
when {
process {
"""
- input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
- []])
-
- input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true)
- input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
- input[3] = Channel.of(
+ [],
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+ ]
+ input[1] = Channel.of(
'##INFO=',
'##INFO='
).collectFile(name:"headers.vcf", newLine:true)
@@ -199,7 +205,7 @@ nextflow_process {
}
- test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - stub") {
+ test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - stub") {
config "./vcf.config"
options "-stub"
@@ -207,13 +213,14 @@ nextflow_process {
when {
process {
"""
- input[0] = [ [ id:'test', single_end:false ], // meta map
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
- file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)]
-
- input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true)
- input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
- input[3] = []
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+ ]
+ input[1] = []
"""
}
}
@@ -227,7 +234,7 @@ nextflow_process {
}
- test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index - stub") {
+ test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub") {
config "./vcf_gz_index.config"
options "-stub"
@@ -235,13 +242,14 @@ nextflow_process {
when {
process {
"""
- input[0] = [ [ id:'test', single_end:false ], // meta map
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
- file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)]
-
- input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true)
- input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
- input[3] = []
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+ ]
+ input[1] = []
"""
}
}
@@ -256,7 +264,7 @@ nextflow_process {
}
- test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index_csi - stub") {
+ test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub") {
config "./vcf_gz_index_csi.config"
options "-stub"
@@ -264,13 +272,14 @@ nextflow_process {
when {
process {
"""
- input[0] = [ [ id:'test', single_end:false ], // meta map
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
- file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)]
-
- input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true)
- input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
- input[3] = []
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+ ]
+ input[1] = []
"""
}
}
@@ -285,7 +294,7 @@ nextflow_process {
}
- test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index_tbi - stub") {
+ test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi - stub") {
config "./vcf_gz_index_tbi.config"
options "-stub"
@@ -293,13 +302,14 @@ nextflow_process {
when {
process {
"""
- input[0] = [ [ id:'test', single_end:false ], // meta map
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
- file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)]
-
- input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true)
- input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
- input[3] = []
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true)
+ ]
+ input[1] = []
"""
}
}
diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap
index 8fd8d11dccf..bac2224a3b5 100644
--- a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap
@@ -1,38 +1,5 @@
{
- "sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index_tbi": {
- "content": [
- [
- [
- {
- "id": "test",
- "single_end": false
- },
- "test_vcf.vcf.gz"
- ]
- ],
- [
- [
- {
- "id": "test",
- "single_end": false
- },
- "test_vcf.vcf.gz.tbi"
- ]
- ],
- [
-
- ],
- [
- "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
- ]
- ],
- "meta": {
- "nf-test": "0.8.4",
- "nextflow": "24.04.2"
- },
- "timestamp": "2024-06-12T16:39:23.802873"
- },
- "sarscov2 - [vcf, []] annotation, annotation_tbi, [] - vcf_output": {
+ "bcf": {
"content": [
[
[
@@ -40,7 +7,7 @@
"id": "test",
"single_end": false
},
- "test_vcf.vcf.gz"
+ "test_ann.bcf"
]
],
[
@@ -51,9 +18,9 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-12T16:38:57.039285"
+ "timestamp": "2024-06-12T16:39:33.331888"
},
- "sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index_csi": {
+ "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index": {
"content": [
[
[
@@ -84,9 +51,9 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-12T16:39:15.152697"
+ "timestamp": "2024-08-15T10:07:59.658031137"
},
- "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - stub": {
+ "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub": {
"content": [
{
"0": [
@@ -102,13 +69,25 @@
],
"2": [
-
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
],
"3": [
"versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
],
"csi": [
-
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
],
"tbi": [
@@ -131,9 +110,9 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-12T16:39:41.994785"
+ "timestamp": "2024-08-15T10:09:05.096883418"
},
- "bcf": {
+ "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi": {
"content": [
[
[
@@ -141,7 +120,19 @@
"id": "test",
"single_end": false
},
- "test_ann.bcf"
+ "test_vcf.vcf.gz"
+ ]
+ ],
+ [
+
+ ],
+ [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test_vcf.vcf.gz.csi"
]
],
[
@@ -152,9 +143,9 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-12T16:39:33.331888"
+ "timestamp": "2024-08-15T10:08:10.581301219"
},
- "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index_tbi - stub": {
+ "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - stub": {
"content": [
{
"0": [
@@ -167,13 +158,7 @@
]
],
"1": [
- [
- {
- "id": "test",
- "single_end": false
- },
- "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
- ]
+
],
"2": [
@@ -185,13 +170,7 @@
],
"tbi": [
- [
- {
- "id": "test",
- "single_end": false
- },
- "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
- ]
+
],
"vcf": [
[
@@ -211,9 +190,9 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-12T16:40:13.835994"
+ "timestamp": "2024-08-15T10:08:43.975017625"
},
- "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_output": {
+ "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi": {
"content": [
[
[
@@ -223,6 +202,18 @@
},
"test_vcf.vcf.gz"
]
+ ],
+ [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test_vcf.vcf.gz.tbi"
+ ]
+ ],
+ [
+
],
[
"versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
@@ -232,9 +223,9 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-12T16:38:48.368629"
+ "timestamp": "2024-08-15T10:08:21.354059092"
},
- "sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index": {
+ "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_output": {
"content": [
[
[
@@ -246,15 +237,24 @@
]
],
[
-
- ],
+ "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.2"
+ },
+ "timestamp": "2024-08-15T10:07:37.788393317"
+ },
+ "sarscov2 - [vcf, [], annotation, annotation_tbi], [] - vcf_output": {
+ "content": [
[
[
{
"id": "test",
"single_end": false
},
- "test_vcf.vcf.gz.csi"
+ "test_vcf.vcf.gz"
]
],
[
@@ -265,9 +265,9 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-12T16:39:05.608108"
+ "timestamp": "2024-08-15T10:07:48.500746325"
},
- "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index - stub": {
+ "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi - stub": {
"content": [
{
"0": [
@@ -280,31 +280,31 @@
]
],
"1": [
-
- ],
- "2": [
[
{
"id": "test",
"single_end": false
},
- "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+ "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
]
+ ],
+ "2": [
+
],
"3": [
"versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204"
],
"csi": [
+
+ ],
+ "tbi": [
[
{
"id": "test",
"single_end": false
},
- "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+ "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
]
- ],
- "tbi": [
-
],
"vcf": [
[
@@ -324,9 +324,9 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-12T16:39:54.842082"
+ "timestamp": "2024-08-15T10:09:16.094918834"
},
- "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index_csi - stub": {
+ "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub": {
"content": [
{
"0": [
@@ -383,6 +383,6 @@
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
- "timestamp": "2024-06-12T16:40:04.074052"
+ "timestamp": "2024-08-15T10:08:54.366358502"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/roh/tests/main.nf.test b/modules/nf-core/bcftools/roh/tests/main.nf.test
new file mode 100644
index 00000000000..bb73b80c024
--- /dev/null
+++ b/modules/nf-core/bcftools/roh/tests/main.nf.test
@@ -0,0 +1,67 @@
+
+nextflow_process {
+
+ name "Test Process BCFTOOLS_ROH"
+ script "../main.nf"
+ process "BCFTOOLS_ROH"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "bcftools"
+ tag "bcftools/roh"
+
+ test("test-bcftools-roh") {
+
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
+ ]
+ input[1] = [[],[]]
+ input[2] = []
+ input[3] = []
+ input[4] = []
+ input[5] = []
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("test-bcftools-roh-stub") {
+ options '-stub'
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
+ ]
+ input[1] = [[],[]]
+ input[2] = []
+ input[3] = []
+ input[4] = []
+ input[5] = []
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/bcftools/roh/tests/main.nf.test.snap b/modules/nf-core/bcftools/roh/tests/main.nf.test.snap
new file mode 100644
index 00000000000..3b008a01e98
--- /dev/null
+++ b/modules/nf-core/bcftools/roh/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+ "test-bcftools-roh": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test"
+ },
+ "test.roh:md5,853de778be3030754be40e11be0aa557"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,684b9cddcfaf57299e6e245b12b7d710"
+ ],
+ "roh": [
+ [
+ {
+ "id": "test"
+ },
+ "test.roh:md5,853de778be3030754be40e11be0aa557"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,684b9cddcfaf57299e6e245b12b7d710"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T14:19:06.961553"
+ },
+ "test-bcftools-roh-stub": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test"
+ },
+ "test.roh:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,684b9cddcfaf57299e6e245b12b7d710"
+ ],
+ "roh": [
+ [
+ {
+ "id": "test"
+ },
+ "test.roh:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,684b9cddcfaf57299e6e245b12b7d710"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T14:19:11.161719"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/split/tests/main.nf.test b/modules/nf-core/bcftools/split/tests/main.nf.test
new file mode 100644
index 00000000000..00328b2004c
--- /dev/null
+++ b/modules/nf-core/bcftools/split/tests/main.nf.test
@@ -0,0 +1,40 @@
+
+nextflow_process {
+
+ name "Test Process BCFTOOLS_SPLIT"
+ script "../main.nf"
+ process "BCFTOOLS_SPLIT"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "bcftools"
+ tag "bcftools/split"
+
+ test("test-bcftools-split") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.split_vcf[0][1]).vcf.variantsMD5,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/bcftools/split/tests/main.nf.test.snap b/modules/nf-core/bcftools/split/tests/main.nf.test.snap
new file mode 100644
index 00000000000..c1a3c98578c
--- /dev/null
+++ b/modules/nf-core/bcftools/split/tests/main.nf.test.snap
@@ -0,0 +1,15 @@
+{
+ "test-bcftools-split": {
+ "content": [
+ "ecf3973f634b7baa1c13e60bfb77a174",
+ [
+ "versions.yml:md5,a1c58d82f1e5c0fed394bfb865f57fd9"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T14:16:45.077115"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/beagle5/beagle/meta.yml b/modules/nf-core/beagle5/beagle/meta.yml
index 03b50869270..51b9c6b6997 100644
--- a/modules/nf-core/beagle5/beagle/meta.yml
+++ b/modules/nf-core/beagle5/beagle/meta.yml
@@ -3,13 +3,14 @@ description: Beagle v5.2 is a software package for phasing genotypes and for imp
keywords:
- phasing
- imputation
+ - genotype
tools:
- "beagle5":
description: "Beagle is a software package for phasing genotypes and for imputing ungenotyped markers."
homepage: "https://faculty.washington.edu/browning/beagle/b5_2.html"
documentation: "https://faculty.washington.edu/browning/beagle/beagle_5.2_13Oct21.pdf"
doi: "10.1016/j.ajhg.2021.08.005; doi:10.1016/j.ajhg.2018.07.015"
- licence: "['GPL v3']"
+ licence: ["GPL v3"]
input:
- meta:
type: map
diff --git a/modules/nf-core/beagle5/beagle/tests/main.nf.test b/modules/nf-core/beagle5/beagle/tests/main.nf.test
new file mode 100644
index 00000000000..2763708e273
--- /dev/null
+++ b/modules/nf-core/beagle5/beagle/tests/main.nf.test
@@ -0,0 +1,106 @@
+
+nextflow_process {
+
+ name "Test Process BEAGLE5_BEAGLE"
+ script "../main.nf"
+ process "BEAGLE5_BEAGLE"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "beagle5"
+ tag "beagle5/beagle"
+
+ test("test-beagle5-beagle") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/target.22Jul22.46e.vcf.gz", checkIfExists: true)
+ ]
+ input[1] = []
+ input[2] = []
+ input[3] = []
+ input[4] = []
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.vcf[0][1]).vcf.variantsMD5,
+ file(process.out.log[0][1]).name,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-beagle5-beagle-ref") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/target.22Jul22.46e.vcf.gz", checkIfExists: true)
+ ]
+ input[1] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/ref.22Jul22.46e.vcf.gz", checkIfExists: true)
+ input[2] = []
+ input[3] = []
+ input[4] = []
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.vcf[0][1]).vcf.variantsMD5,
+ file(process.out.log[0][1]).name,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-beagle5-beagle-ref-map") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/target.22Jul22.46e.vcf.gz", checkIfExists: true)
+ ]
+ input[1] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/ref.22Jul22.46e.vcf.gz", checkIfExists: true)
+ input[2] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/plink.chr22.GRCh38.map", checkIfExists: true)
+ input[3] = []
+ input[4] = []
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.vcf[0][1]).vcf.variantsMD5,
+ file(process.out.log[0][1]).name,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/beagle5/beagle/tests/main.nf.test.snap b/modules/nf-core/beagle5/beagle/tests/main.nf.test.snap
new file mode 100644
index 00000000000..e956af5c451
--- /dev/null
+++ b/modules/nf-core/beagle5/beagle/tests/main.nf.test.snap
@@ -0,0 +1,44 @@
+{
+ "test-beagle5-beagle": {
+ "content": [
+ "c64dae0a50a33b6083b8bfa0991f6eb0",
+ "test.bglout.log",
+ [
+ "versions.yml:md5,d2b2dffb6ef6c2a1dd4f718a38c83a48"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T14:14:00.293016"
+ },
+ "test-beagle5-beagle-ref-map": {
+ "content": [
+ "aba50d8debbfe25cd71b50f8fd8f7ce5",
+ "test.bglout.log",
+ [
+ "versions.yml:md5,d2b2dffb6ef6c2a1dd4f718a38c83a48"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T14:14:25.525094"
+ },
+ "test-beagle5-beagle-ref": {
+ "content": [
+ "bd8d96bed907d22e569746f2754f5469",
+ "test.bglout.log",
+ [
+ "versions.yml:md5,d2b2dffb6ef6c2a1dd4f718a38c83a48"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T14:14:13.328146"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bedtools/groupby/tests/main.nf.test b/modules/nf-core/bedtools/groupby/tests/main.nf.test
new file mode 100644
index 00000000000..b7dedcc2aa5
--- /dev/null
+++ b/modules/nf-core/bedtools/groupby/tests/main.nf.test
@@ -0,0 +1,37 @@
+
+nextflow_process {
+
+ name "Test Process BEDTOOLS_GROUPBY"
+ script "../main.nf"
+ process "BEDTOOLS_GROUPBY"
+ config "./nextflow.config"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "bedtools"
+ tag "bedtools/groupby"
+
+ test("test-bedtools-groupby") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true),
+ ]
+ input[1] = 5
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/bedtools/groupby/tests/main.nf.test.snap b/modules/nf-core/bedtools/groupby/tests/main.nf.test.snap
new file mode 100644
index 00000000000..956487d0f5a
--- /dev/null
+++ b/modules/nf-core/bedtools/groupby/tests/main.nf.test.snap
@@ -0,0 +1,37 @@
+{
+ "test-bedtools-groupby": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.grouped.bed:md5,ba080b3d282f206f6312122c71a66745"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,8f48acf848ff45a4fff4e10a806f29f5"
+ ],
+ "bed": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.grouped.bed:md5,ba080b3d282f206f6312122c71a66745"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,8f48acf848ff45a4fff4e10a806f29f5"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T14:10:16.714787"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bedtools/groupby/tests/nextflow.config b/modules/nf-core/bedtools/groupby/tests/nextflow.config
new file mode 100644
index 00000000000..3b6019fb28d
--- /dev/null
+++ b/modules/nf-core/bedtools/groupby/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+ withName: BEDTOOLS_GROUPBY {
+ ext.args = "-g 1"
+ }
+}
diff --git a/modules/nf-core/bedtools/jaccard/tests/main.nf.test b/modules/nf-core/bedtools/jaccard/tests/main.nf.test
new file mode 100644
index 00000000000..839266b5fcc
--- /dev/null
+++ b/modules/nf-core/bedtools/jaccard/tests/main.nf.test
@@ -0,0 +1,66 @@
+
+nextflow_process {
+
+ name "Test Process BEDTOOLS_JACCARD"
+ script "../main.nf"
+ process "BEDTOOLS_JACCARD"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "bedtools"
+ tag "bedtools/jaccard"
+
+ test("test-bedtools-jaccard") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true)
+ ]
+ input[1] = [[],[]]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("test-bedtools-jaccard-genome") {
+
+ config "./nextflow.config"
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true)
+ ]
+ input[1] = [
+ [ id:'genome' ],
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/bedtools/jaccard/tests/main.nf.test.snap b/modules/nf-core/bedtools/jaccard/tests/main.nf.test.snap
new file mode 100644
index 00000000000..4783d48960f
--- /dev/null
+++ b/modules/nf-core/bedtools/jaccard/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+ "test-bedtools-jaccard-genome": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.tsv:md5,b737742026a3b512a494f3aa7935fded"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,4d8267abd99c41fb6056d5162b380d23"
+ ],
+ "tsv": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.tsv:md5,b737742026a3b512a494f3aa7935fded"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,4d8267abd99c41fb6056d5162b380d23"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T14:08:36.70775"
+ },
+ "test-bedtools-jaccard": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.tsv:md5,b737742026a3b512a494f3aa7935fded"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,4d8267abd99c41fb6056d5162b380d23"
+ ],
+ "tsv": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.tsv:md5,b737742026a3b512a494f3aa7935fded"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,4d8267abd99c41fb6056d5162b380d23"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T14:08:32.019101"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bedtools/jaccard/tests/nextflow.config b/modules/nf-core/bedtools/jaccard/tests/nextflow.config
new file mode 100644
index 00000000000..5208fee9b6a
--- /dev/null
+++ b/modules/nf-core/bedtools/jaccard/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+ withName: "BEDTOOLS_JACCARD" {
+ ext.args = "-sorted"
+ }
+}
diff --git a/modules/nf-core/bedtools/makewindows/tests/main.nf.test b/modules/nf-core/bedtools/makewindows/tests/main.nf.test
new file mode 100644
index 00000000000..b27e59b6e04
--- /dev/null
+++ b/modules/nf-core/bedtools/makewindows/tests/main.nf.test
@@ -0,0 +1,58 @@
+
+nextflow_process {
+
+ name "Test Process BEDTOOLS_MAKEWINDOWS"
+ script "../main.nf"
+ process "BEDTOOLS_MAKEWINDOWS"
+ config "./nextflow.config"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "bedtools"
+ tag "bedtools/makewindows"
+
+ test("test-bedtools-makewindows-bed") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test2'],
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("test-bedtools-makewindows-fai") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test2'],
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/bedtools/makewindows/tests/main.nf.test.snap b/modules/nf-core/bedtools/makewindows/tests/main.nf.test.snap
new file mode 100644
index 00000000000..22cfbc17253
--- /dev/null
+++ b/modules/nf-core/bedtools/makewindows/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+ "test-bedtools-makewindows-fai": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test2"
+ },
+ "test2.bed:md5,622d1f62786fe4239b76c53168f21c54"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,f797078cc8b8bac7e6906685d4867be5"
+ ],
+ "bed": [
+ [
+ {
+ "id": "test2"
+ },
+ "test2.bed:md5,622d1f62786fe4239b76c53168f21c54"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,f797078cc8b8bac7e6906685d4867be5"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T14:03:31.430455"
+ },
+ "test-bedtools-makewindows-bed": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test2"
+ },
+ "test2.bed:md5,0cf6ed2b6f470cd44a247da74ca4fe4e"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,f797078cc8b8bac7e6906685d4867be5"
+ ],
+ "bed": [
+ [
+ {
+ "id": "test2"
+ },
+ "test2.bed:md5,0cf6ed2b6f470cd44a247da74ca4fe4e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,f797078cc8b8bac7e6906685d4867be5"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T14:03:27.118372"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bedtools/makewindows/tests/nextflow.config b/modules/nf-core/bedtools/makewindows/tests/nextflow.config
new file mode 100644
index 00000000000..fa16733f166
--- /dev/null
+++ b/modules/nf-core/bedtools/makewindows/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+ withName: BEDTOOLS_MAKEWINDOWS {
+ ext.args = '-w 50 '
+ }
+}
diff --git a/modules/nf-core/bedtools/maskfasta/tests/main.nf.test b/modules/nf-core/bedtools/maskfasta/tests/main.nf.test
new file mode 100644
index 00000000000..14dfc33e31a
--- /dev/null
+++ b/modules/nf-core/bedtools/maskfasta/tests/main.nf.test
@@ -0,0 +1,35 @@
+
+nextflow_process {
+
+ name "Test Process BEDTOOLS_MASKFASTA"
+ script "../main.nf"
+ process "BEDTOOLS_MASKFASTA"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "bedtools"
+ tag "bedtools/maskfasta"
+
+ test("test-bedtools-maskfasta") {
+
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test'],
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+ ]
+ input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/bedtools/maskfasta/tests/main.nf.test.snap b/modules/nf-core/bedtools/maskfasta/tests/main.nf.test.snap
new file mode 100644
index 00000000000..48887161bcb
--- /dev/null
+++ b/modules/nf-core/bedtools/maskfasta/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+ "test-bedtools-maskfasta": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test"
+ },
+ "test.fa:md5,f4f6749698f11074228d2c79338e3b9c"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,441689b51fc99b551e274857bb36445a"
+ ],
+ "fasta": [
+ [
+ {
+ "id": "test"
+ },
+ "test.fa:md5,f4f6749698f11074228d2c79338e3b9c"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,441689b51fc99b551e274857bb36445a"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T13:57:44.016613"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bedtools/multiinter/tests/main.nf.test b/modules/nf-core/bedtools/multiinter/tests/main.nf.test
new file mode 100644
index 00000000000..ed46cf0d3bc
--- /dev/null
+++ b/modules/nf-core/bedtools/multiinter/tests/main.nf.test
@@ -0,0 +1,65 @@
+
+nextflow_process {
+
+ name "Test Process BEDTOOLS_MULTIINTER"
+ script "../main.nf"
+ process "BEDTOOLS_MULTIINTER"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "bedtools"
+ tag "bedtools/multiinter"
+
+ test("test-bedtools-multiinter") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test2.bed', checkIfExists: true)
+ ]
+ ]
+ input[1] = []
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("test-bedtools-multiinter-genome") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test2.bed', checkIfExists: true)
+ ]
+ ]
+ input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true)
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/bedtools/multiinter/tests/main.nf.test.snap b/modules/nf-core/bedtools/multiinter/tests/main.nf.test.snap
new file mode 100644
index 00000000000..14cad906c41
--- /dev/null
+++ b/modules/nf-core/bedtools/multiinter/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+ "test-bedtools-multiinter": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.bed:md5,03d8d889a19cf26e038868775bbcbaa7"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,d50d8662e6ba7227f29713a252d0b51c"
+ ],
+ "bed": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.bed:md5,03d8d889a19cf26e038868775bbcbaa7"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,d50d8662e6ba7227f29713a252d0b51c"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T13:55:57.797405"
+ },
+ "test-bedtools-multiinter-genome": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.bed:md5,03d8d889a19cf26e038868775bbcbaa7"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,d50d8662e6ba7227f29713a252d0b51c"
+ ],
+ "bed": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.bed:md5,03d8d889a19cf26e038868775bbcbaa7"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,d50d8662e6ba7227f29713a252d0b51c"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T13:56:02.192345"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bedtools/shift/tests/main.nf.test b/modules/nf-core/bedtools/shift/tests/main.nf.test
new file mode 100644
index 00000000000..5c251401aea
--- /dev/null
+++ b/modules/nf-core/bedtools/shift/tests/main.nf.test
@@ -0,0 +1,36 @@
+
+nextflow_process {
+
+ name "Test Process BEDTOOLS_SHIFT"
+ script "../main.nf"
+ process "BEDTOOLS_SHIFT"
+ config "./nextflow.config"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "bedtools"
+ tag "bedtools/shift"
+
+ test("test-bedtools-shift") {
+
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test'],
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+ ]
+ input[1] = [[id:'sizes'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true)]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/bedtools/shift/tests/main.nf.test.snap b/modules/nf-core/bedtools/shift/tests/main.nf.test.snap
new file mode 100644
index 00000000000..8d5d6eba419
--- /dev/null
+++ b/modules/nf-core/bedtools/shift/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+ "test-bedtools-shift": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test"
+ },
+ "test_out.bed:md5,fdfa2c33084f1f8e42505076a449afdc"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,1a2d22a8a7a1de74d4316895e2d97701"
+ ],
+ "bed": [
+ [
+ {
+ "id": "test"
+ },
+ "test_out.bed:md5,fdfa2c33084f1f8e42505076a449afdc"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,1a2d22a8a7a1de74d4316895e2d97701"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T13:53:47.543861"
+ }
+}
\ No newline at end of file
diff --git a/tests/modules/nf-core/bedtools/shift/nextflow.config b/modules/nf-core/bedtools/shift/tests/nextflow.config
similarity index 52%
rename from tests/modules/nf-core/bedtools/shift/nextflow.config
rename to modules/nf-core/bedtools/shift/tests/nextflow.config
index 19cf58773f0..229ddd6bf8b 100644
--- a/tests/modules/nf-core/bedtools/shift/nextflow.config
+++ b/modules/nf-core/bedtools/shift/tests/nextflow.config
@@ -1,10 +1,6 @@
process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
withName: BEDTOOLS_SHIFT {
ext.args = '-s 5'
ext.prefix = { "${meta.id}_out" }
}
-
}
diff --git a/modules/nf-core/bedtools/slop/tests/main.nf.test b/modules/nf-core/bedtools/slop/tests/main.nf.test
new file mode 100644
index 00000000000..c8dccc8e6ed
--- /dev/null
+++ b/modules/nf-core/bedtools/slop/tests/main.nf.test
@@ -0,0 +1,36 @@
+
+nextflow_process {
+
+ name "Test Process BEDTOOLS_SLOP"
+ script "../main.nf"
+ process "BEDTOOLS_SLOP"
+ config "./nextflow.config"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "bedtools"
+ tag "bedtools/slop"
+
+ test("test-bedtools-slop") {
+
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test'],
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+ ]
+ input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true)
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/bedtools/slop/tests/main.nf.test.snap b/modules/nf-core/bedtools/slop/tests/main.nf.test.snap
new file mode 100644
index 00000000000..899ac21bac9
--- /dev/null
+++ b/modules/nf-core/bedtools/slop/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+ "test-bedtools-slop": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test"
+ },
+ "test_out.bed:md5,4f1d8924925fe5d205c9e1981fe290a4"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,ee6210f0a2c4a60d9cad324bfe18e0cf"
+ ],
+ "bed": [
+ [
+ {
+ "id": "test"
+ },
+ "test_out.bed:md5,4f1d8924925fe5d205c9e1981fe290a4"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,ee6210f0a2c4a60d9cad324bfe18e0cf"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T13:52:04.945029"
+ }
+}
\ No newline at end of file
diff --git a/tests/modules/nf-core/bedtools/slop/nextflow.config b/modules/nf-core/bedtools/slop/tests/nextflow.config
similarity index 53%
rename from tests/modules/nf-core/bedtools/slop/nextflow.config
rename to modules/nf-core/bedtools/slop/tests/nextflow.config
index 09abb51aabb..fef7548168e 100644
--- a/tests/modules/nf-core/bedtools/slop/nextflow.config
+++ b/modules/nf-core/bedtools/slop/tests/nextflow.config
@@ -1,10 +1,6 @@
process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
withName: BEDTOOLS_SLOP {
ext.args = '-l 15 -r 30'
ext.prefix = { "${meta.id}_out" }
}
-
}
diff --git a/modules/nf-core/bedtools/split/tests/main.nf.test b/modules/nf-core/bedtools/split/tests/main.nf.test
new file mode 100644
index 00000000000..a59891b7936
--- /dev/null
+++ b/modules/nf-core/bedtools/split/tests/main.nf.test
@@ -0,0 +1,36 @@
+
+nextflow_process {
+
+ name "Test Process BEDTOOLS_SPLIT"
+ script "../main.nf"
+ process "BEDTOOLS_SPLIT"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "bedtools"
+ tag "bedtools/split"
+
+ test("test-bedtools-split") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true),
+ 2
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/bedtools/split/tests/main.nf.test.snap b/modules/nf-core/bedtools/split/tests/main.nf.test.snap
new file mode 100644
index 00000000000..359b3aa93b7
--- /dev/null
+++ b/modules/nf-core/bedtools/split/tests/main.nf.test.snap
@@ -0,0 +1,41 @@
+{
+ "test-bedtools-split": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test"
+ },
+ [
+ "test.00001.bed:md5,d58e5e46c2fcc3b8be5db0f023e93cb5",
+ "test.00002.bed:md5,03caf952e9297a54620d2bbba8dc2823"
+ ]
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,33e0d5f886b7f0ed6f9c3e19b049357f"
+ ],
+ "beds": [
+ [
+ {
+ "id": "test"
+ },
+ [
+ "test.00001.bed:md5,d58e5e46c2fcc3b8be5db0f023e93cb5",
+ "test.00002.bed:md5,03caf952e9297a54620d2bbba8dc2823"
+ ]
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,33e0d5f886b7f0ed6f9c3e19b049357f"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T13:50:28.137857"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bedtools/subtract/tests/main.nf.test b/modules/nf-core/bedtools/subtract/tests/main.nf.test
new file mode 100644
index 00000000000..cc4729c8bf2
--- /dev/null
+++ b/modules/nf-core/bedtools/subtract/tests/main.nf.test
@@ -0,0 +1,36 @@
+
+nextflow_process {
+
+ name "Test Process BEDTOOLS_SUBTRACT"
+ script "../main.nf"
+ process "BEDTOOLS_SUBTRACT"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "bedtools"
+ tag "bedtools/subtract"
+
+ test("test-bedtools-subtract") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test_subtract' ],
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/bedtools/subtract/tests/main.nf.test.snap b/modules/nf-core/bedtools/subtract/tests/main.nf.test.snap
new file mode 100644
index 00000000000..1dc0e6e7464
--- /dev/null
+++ b/modules/nf-core/bedtools/subtract/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+ "test-bedtools-subtract": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test_subtract"
+ },
+ "test_subtract.bed:md5,63513c4dc69e8b481ce3b4b2a9f24259"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,1424765d0d00cc3f44f5e7745607effe"
+ ],
+ "bed": [
+ [
+ {
+ "id": "test_subtract"
+ },
+ "test_subtract.bed:md5,63513c4dc69e8b481ce3b4b2a9f24259"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,1424765d0d00cc3f44f5e7745607effe"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T13:47:34.662548"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gatk/unifiedgenotyper/tests/main.nf.test b/modules/nf-core/gatk/unifiedgenotyper/tests/main.nf.test
new file mode 100644
index 00000000000..8d22aabdcfc
--- /dev/null
+++ b/modules/nf-core/gatk/unifiedgenotyper/tests/main.nf.test
@@ -0,0 +1,56 @@
+
+nextflow_process {
+
+ name "Test Process GATK_UNIFIEDGENOTYPER"
+ script "../main.nf"
+ process "GATK_UNIFIEDGENOTYPER"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gatk"
+ tag "gatk/unifiedgenotyper"
+
+ test("test-gatk-unifiedgenotyper") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+ ]
+ input[1] = [
+ [id: 'test'],
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+ ]
+ input[2] = [
+ [id: 'test'],
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+ ]
+ input[3] = [
+ [id: 'test'],
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
+ ]
+ input[4] = [[],[]]
+ input[5] = [[],[]]
+ input[6] = [[],[]]
+ input[7] = [[],[]]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.vcf[0][1]).vcf.variantsMD5,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gatk/unifiedgenotyper/tests/main.nf.test.snap b/modules/nf-core/gatk/unifiedgenotyper/tests/main.nf.test.snap
new file mode 100644
index 00000000000..51c93dc5e63
--- /dev/null
+++ b/modules/nf-core/gatk/unifiedgenotyper/tests/main.nf.test.snap
@@ -0,0 +1,15 @@
+{
+ "test-gatk-unifiedgenotyper": {
+ "content": [
+ "577c77d9323f6256931a6846eaac3f40",
+ [
+ "versions.yml:md5,f0dfc5a0252a665c12a2b27444f73e67"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T13:30:01.119639"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test
new file mode 100644
index 00000000000..f06292f2eed
--- /dev/null
+++ b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test
@@ -0,0 +1,137 @@
+
+nextflow_process {
+
+ name "Test Process GATK4_CALIBRATEDRAGSTRMODEL"
+ script "../main.nf"
+ process "GATK4_CALIBRATEDRAGSTRMODEL"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gatk4"
+ tag "gatk4/calibratedragstrmodel"
+
+ test("test-gatk4-calibratedragstrmodel-bam") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+ ]
+ input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+ input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+ input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+ input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_strtablefile.zip', checkIfExists: true)
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ file(process.out.dragstr_model[0][1]).readLines()[3..7],
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-gatk4-calibratedragstrmodel-cram") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
+ ]
+ input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+ input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+ input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+ input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_strtablefile.zip', checkIfExists: true)
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ file(process.out.dragstr_model[0][1]).readLines()[3..7],
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-gatk4-calibratedragstrmodel-beds") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
+ ]
+ input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+ input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+ input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+ input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_strtablefile.zip', checkIfExists: true)
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ file(process.out.dragstr_model[0][1]).readLines()[3..7],
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-gatk4-calibratedragstrmodel-gzipped-beds") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
+ ]
+ input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+ input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+ input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+ input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_strtablefile.zip', checkIfExists: true)
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ file(process.out.dragstr_model[0][1]).readLines()[3..7],
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap
new file mode 100644
index 00000000000..d0d7b8b9dce
--- /dev/null
+++ b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap
@@ -0,0 +1,78 @@
+{
+ "test-gatk4-calibratedragstrmodel-bam": {
+ "content": [
+ [
+ "# sample = testN",
+ "# readGroups = 1",
+ "# estimatedOrDefaults = defaults",
+ "# commandLine = CalibrateDragstrModel --str-table-path genome_strtablefile.zip --threads 2 --output test.txt --input test.paired_end.sorted.bam --reference genome.fasta --tmp-dir . --gp-values 10:1.0:50 --api-values 0:1.0:40 --gop-values 10:.25:50 --het-to-hom-ratio 2.0 --min-loci-count 50 --api-mono-threshold 3 --max-period 8 --max-repeats 20 --minimum-depth 10 --pileup-padding 5 --sampling-min-mq 20 --parallel false --shard-size 1000000 --down-sample-size 4096 --force-estimation false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",
+ "############################################################################################"
+ ],
+ [
+ "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T13:22:17.584362"
+ },
+ "test-gatk4-calibratedragstrmodel-cram": {
+ "content": [
+ [
+ "# sample = testN",
+ "# readGroups = 1",
+ "# estimatedOrDefaults = defaults",
+ "# commandLine = CalibrateDragstrModel --str-table-path genome_strtablefile.zip --threads 2 --output test.txt --input test.paired_end.sorted.cram --reference genome.fasta --tmp-dir . --gp-values 10:1.0:50 --api-values 0:1.0:40 --gop-values 10:.25:50 --het-to-hom-ratio 2.0 --min-loci-count 50 --api-mono-threshold 3 --max-period 8 --max-repeats 20 --minimum-depth 10 --pileup-padding 5 --sampling-min-mq 20 --parallel false --shard-size 1000000 --down-sample-size 4096 --force-estimation false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",
+ "############################################################################################"
+ ],
+ [
+ "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T13:22:30.21551"
+ },
+ "test-gatk4-calibratedragstrmodel-gzipped-beds": {
+ "content": [
+ [
+ "# sample = testN",
+ "# readGroups = 1",
+ "# estimatedOrDefaults = defaults",
+ "# commandLine = CalibrateDragstrModel --str-table-path genome_strtablefile.zip --threads 2 --output test.txt --input test.paired_end.sorted.cram --reference genome.fasta --tmp-dir . --gp-values 10:1.0:50 --api-values 0:1.0:40 --gop-values 10:.25:50 --het-to-hom-ratio 2.0 --min-loci-count 50 --api-mono-threshold 3 --max-period 8 --max-repeats 20 --minimum-depth 10 --pileup-padding 5 --sampling-min-mq 20 --parallel false --shard-size 1000000 --down-sample-size 4096 --force-estimation false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",
+ "############################################################################################"
+ ],
+ [
+ "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T13:22:53.619871"
+ },
+ "test-gatk4-calibratedragstrmodel-beds": {
+ "content": [
+ [
+ "# sample = testN",
+ "# readGroups = 1",
+ "# estimatedOrDefaults = defaults",
+ "# commandLine = CalibrateDragstrModel --str-table-path genome_strtablefile.zip --threads 2 --output test.txt --input test.paired_end.sorted.cram --reference genome.fasta --tmp-dir . --gp-values 10:1.0:50 --api-values 0:1.0:40 --gop-values 10:.25:50 --het-to-hom-ratio 2.0 --min-loci-count 50 --api-mono-threshold 3 --max-period 8 --max-repeats 20 --minimum-depth 10 --pileup-padding 5 --sampling-min-mq 20 --parallel false --shard-size 1000000 --down-sample-size 4096 --force-estimation false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",
+ "############################################################################################"
+ ],
+ [
+ "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T13:22:41.938548"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test
new file mode 100644
index 00000000000..0832cf85a24
--- /dev/null
+++ b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test
@@ -0,0 +1,104 @@
+
+nextflow_process {
+
+ name "Test Process GATK4_COLLECTREADCOUNTS"
+ script "../main.nf"
+ process "GATK4_COLLECTREADCOUNTS"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gatk4"
+ tag "gatk4/collectreadcounts"
+
+ test("test-gatk4-collectreadcounts-hdf5") {
+
+ config "./nextflow.hdf5.config"
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true),
+ ]
+ input[1] = [[],[]]
+ input[2] = [[],[]]
+ input[3] = [[],[]]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ file(process.out.hdf5[0][1]).name,
+ process.out.tsv,
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-gatk4-collectreadcounts-tsv") {
+
+ config "./nextflow.tsv.config"
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true),
+ ]
+ input[1] = [[],[]]
+ input[2] = [[],[]]
+ input[3] = [[],[]]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("test-gatk4-collectreadcounts-cram") {
+
+ config "./nextflow.cram.config"
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true),
+ ]
+ input[1] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]
+ input[2] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]
+ input[3] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap
new file mode 100644
index 00000000000..28a3a6e151b
--- /dev/null
+++ b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap
@@ -0,0 +1,97 @@
+{
+ "test-gatk4-collectreadcounts-cram": {
+ "content": [
+ {
+ "0": [
+
+ ],
+ "1": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.tsv:md5,d9a32039b7a84f5bb74e8382e5427670"
+ ]
+ ],
+ "2": [
+ "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659"
+ ],
+ "hdf5": [
+
+ ],
+ "tsv": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.tsv:md5,d9a32039b7a84f5bb74e8382e5427670"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T12:58:19.610687"
+ },
+ "test-gatk4-collectreadcounts-hdf5": {
+ "content": [
+ "test.hdf5",
+ [
+
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T13:02:48.607644"
+ },
+ "test-gatk4-collectreadcounts-tsv": {
+ "content": [
+ {
+ "0": [
+
+ ],
+ "1": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.tsv:md5,8e45a6164916c303387f39f02ce45841"
+ ]
+ ],
+ "2": [
+ "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659"
+ ],
+ "hdf5": [
+
+ ],
+ "tsv": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.tsv:md5,8e45a6164916c303387f39f02ce45841"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T12:58:07.500024"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/collectreadcounts/tests/nextflow.cram.config b/modules/nf-core/gatk4/collectreadcounts/tests/nextflow.cram.config
new file mode 100644
index 00000000000..682bdcad1e5
--- /dev/null
+++ b/modules/nf-core/gatk4/collectreadcounts/tests/nextflow.cram.config
@@ -0,0 +1,5 @@
+process {
+ withName: 'GATK4_COLLECTREADCOUNTS' {
+ ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY"
+ }
+}
diff --git a/modules/nf-core/gatk4/collectreadcounts/tests/nextflow.hdf5.config b/modules/nf-core/gatk4/collectreadcounts/tests/nextflow.hdf5.config
new file mode 100644
index 00000000000..d6ca881b7e3
--- /dev/null
+++ b/modules/nf-core/gatk4/collectreadcounts/tests/nextflow.hdf5.config
@@ -0,0 +1,5 @@
+process {
+ withName: 'GATK4_COLLECTREADCOUNTS'{
+ ext.args = "--interval-merging-rule OVERLAPPING_ONLY"
+ }
+}
diff --git a/modules/nf-core/gatk4/collectreadcounts/tests/nextflow.tsv.config b/modules/nf-core/gatk4/collectreadcounts/tests/nextflow.tsv.config
new file mode 100644
index 00000000000..682bdcad1e5
--- /dev/null
+++ b/modules/nf-core/gatk4/collectreadcounts/tests/nextflow.tsv.config
@@ -0,0 +1,5 @@
+process {
+ withName: 'GATK4_COLLECTREADCOUNTS' {
+ ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY"
+ }
+}
diff --git a/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test
new file mode 100644
index 00000000000..308fc7f678e
--- /dev/null
+++ b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test
@@ -0,0 +1,121 @@
+
+nextflow_process {
+
+ name "Test Process GATK4_COLLECTSVEVIDENCE"
+ script "../main.nf"
+ process "GATK4_COLLECTSVEVIDENCE"
+ config "./nextflow.config"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gatk4"
+ tag "gatk4/collectsvevidence"
+
+ test("test-gatk4-collectsvevidence-cram") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
+ [],
+ []
+ ]
+ input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+ input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+ input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.split_read_evidence[0][1]).linesGzip[0],
+ file(process.out.split_read_evidence_index[0][1]).name,
+ path(process.out.paired_end_evidence[0][1]).linesGzip[0],
+ file(process.out.paired_end_evidence_index[0][1]).name,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-gatk4-collectsvevidence-bam") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+ [],
+ []
+ ]
+ input[1] = []
+ input[2] = []
+ input[3] = []
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.split_read_evidence[0][1]).linesGzip[0],
+ file(process.out.split_read_evidence_index[0][1]).name,
+ path(process.out.paired_end_evidence[0][1]).linesGzip[0],
+ file(process.out.paired_end_evidence_index[0][1]).name,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-gatk4-collectsvevidence-allele-count") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true)
+ ]
+ input[1] = []
+ input[2] = []
+ input[3] = []
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.split_read_evidence[0][1]).linesGzip[0],
+ file(process.out.split_read_evidence_index[0][1]).name,
+ path(process.out.paired_end_evidence[0][1]).linesGzip[0],
+ file(process.out.paired_end_evidence_index[0][1]).name,
+ path(process.out.site_depths[0][1]).linesGzip[0],
+ file(process.out.site_depths_index[0][1]).name,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap
new file mode 100644
index 00000000000..5143cf3c0be
--- /dev/null
+++ b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap
@@ -0,0 +1,52 @@
+{
+ "test-gatk4-collectsvevidence-cram": {
+ "content": [
+ "chr22\t2008\tleft\t1\tnormal",
+ "test.sr.txt.gz.tbi",
+ "chr22\t3320\t+\tchr22\t3482\t-\tnormal",
+ "test.pe.txt.gz.tbi",
+ [
+ "versions.yml:md5,eb641a78898f7bfe135ef01b77647079"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T12:51:11.44656"
+ },
+ "test-gatk4-collectsvevidence-allele-count": {
+ "content": [
+ "chr22\t2008\tleft\t1\tnormal",
+ "test.sr.txt.gz.tbi",
+ "chr22\t3320\t+\tchr22\t3482\t-\tnormal",
+ "test.pe.txt.gz.tbi",
+ "chr22\t1981\tnormal\t235\t0\t48\t0",
+ "test.sd.txt.gz.tbi",
+ [
+ "versions.yml:md5,eb641a78898f7bfe135ef01b77647079"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T12:48:13.663238"
+ },
+ "test-gatk4-collectsvevidence-bam": {
+ "content": [
+ "chr22\t2008\tleft\t1\tnormal",
+ "test.sr.txt.gz.tbi",
+ "chr22\t3320\t+\tchr22\t3482\t-\tnormal",
+ "test.pe.txt.gz.tbi",
+ [
+ "versions.yml:md5,eb641a78898f7bfe135ef01b77647079"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T12:51:22.087808"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/collectsvevidence/tests/nextflow.config b/modules/nf-core/gatk4/collectsvevidence/tests/nextflow.config
new file mode 100644
index 00000000000..ca7c056227f
--- /dev/null
+++ b/modules/nf-core/gatk4/collectsvevidence/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+ withName: GATK4_COLLECTSVEVIDENCE {
+ ext.args = "--sample-name normal"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test
new file mode 100644
index 00000000000..7d066cf1ffb
--- /dev/null
+++ b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test
@@ -0,0 +1,38 @@
+
+nextflow_process {
+
+ name "Test Process GATK4_COMPOSESTRTABLEFILE"
+ script "../main.nf"
+ process "GATK4_COMPOSESTRTABLEFILE"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gatk4"
+ tag "gatk4/composestrtablefile"
+
+ test("test-gatk4-composestrtablefile") {
+
+ when {
+ process {
+ """
+ input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+ input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+ input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ file(process.out.str_table[0]).name,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap
new file mode 100644
index 00000000000..02136a8b365
--- /dev/null
+++ b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap
@@ -0,0 +1,15 @@
+{
+ "test-gatk4-composestrtablefile": {
+ "content": [
+ "genome.zip",
+ [
+ "versions.yml:md5,755f9a44a99148151b624d70eb6ce260"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T13:37:10.366333"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test
new file mode 100644
index 00000000000..0f65f542891
--- /dev/null
+++ b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test
@@ -0,0 +1,44 @@
+
+nextflow_process {
+
+ name "Test Process GATK4_CONDENSEDEPTHEVIDENCE"
+ script "../main.nf"
+ process "GATK4_CONDENSEDEPTHEVIDENCE"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gatk4"
+ tag "gatk4/condensedepthevidence"
+
+ test("test-gatk4-condensdepthevidence") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/condensedepthevidence/testN.rd.txt.gz", checkIfExists: true),
+ file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/condensedepthevidence/testN.rd.txt.gz.tbi", checkIfExists: true)
+ ]
+ input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+ input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+ input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.condensed_evidence[0][1]).linesGzip[0..1],
+ file(process.out.condensed_evidence_index[0][1]).name,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap
new file mode 100644
index 00000000000..d8da0978b2b
--- /dev/null
+++ b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap
@@ -0,0 +1,19 @@
+{
+ "test-gatk4-condensdepthevidence": {
+ "content": [
+ [
+ "#Chr\tStart\tEnd\ttestN",
+ "chr22\t0\t40001\t5642"
+ ],
+ "test.rd.txt.gz.tbi",
+ [
+ "versions.yml:md5,d1d29007b92a10b3e50bdd25335013a8"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T12:33:21.910858"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test
new file mode 100644
index 00000000000..2e3688a779d
--- /dev/null
+++ b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test
@@ -0,0 +1,64 @@
+
+nextflow_process {
+
+ name "Test Process GATK4_FASTQTOSAM"
+ script "../main.nf"
+ process "GATK4_FASTQTOSAM"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gatk4"
+ tag "gatk4/fastqtosam"
+
+ test("test-gatk4-fastqtosam-single-end") {
+
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test', single_end:true ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ bam(process.out.bam[0][1]).getReadsMD5(),
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-gatk4-fastqtosam-paired-end") {
+
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ bam(process.out.bam[0][1]).getReadsMD5(),
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap
new file mode 100644
index 00000000000..554480a24b7
--- /dev/null
+++ b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap
@@ -0,0 +1,28 @@
+{
+ "test-gatk4-fastqtosam-single-end": {
+ "content": [
+ "e6a4aa204d980e177a0458596f0a70ac",
+ [
+ "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T12:29:12.362942"
+ },
+ "test-gatk4-fastqtosam-paired-end": {
+ "content": [
+ "e6a4aa204d980e177a0458596f0a70ac",
+ [
+ "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T12:29:22.385798"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/filterintervals/tests/main.nf.test b/modules/nf-core/gatk4/filterintervals/tests/main.nf.test
new file mode 100644
index 00000000000..a84f562e394
--- /dev/null
+++ b/modules/nf-core/gatk4/filterintervals/tests/main.nf.test
@@ -0,0 +1,38 @@
+
+nextflow_process {
+
+ name "Test Process GATK4_FILTERINTERVALS"
+ script "../main.nf"
+ process "GATK4_FILTERINTERVALS"
+ config "./nextflow.config"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gatk4"
+ tag "gatk4/filterintervals"
+
+ test("test-gatk4-filterintervals") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.preprocessed_intervals.interval_list', checkIfExists: true)
+ ]
+ input[1] = [ [:], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.preprocessed_intervals.counts.tsv', checkIfExists: true) ] ]
+ input[2] = [ [:], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.annotated_intervals.tsv', checkIfExists: true) ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap
new file mode 100644
index 00000000000..c9626666948
--- /dev/null
+++ b/modules/nf-core/gatk4/filterintervals/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+ "test-gatk4-filterintervals": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test"
+ },
+ "test.interval_list:md5,67b15dff732693db3542e6b1dc30a5da"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,9a445090a815c06982d5deb5ed7d5e30"
+ ],
+ "interval_list": [
+ [
+ {
+ "id": "test"
+ },
+ "test.interval_list:md5,67b15dff732693db3542e6b1dc30a5da"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,9a445090a815c06982d5deb5ed7d5e30"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T12:25:35.933532"
+ }
+}
\ No newline at end of file
diff --git a/tests/modules/nf-core/gatk4/filterintervals/nextflow.config b/modules/nf-core/gatk4/filterintervals/tests/nextflow.config
similarity index 51%
rename from tests/modules/nf-core/gatk4/filterintervals/nextflow.config
rename to modules/nf-core/gatk4/filterintervals/tests/nextflow.config
index 7cdcd35fb86..93ea379c8d4 100644
--- a/tests/modules/nf-core/gatk4/filterintervals/nextflow.config
+++ b/modules/nf-core/gatk4/filterintervals/tests/nextflow.config
@@ -1,9 +1,5 @@
process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
withName: GATK4_FILTERINTERVALS {
ext.args = "--interval-merging-rule OVERLAPPING_ONLY"
}
-
}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test b/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test
new file mode 100644
index 00000000000..173b149b547
--- /dev/null
+++ b/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test
@@ -0,0 +1,60 @@
+
+nextflow_process {
+
+ name "Test Process GATK4_GATHERBQSRREPORTS"
+ script "../main.nf"
+ process "GATK4_GATHERBQSRREPORTS"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gatk4"
+ tag "gatk4/gatherbqsrreports"
+
+ test("test-gatk4-gatherbqsrreports") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("test-gatk4-gatherbqsrreports-multiple") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table', checkIfExists: true)
+ ]
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap b/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap
new file mode 100644
index 00000000000..bc5d4bd1332
--- /dev/null
+++ b/modules/nf-core/gatk4/gatherbqsrreports/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+ "test-gatk4-gatherbqsrreports-multiple": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.table:md5,0c1257eececf95db8ca378272d0f21f9"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0"
+ ],
+ "table": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.table:md5,0c1257eececf95db8ca378272d0f21f9"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T12:22:34.490694"
+ },
+ "test-gatk4-gatherbqsrreports": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.table:md5,9603b69fdc3b5090de2e0dd78bfcc4bf"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0"
+ ],
+ "table": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.table:md5,9603b69fdc3b5090de2e0dd78bfcc4bf"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,413fc0014d5dc41ab67d65f59f61a4a0"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T12:22:10.552951"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf
index 561e9bb8b88..c784d59ab26 100644
--- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf
+++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf
@@ -14,7 +14,7 @@ process GATK4_GATHERPILEUPSUMMARIES {
output:
tuple val(meta), path("*.pileups.table"), emit: table
- path "versions.yml" , emit: versions
+ path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test
new file mode 100644
index 00000000000..8497e64db37
--- /dev/null
+++ b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test
@@ -0,0 +1,37 @@
+
+nextflow_process {
+
+ name "Test Process GATK4_GATHERPILEUPSUMMARIES"
+ script "../main.nf"
+ process "GATK4_GATHERPILEUPSUMMARIES"
+ config "./nextflow.config"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gatk4"
+ tag "gatk4/gatherpileupsummaries"
+
+ test("test-gatk4-gatherpileupsummaries") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.pileups.table', checkIfExists: true) ]
+ ]
+ input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap
new file mode 100644
index 00000000000..f05a7ef0d11
--- /dev/null
+++ b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap
@@ -0,0 +1,37 @@
+{
+ "test-gatk4-gatherpileupsummaries": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.out.pileups.table:md5,8e0ca6f66e112bd2f7ec1d31a2d62469"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02"
+ ],
+ "table": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.out.pileups.table:md5,8e0ca6f66e112bd2f7ec1d31a2d62469"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T12:18:40.835226"
+ }
+}
\ No newline at end of file
diff --git a/tests/modules/nf-core/gatk4/gatherpileupsummaries/nextflow.config b/modules/nf-core/gatk4/gatherpileupsummaries/tests/nextflow.config
similarity index 51%
rename from tests/modules/nf-core/gatk4/gatherpileupsummaries/nextflow.config
rename to modules/nf-core/gatk4/gatherpileupsummaries/tests/nextflow.config
index 48afc706e6c..2b49a6fa39d 100644
--- a/tests/modules/nf-core/gatk4/gatherpileupsummaries/nextflow.config
+++ b/modules/nf-core/gatk4/gatherpileupsummaries/tests/nextflow.config
@@ -1,7 +1,4 @@
process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
withName: 'GATK4_GATHERPILEUPSUMMARIES' {
ext.prefix = { "${meta.id}.out" }
}
diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test b/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test
new file mode 100644
index 00000000000..bffe02e4f6c
--- /dev/null
+++ b/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test
@@ -0,0 +1,38 @@
+
+nextflow_process {
+
+ name "Test Process GATK4_LEARNREADORIENTATIONMODEL"
+ script "../main.nf"
+ process "GATK4_LEARNREADORIENTATIONMODEL"
+ config "./nextflow.config"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gatk4"
+ tag "gatk4/learnreadorientationmodel"
+
+ test("test-gatk4-learnreadorientationmodel") {
+
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test' ], // meta map
+ [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz', checkIfExists: true)] ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.artifactprior[0][1]).linesGzip[3..7],
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test.snap b/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test.snap
new file mode 100644
index 00000000000..b829bd9c4aa
--- /dev/null
+++ b/modules/nf-core/gatk4/learnreadorientationmodel/tests/main.nf.test.snap
@@ -0,0 +1,21 @@
+{
+ "test-gatk4-learnreadorientationmodel": {
+ "content": [
+ [
+ "CTT\tAAG\t2.7114986684474486E-6\t3.2076972826656866E-5\t2.6085822355549755E-6\t0.0\t2.6371799896540086E-6\t3.3869355267901446E-6\t2.6085822355549755E-6\t0.0\t0.9995881552107633\t4.6590850211691583E-5\t2.8848017683240004E-4\t3.0744010710100574E-5\t38334\t116",
+ "GTT\tAAC\t0.1\t0.1\t0.1\t0.0\t0.1\t0.1\t0.1\t0.0\t0.1\t0.1\t0.1\t0.1\t0\t0",
+ "TAT\tATA\t0.0\t5.548307163536064E-6\t5.144357865084592E-6\t6.205892051757818E-6\t0.0\t5.907388162200423E-6\t5.176730417709638E-6\t6.083872804985981E-6\t0.9924019419831304\t3.946972069386949E-5\t0.007516612822150651\t7.908925559851714E-6\t19439\t95",
+ "AAA\tTTT\t0.0\t1.7634470563520664E-6\t2.8327478284981175E-6\t1.8084237600021914E-6\t0.0\t1.7692606885284446E-6\t2.263339968296726E-6\t1.8660094002474611E-6\t0.9990845693211764\t1.8004690536795885E-5\t8.701192700921183E-4\t1.5003489492700572E-5\t56708\t130",
+ "CAA\tTTG\t0.0\t3.4445551925564533E-6\t3.435193155024585E-6\t5.139879646597498E-6\t0.0\t3.4674461103560476E-6\t3.428570449688764E-6\t6.343168047383713E-6\t0.9945238954147358\t1.3629167993931722E-4\t0.0052793454402581125\t3.5208652465150646E-5\t29263\t197"
+ ],
+ [
+ "versions.yml:md5,88928ff140a0967e574e66944fd2a2f2"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T12:16:08.296564"
+ }
+}
\ No newline at end of file
diff --git a/tests/modules/nf-core/gatk4/learnreadorientationmodel/nextflow.config b/modules/nf-core/gatk4/learnreadorientationmodel/tests/nextflow.config
similarity index 52%
rename from tests/modules/nf-core/gatk4/learnreadorientationmodel/nextflow.config
rename to modules/nf-core/gatk4/learnreadorientationmodel/tests/nextflow.config
index 463e2d54932..79e4f67df3e 100644
--- a/tests/modules/nf-core/gatk4/learnreadorientationmodel/nextflow.config
+++ b/modules/nf-core/gatk4/learnreadorientationmodel/tests/nextflow.config
@@ -1,9 +1,5 @@
process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
withName: GATK4_LEARNREADORIENTATIONMODEL {
ext.prefix = { "${meta.id}.artifact-prior" }
}
-
}
diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test
new file mode 100644
index 00000000000..581d730e5ac
--- /dev/null
+++ b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test
@@ -0,0 +1,76 @@
+
+nextflow_process {
+
+ name "Test Process GATK4_LEFTALIGNANDTRIMVARIANTS"
+ script "../main.nf"
+ process "GATK4_LEFTALIGNANDTRIMVARIANTS"
+ config "./nextflow.config"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gatk4"
+ tag "gatk4/leftalignandtrimvariants"
+
+ test("test-gatk4-leftalignandtrimvariants-interval") {
+
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true),
+ ]
+ input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+ input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+ input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.vcf[0][1]).vcf.summary,
+ file(process.out.tbi[0][1]).name,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-gatk4-leftalignandtrimvariants-no-interval") {
+
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
+ []
+ ]
+ input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+ input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+ input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.vcf[0][1]).vcf.variantsMD5,
+ file(process.out.tbi[0][1]).name,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test.snap b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test.snap
new file mode 100644
index 00000000000..f500c0dcc08
--- /dev/null
+++ b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/main.nf.test.snap
@@ -0,0 +1,30 @@
+{
+ "test-gatk4-leftalignandtrimvariants-no-interval": {
+ "content": [
+ "85745045e9c55d3846d80bfde08a7d34",
+ "test.normalised.vcf.gz.tbi",
+ [
+ "versions.yml:md5,2c2a0a8745e7517e028d257d39b07d61"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T12:09:35.03744"
+ },
+ "test-gatk4-leftalignandtrimvariants-interval": {
+ "content": [
+ "VcfFile [chromosomes=[], sampleCount=1, variantCount=0, phased=true, phasedAutodetect=true]",
+ "test.normalised.vcf.gz.tbi",
+ [
+ "versions.yml:md5,2c2a0a8745e7517e028d257d39b07d61"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T12:11:42.893725"
+ }
+}
\ No newline at end of file
diff --git a/tests/modules/nf-core/gatk4/leftalignandtrimvariants/nextflow.config b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/nextflow.config
similarity index 65%
rename from tests/modules/nf-core/gatk4/leftalignandtrimvariants/nextflow.config
rename to modules/nf-core/gatk4/leftalignandtrimvariants/tests/nextflow.config
index 56fcee59a9a..dfe16334636 100644
--- a/tests/modules/nf-core/gatk4/leftalignandtrimvariants/nextflow.config
+++ b/modules/nf-core/gatk4/leftalignandtrimvariants/tests/nextflow.config
@@ -1,7 +1,4 @@
process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
withName: 'GATK4_LEFTALIGNANDTRIMVARIANTS' {
ext.args = "--split-multi-allelics --dont-trim-alleles --keep-original-ac"
ext.prefix = { "${meta.id}.normalised" }
diff --git a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test
new file mode 100644
index 00000000000..96e93bb1995
--- /dev/null
+++ b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test
@@ -0,0 +1,73 @@
+
+nextflow_process {
+
+ name "Test Process GATK4_MERGEBAMALIGNMENT"
+ script "../main.nf"
+ process "GATK4_MERGEBAMALIGNMENT"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gatk4"
+ tag "gatk4/mergebamalignment"
+
+ test("test-gatk4-mergebamalignment") {
+
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.unaligned.bam', checkIfExists: true)
+ ]
+ input[1] = [ [ id:'genome' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+ ]
+ input[2] = [ [ id:'genome' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ bam(process.out.bam[0][1]).getReadsMD5(),
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-gatk4-mergebamalignment-stubs") {
+ options '-stub'
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.unaligned.bam', checkIfExists: true)
+ ]
+ input[1] = [ [ id:'genome' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+ ]
+ input[2] = [ [ id:'genome' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap
new file mode 100644
index 00000000000..719a7bb3311
--- /dev/null
+++ b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap
@@ -0,0 +1,48 @@
+{
+ "test-gatk4-mergebamalignment-stubs": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test"
+ },
+ "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,a72cfce8c9d171260cbb82b492be4372"
+ ],
+ "bam": [
+ [
+ {
+ "id": "test"
+ },
+ "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,a72cfce8c9d171260cbb82b492be4372"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T12:02:15.41024"
+ },
+ "test-gatk4-mergebamalignment": {
+ "content": [
+ "30c325e1e032eb1782a280d34c0fb1c7",
+ [
+ "versions.yml:md5,a72cfce8c9d171260cbb82b492be4372"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T12:02:08.379035"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test b/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test
new file mode 100644
index 00000000000..a546fac5aa3
--- /dev/null
+++ b/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test
@@ -0,0 +1,49 @@
+
+nextflow_process {
+
+ name "Test Process GATK4_PREPROCESSINTERVALS"
+ script "../main.nf"
+ process "GATK4_PREPROCESSINTERVALS"
+ config "./nextflow.config"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gatk4"
+ tag "gatk4/preprocessintervals"
+
+ test("test-gatk4-preprocessintervals") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+ ]
+ input[1] = [
+ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+ ]
+ input[2] = [
+ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+ ]
+ input[3] = [[],[]]
+ input[4] = [
+ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.blacklist_intervals.bed', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test.snap
new file mode 100644
index 00000000000..5365291dab8
--- /dev/null
+++ b/modules/nf-core/gatk4/preprocessintervals/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+ "test-gatk4-preprocessintervals": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test"
+ },
+ "test.interval_list:md5,ce14b8fb47a60483fe44473ba40e1583"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,fc3037804d90d3d3424047cfac85d5e4"
+ ],
+ "interval_list": [
+ [
+ {
+ "id": "test"
+ },
+ "test.interval_list:md5,ce14b8fb47a60483fe44473ba40e1583"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,fc3037804d90d3d3424047cfac85d5e4"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T11:58:51.314382"
+ }
+}
\ No newline at end of file
diff --git a/tests/modules/nf-core/gatk4/preprocessintervals/nextflow.config b/modules/nf-core/gatk4/preprocessintervals/tests/nextflow.config
similarity index 53%
rename from tests/modules/nf-core/gatk4/preprocessintervals/nextflow.config
rename to modules/nf-core/gatk4/preprocessintervals/tests/nextflow.config
index b1fa3d68db9..a53707fb36a 100644
--- a/tests/modules/nf-core/gatk4/preprocessintervals/nextflow.config
+++ b/modules/nf-core/gatk4/preprocessintervals/tests/nextflow.config
@@ -1,9 +1,5 @@
process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
withName: GATK4_PREPROCESSINTERVALS {
ext.args = "--padding 0 --interval-merging-rule OVERLAPPING_ONLY"
}
-
}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/printreads/tests/main.nf.test b/modules/nf-core/gatk4/printreads/tests/main.nf.test
new file mode 100644
index 00000000000..c0788619700
--- /dev/null
+++ b/modules/nf-core/gatk4/printreads/tests/main.nf.test
@@ -0,0 +1,95 @@
+
+nextflow_process {
+
+ name "Test Process GATK4_PRINTREADS"
+ script "../main.nf"
+ process "GATK4_PRINTREADS"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gatk4"
+ tag "gatk4/printreads"
+
+ test("test-gatk4-printreads-bam") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+ ]
+
+ input[1] = [ [ id:'genome' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+ ]
+
+ input[2] = [ [ id:'genome' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+ ]
+
+ input[3] = [ [ id:'genome' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ bam(process.out.bam[0][1]).getReadsMD5(),
+ process.out.cram,
+ process.out.sam,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-gatk4-printreads-cram") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true)
+ ]
+
+ input[1] = [ [ id:'genome' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+ ]
+
+ input[2] = [ [ id:'genome' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+ ]
+
+ input[3] = [ [ id:'genome' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ process.out.bam,
+ bam(process.out.cram[0][1]).getHeaderMD5(),
+ process.out.sam,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap b/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap
new file mode 100644
index 00000000000..7f1266f2641
--- /dev/null
+++ b/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap
@@ -0,0 +1,40 @@
+{
+ "test-gatk4-printreads-bam": {
+ "content": [
+ "894549ee3ced6b5ca2eed2563a985217",
+ [
+
+ ],
+ [
+
+ ],
+ [
+ "versions.yml:md5,9b368270d802ed95c530a7f0105f6453"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T11:48:53.871683"
+ },
+ "test-gatk4-printreads-cram": {
+ "content": [
+ [
+
+ ],
+ "591299d00e262474250c5ccc241bba59",
+ [
+
+ ],
+ [
+ "versions.yml:md5,9b368270d802ed95c530a7f0105f6453"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T13:42:29.968056"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/revertsam/tests/main.nf.test b/modules/nf-core/gatk4/revertsam/tests/main.nf.test
new file mode 100644
index 00000000000..b5268048587
--- /dev/null
+++ b/modules/nf-core/gatk4/revertsam/tests/main.nf.test
@@ -0,0 +1,59 @@
+
+nextflow_process {
+
+ name "Test Process GATK4_REVERTSAM"
+ script "../main.nf"
+ process "GATK4_REVERTSAM"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gatk4"
+ tag "gatk4/revertsam"
+
+ test("test-gatk4-revertsam") {
+
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ bam(process.out.bam[0][1]).getReadsMD5(),
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-gatk4-revertsam-stubs") {
+ options '-stub'
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap b/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap
new file mode 100644
index 00000000000..1cbb5ce6e79
--- /dev/null
+++ b/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap
@@ -0,0 +1,48 @@
+{
+ "test-gatk4-revertsam": {
+ "content": [
+ "e3cfa46b13cc4fc425cccae944f43b10",
+ [
+ "versions.yml:md5,ee8dfa21abb49349e4865984cc122b9e"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T11:45:39.712635"
+ },
+ "test-gatk4-revertsam-stubs": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test"
+ },
+ "test.reverted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,ee8dfa21abb49349e4865984cc122b9e"
+ ],
+ "bam": [
+ [
+ {
+ "id": "test"
+ },
+ "test.reverted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,ee8dfa21abb49349e4865984cc122b9e"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T11:45:46.856318"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test
new file mode 100644
index 00000000000..30a41adddf6
--- /dev/null
+++ b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test
@@ -0,0 +1,88 @@
+
+nextflow_process {
+
+ name "Test Process GATK4_SAMTOFASTQ"
+ script "../main.nf"
+ process "GATK4_SAMTOFASTQ"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gatk4"
+ tag "gatk4/samtofastq"
+
+ test("test-gatk4-samtofastq-single-end") {
+
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test', single_end: true ], // meta map
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) ]
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.fastq[0][1]).linesGzip[3..7],
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-gatk4-samtofastq-paired-end") {
+
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test', single_end: false ], // meta map
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ]
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ process.out.fastq[0][1].collect { path(it).linesGzip[3..7] },
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-gatk4-samtofastq-paired-end-stubs") {
+ options '-stub'
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test', single_end: true ], // meta map
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) ]
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ process.out.fastq[0][1].collect { file(it).name },
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap
new file mode 100644
index 00000000000..0e1ec4b79d4
--- /dev/null
+++ b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap
@@ -0,0 +1,66 @@
+{
+ "test-gatk4-samtofastq-single-end": {
+ "content": [
+ [
+ "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE0\t0,0,0,0,0>0,0,0,0,0\t0>0\t__________>__________\t16=1X20=1X19=1X58=1X40=1X7=1X12=1X2=1X41=1X93=1X48=1X5=1X4=1X40=1X10=1X27=2X25=1X2=1X4=1X24=1X7=2X14=1X52=1X5=1X6=2X8=1X21=1X4=1X35=1X40=1X75=1X3=1X21=1X20=1X23=2X31=1X19=1X27=1X3=1X52=1X40=1X10=1X28=1X34=1X33=1X26=1X13=1X56=2X31=2X11=1X94=1X41=1X1=1X20=1X32=1X10=1X64=1X4=1X39=2X6=2X15=1X63=1X28=1X34=1X33=1X7=1X3=1X17=1X20=1X47=1X7=2X11=1X2=1X5=1X6=1X41=1X7=1X77=1X14=1X35=1X14=1X32=1X52=1I10=1X30=1X9=1X36=1X2=1X66=1X4=1X38=1X5=1X12=1X19=1X75=1X26=2D11=1X20=1X3=1X1=1X14=1X20=1X7=1X14=1X24=1X2=1X25=1X4=1X81=1X15=1X15=1X27=2X17=28149N22=9S",
+ "m64014_190506_005857/6294364/ccs\tlde_pass\tchr22:16600000-16800000\t168536\t199436\t+\t2\t0\t1>0\t0,0,1,0,0>0,0,0,0,0\t4.T.A_3M>0\t_____X____>__________\t6=1X7=1X2=1X8=1D3=1X14=1X23=1X2=1X4=1X35=1X11=1X40=1X6=1X41=1X2=1X59=1X23=1X3=2X16=1X8=1X7=1X33=1X38=8I1=2I28=1X5=1X3=1X2=1X9=1X19=1X1=1X4=1X35=1X9=1X29=5D20=2D16=1X8=1X3=1X20=1X24=1X45=2X4=1I27=1X19=2X26=1X2=1X94=1X4=1X5=1X12=1X15=1X7=1X6=1X19=1X20=1X9=1I3=2X25=1X5=1X7=1X42=1X17=1X29=1X11=1X79=1X14=1X10=1X30=1X1=1X43=1X2=1X6=1X30=1I45=1X1=1I32=1X11=1X6=1X12=1X3=1X63=1X63=1X41=1X20=1X16=1I5=1X32=1I9=1X5=1X1=1I6=2X11=1X2=1X11=4D38=2X22=1X46=1X1=1I40=1X24=1X29=1X25=1X23=2X17=1X3=1X7=1X31=1X3=1X4=1X36=1X10=1X31=1D17=1X8=1X4=1X38=1X1=2X1=2X9=1X2=1X95=1X22=9D33=1X1=1X14=1X20=1X22=1X8=1X44=1X4=1X41=1X55=2X12=1X30=1X3=28161N24=7S",
+ "m64014_190506_005857/9307762/ccs\tlde_pass\tchr22:16600000-16800000\t169225\t199436\t+\t2\t0\t0>3\t0,0,0,0,0>2,0,1,0,0\t0>2M_2.A.C_1M_2I\t__________>__X_II____\t3S4=1X23=3X26=1X3=1X19=1X27=1X14=1X30=1X10=1X40=1X10=1X1=1X26=1X5=1X28=1X60=1X7=1X5=1X6=1X50=1X32=1X11=1X41=1X52=1X41=1X1=1X20=1X32=1X10=1X17=1X51=1X40=1X6=1X16=1X43=1X19=1X37=1X8=1X11=1X4=1X33=1X7=1X34=1X4=1X2=1X47=1X7=2X11=1X2=1X5=1X6=1X26=1X14=1X9=1X23=1X12=1X27=1X10=1X28=1X8=1X8=1X3=1X47=1X16=1X16=1X28=1X31=1X4=1X3=1X36=1X2=1X36=1X29=1X4=1X37=2X1=2X2=1X12=1X19=1X75=1X26=2D11=1X8=1X15=1X1=1X14=1X18=1X1=1X7=1X14=1X22=1X30=1X4=1X15=1X9=1X71=2X25=1X17=1X17=1X17=1X28=4D21=1X8=1X16=1X140=1X43=1X51=1X14=1X11=1X17=2X15=1X24=1X25=1X7=1X2=1X8=1X5=1X4=1X15=1X11=1X18=1D42=1X19=1X5=1X7=1X15=9D5=4D18=1X3=1X4=1X17=1X7=1X1=1X17=1X7=1X11=1X4=1X4=1X14=1X11=1X8=1X2=1X4=1X11=1X13=1X10=1X8=1X17=27297N2=1X1=2I22=8S"
+ ],
+ "cluster_id\ttrans_id\tstrand\ta_percent\ta_count\tsequence",
+ [
+ "m64014_190506_005857/13631523/ccs\tchimeric\tchimeric\tNA\tNA\tNA\tNA\tNA",
+ "m64014_190506_005857/13238379/ccs\tforward_strand\tdiscarded\t7.53\t6.24\t0;3600;8;2;40\t3893\t2807S12=1X2=1D2=2X5=1X7=2X5=2I2=5I1X6=1X6=1X17=2X6=1X7=1X2=1X6=1X1=1X9=2X7=1X3=1X6=2X7=1X1=1X3=3030N1=2X12=1X17=2X4=1I7=1X5=1X8=1X25=1X5=1X2=1D8=1X12=1X1=2X9=2X7=793S",
+ "m64014_190506_005857/5048548/ccs\tnot_primary\tnot_primary\tNA\tNA\tNA\tNA\tNA",
+ "m64014_190506_005857/2491688/ccs\tchimeric\tchimeric\tNA\tNA\tNA\tNA\tNA",
+ "m64014_190506_005857/10945888/ccs\tnot_primary\tnot_primary\tNA\tNA\tNA\tNA\tNA"
+ ],
+ "read_id\tscaff_name\tstart_pos\tcigar\tstrands",
+ [
+ "G1.3\t1\t99.21\t99.21\t92.96\t92.96\t0\t0\t0\t0\tna",
+ "G1.4\t1\t99.31\t99.31\t93.56\t93.56\t0\t0\t0\t0\tna",
+ "G1.5\t1\t99.69\t99.69\t95.46\t95.46\t0,0\t0,0\t0,0\t0,0\t0>0",
+ "G1.6\t1\t99.74\t99.74\t93.58\t93.58\t0,0\t0,0\t0,0\t0,0\t4.T.A_3M>0",
+ "G1.7\t1\t99.62\t99.62\t93.7\t93.7\t0,0\t0,0\t0,0\t0,0\t0>2M_2.A.C_1M_2I"
+ ],
+ [
+ "chr22:16600000-16800000_6225\tm64014_190506_005857/11141276/ccs,m64014_190506_005857/13501955/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/6228265/ccs,m64014_190506_005857/7211438/ccs,m64014_190506_005857/8258125/ccs,m64014_190506_005857/9045622/ccs,m64014_190506_005857/9896837/ccs",
+ "chr22:16600000-16800000_6234\tm64014_190506_005857/10945789/ccs,m64014_190506_005857/11403968/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/6228265/ccs,m64014_190506_005857/9045622/ccs,m64014_190506_005857/9896837/ccs",
+ "chr22:16600000-16800000_6244\tm64014_190506_005857/10945789/ccs,m64014_190506_005857/11141276/ccs,m64014_190506_005857/11403968/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/13501955/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/3735911/ccs,m64014_190506_005857/6228265/ccs,m64014_190506_005857/8258125/ccs,m64014_190506_005857/8586246/ccs,m64014_190506_005857/9045622/ccs,m64014_190506_005857/9896837/ccs",
+ "chr22:16600000-16800000_6255\tm64014_190506_005857/11403968/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/3735911/ccs,m64014_190506_005857/7538257/ccs,m64014_190506_005857/8586246/ccs,m64014_190506_005857/9896837/ccs",
+ "chr22:16600000-16800000_6256\tm64014_190506_005857/11403968/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/13501955/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/3735911/ccs,m64014_190506_005857/7538257/ccs,m64014_190506_005857/8586246/ccs,m64014_190506_005857/9896837/ccs"
+ ],
+ [
+ "chr22:16600000-16800000\t6225\tM\tT\tC\t8\t8\tm64014_190506_005857/9045622/ccs,m64014_190506_005857/8258125/ccs,m64014_190506_005857/11141276/ccs,m64014_190506_005857/6228265/ccs,m64014_190506_005857/9896837/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/7211438/ccs,m64014_190506_005857/13501955/ccs",
+ "chr22:16600000-16800000\t6234\tM\tG\tA\t5\t7\tm64014_190506_005857/9896837/ccs,m64014_190506_005857/6228265/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/9045622/ccs",
+ "chr22:16600000-16800000\t6244\tM\tC\tG\t11\t12\tm64014_190506_005857/9045622/ccs,m64014_190506_005857/8586246/ccs,m64014_190506_005857/11141276/ccs,m64014_190506_005857/6228265/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/9896837/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/8258125/ccs,m64014_190506_005857/10945789/ccs,m64014_190506_005857/3735911/ccs,m64014_190506_005857/13501955/ccs",
+ "chr22:16600000-16800000\t6255\tM\tT\tC\t7\t7\tm64014_190506_005857/7538257/ccs,m64014_190506_005857/8586246/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/11403968/ccs,m64014_190506_005857/9896837/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/3735911/ccs",
+ "chr22:16600000-16800000\t6256\tM\tG\tA\t7\t8\tm64014_190506_005857/7538257/ccs,m64014_190506_005857/8586246/ccs,m64014_190506_005857/13633438/ccs,m64014_190506_005857/11403968/ccs,m64014_190506_005857/9896837/ccs,m64014_190506_005857/13043967/ccs,m64014_190506_005857/3735911/ccs"
+ ],
+ [
+ "versions.yml:md5,e78d77df56e6434d307e702b7875d005"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T10:53:08.268377"
+ }
+}
\ No newline at end of file
diff --git a/tests/modules/nf-core/gstama/collapse/nextflow.config b/modules/nf-core/gstama/collapse/tests/nextflow.config
similarity index 54%
rename from tests/modules/nf-core/gstama/collapse/nextflow.config
rename to modules/nf-core/gstama/collapse/tests/nextflow.config
index a68f33f2ea0..ea89a16473c 100644
--- a/tests/modules/nf-core/gstama/collapse/nextflow.config
+++ b/modules/nf-core/gstama/collapse/tests/nextflow.config
@@ -1,10 +1,6 @@
process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
withName: GSTAMA_COLLAPSE {
ext.args = '-x capped -b BAM'
ext.prefix = { "${meta.id}_tc" }
}
-
}
diff --git a/modules/nf-core/gstama/merge/tests/main.nf.test b/modules/nf-core/gstama/merge/tests/main.nf.test
new file mode 100644
index 00000000000..c485d3eaafa
--- /dev/null
+++ b/modules/nf-core/gstama/merge/tests/main.nf.test
@@ -0,0 +1,47 @@
+
+nextflow_process {
+
+ name "Test Process GSTAMA_MERGE"
+ script "../main.nf"
+ process "GSTAMA_MERGE"
+ config "./nextflow.config"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gstama"
+ tag "gstama/merge"
+
+ test("test-gstama-merge") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed', checkIfExists: true)
+ ]
+ ]
+ input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/txt/filelist.txt', checkIfExists: true)
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ process.out.bed,
+ file(process.out.gene_report[0][1]).readLines()[3..7],
+ file(process.out.merge[0][1]).readLines()[3..7],
+ file(process.out.trans_report[0][1]).readLines()[3..7],
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gstama/merge/tests/main.nf.test.snap b/modules/nf-core/gstama/merge/tests/main.nf.test.snap
new file mode 100644
index 00000000000..0ac82c39e0f
--- /dev/null
+++ b/modules/nf-core/gstama/merge/tests/main.nf.test.snap
@@ -0,0 +1,44 @@
+{
+ "test-gstama-merge": {
+ "content": [
+ [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test_merged.bed:md5,60ec34e1ff9655d4ce2e83d3f4bbf448"
+ ]
+ ],
+ [
+ "G3\t1\t1\tGM2\t22\t16154707\t16159526\tGM2_G2\tGM2:1",
+ "G4\t1\t1\tGM2\t22\t19520556\t19524409\tGM2_G3\tGM2:1",
+ "G5\t3\t3\tGM2\t22\t20675820\t20834631\tGM2_G4\tGM2:1",
+ "G6\t1\t1\tGM2\t22\t21927942\t21952850\tGM2_G5\tGM2:1",
+ "G7\t1\t1\tGM2\t22\t23226655\t23231517\tGM2_G6\tGM2:1"
+ ],
+ [
+ "22\t11867751\t11883593\tG2.1;GM2_G1.1\t40\t+\t11867751\t11883593\t255,0,0\t5\t2147,85,29,73,1326\t0,6089,8352,8472,14516",
+ "22\t16154707\t16159526\tG3.1;GM2_G2.1\t40\t+\t16154707\t16159526\t255,0,0\t1\t4819\t0",
+ "22\t19520556\t19524409\tG4.1;GM2_G3.1\t40\t-\t19520556\t19524409\t255,0,0\t1\t3853\t0",
+ "22\t20675820\t20726523\tG5.1;GM2_G4.1\t40\t-\t20675820\t20726523\t255,0,0\t15\t22,399,84,90,160,121,126,105,110,71,73,71,130,121,36\t0,31879,33475,34087,34878,35520,36665,36872,37460,38637,38807,41887,42872,45477,50667",
+ "22\t20707690\t20834631\tG5.2;GM2_G4.2\t40\t-\t20707690\t20834631\t255,0,0\t53\t408,84,90,160,121,126,105,110,71,73,71,130,121,54,168,91,194,80,120,128,108,152,159,128,157,93,120,90,84,82,125,71,83,134,137,109,51,169,104,184,96,133,130,101,192,97,66,149,67,260,73,89,70\t0,1605,2217,3008,3650,4795,5002,5590,6767,6937,10017,11002,13607,18797,19539,20083,21622,21941,22201,25280,26045,26352,26704,34537,34917,36937,39892,42214,43602,43983,45212,45419,53613,57126,57409,57894,85502,88455,90893,91402,91980,94282,95500,96609,97283,99671,103276,105667,110792,111950,112848,116635,126871"
+ ],
+ [
+ "G1.3\t1\tGM1\t0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\t0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\tGM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2\tGM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2;GM1_G1.2\tGM1_G1.2",
+ "G2.1\t1\tGM2\t0,0,0,0,0\t0,0,0,0,0\tGM2_G1.1;GM2_G1.1;GM2_G1.1;GM2_G1.1;GM2_G1.1\tGM2_G1.1;GM2_G1.1;GM2_G1.1;GM2_G1.1;GM2_G1.1\tGM2_G1.1",
+ "G3.1\t1\tGM2\t0\t0\tGM2_G2.1\tGM2_G2.1\tGM2_G2.1",
+ "G4.1\t1\tGM2\t0\t0\tGM2_G3.1\tGM2_G3.1\tGM2_G3.1",
+ "G5.1\t1\tGM2\t0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\t0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\tGM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1\tGM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1;GM2_G4.1\tGM2_G4.1"
+ ],
+ [
+ "versions.yml:md5,ceaccf17d15e3fabb193d67b4a822d08"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T10:46:55.890773"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gstama/merge/tests/nextflow.config b/modules/nf-core/gstama/merge/tests/nextflow.config
new file mode 100644
index 00000000000..02d0a81e0d3
--- /dev/null
+++ b/modules/nf-core/gstama/merge/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+ withName: GSTAMA_MERGE {
+ ext.prefix = { "${meta.id}_merged" }
+ }
+}
diff --git a/modules/nf-core/gstama/polyacleanup/tests/main.nf.test b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test
new file mode 100644
index 00000000000..c447f001dc0
--- /dev/null
+++ b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test
@@ -0,0 +1,42 @@
+
+nextflow_process {
+
+ name "Test Process GSTAMA_POLYACLEANUP"
+ script "../main.nf"
+ process "GSTAMA_POLYACLEANUP"
+ config "./nextflow.config"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gstama"
+ tag "gstama/polyacleanup"
+
+ test("test-gstama-polyacleanup") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/transcriptome.fasta', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.report[0][1]).linesGzip[0..2],
+ path(process.out.fasta[0][1]).linesGzip[3..7],
+ path(process.out.tails[0][1]).linesGzip[3..7],
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap
new file mode 100644
index 00000000000..a9cc2aefef1
--- /dev/null
+++ b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap
@@ -0,0 +1,33 @@
+{
+ "test-gstama-polyacleanup": {
+ "content": [
+ [
+ "polya_num\tpolya_num_count",
+ "0\t11",
+ "1\t1"
+ ],
+ [
+ "GGAAGCACTTTTTTCCTGTATAGCAAAATGAGTTCAAGATATTCTTTGCCTAATTTCAGCTCTAGCTAGAACCAGTCAATATGGAAATAAACAATGAGGGTATCTAACCTACTGAACACTGAACCATCAGCCTAACTCTATGCAATATAGTCATACTAAAATATTTCTCATAAAAAAGTTCTTAACAGTTCGTTCACTATATCTTTCACGCAGTTATTTTATAGAATAAGCAAAGTAGGGCATGTGAAACACTTTAGCTTAGCTTCTAGCATCCAGTAGCGGTGCTCAAAAATGTTAGATCATTTATGTAACAATCTGCTAGGTTATAACATTCAGTGAGCCTTGGTACTTTTCATTGAACAGCTGGTATAGAGGCTAGGGATAGGGAGCTGCAGTTCATTTTCCATGCCCCTACCCGAGTTCTCTTGGCTAAATGTGATACGCATTTAAGGCCCAGAACCTGCTGTTTAAAAGGTTGTGGTAAACTATTTTGTATACCAAAGACTTCTCTGTAATAAAGTATGTAAGTACACATGAACATTTTATATGCACGCACATTTTAAATCATCTGCACATTGAGATTCTACACTTTTCTCAAGGGCACATCTCTATTCCGTTTCTTTGTAAATTTGACTTCTACCTAACAATATGCAATTGCTGGGATTTTTTTCCCTAACAGTATGAAAGTTGTCTTTAAATAGTAAAAGCACCACAATCTATTAACACCACATGTTATCTTTAAACTGAAATATTTTAGTGATGTCTTGGACATCAAAATAATTTCTTAAGGTGGACTCTTGAGTATGTGGGTCCAGCCCAGGTCTGCAGTTTGTGCAGACATAGAAAAAAGAGGAACTTTAAATATTCAGAAAAAGTTAACAGGCTAGCTTTAAAATACTGCTGGAAATTAAATTTCTTCAGAGTTGGCAAGCATGGGCTATTGATCAAAATATGAATTAAACGGATTTACATCATTAAGAAAAAAACAAATCCATGTTATTGTGCTGTGAAATTTCCATGATGCCTTTCAAATAGGCTGCTCACAAATTTTTTTATAATTCTAAATCACTCGCTTTTTGATGGAAAAAAGAATACAGATGGACTGTGTTTTACCTATGTGAAAGTCACCAATCCATTTAAAATAAAATCCAAGAGGGCATATACAGTCTAATCAAGTCATCATTTTCCTGATTAATAAGAACTACACTTTACACAAAATACTTTATCAGCAGCTGTTTTCATCAAAAAATCAGTAGTCAGTTTCACAGTTGAAAAAGTTACACATTAAAATATTTTACAATTCATTATATATTCACCAGGTTCCCATTTTCTAAGGGGCTTTTAATATAAAGCAGAATAGAACACTGTCTCTACTAAAAATACAAAAATTAGCTGGGAGTGGTGGCATGCTCCTATAGTCCTAGCTACTCAGGAGGCTGAGGTGGGAGGATGGCTTGAACCCAGGAGGTCAAGGCTGCAGTGAGCCGAAATTGCACCACTGCATTCCAGGCCGGGCAAAAGAGCCAGACCCTGTCTCAAAAAAAAAAGTTTACATTGTATTTCCTACTCTTAGTTACACTAAGCTAGACAGCAGATGACTAGAGGGTGTGATATATTTACTGAGTGACTCGAAATCCATTTTAAACTTGGAAATGTAAAAACTAACTTCTTTCCACTCATTTTCAGGGTCATTACTGAGAGATAATAAATGACAGAATAAGGAAATAATCACTGTAAATACTTAGGGACCTGAATAAGAGAAAGGAAGGGAAAGTAAAGGGATCTAACATTTATTGGGCACCTTCTGTGTTCCAAGGATTGTGATAGGTTCTTTGCATATCTCATGTAATTTAATTCTCACAATGGCCTTACGAAGCAGGTATTATTCCCATTTTACAGACAAAGAAAATGAGTCTTGAGAGCCTGCATAACGTGTCTAACACTACACAGATGAGAGGCAGTGGAACTTGGTTCCAAATCCTAATCTGCTTGATTCCAAGGACCATGATCTGTATATACACTGGGCTTCTAAACAACTCTGCCCCACTGCAGTGAAAAGAGTCTCAAACACAGACTAGAGTCACACAACTTTTGTGTTTCATCCTTCTTCTCCTGTTTGACAATGTCAGTTAAGTTAATGAGCTTTTCCATTGCCTCGACTTGCCTATTCAGGTGCTTCAAATACATCCCACATGCACGACAATAGGACTCCAAAAGCAGGCCAAACCTCTGGCTAAGTGTTTTATTGTGCATCTCAGATCTAAAAGAATCATGCAAAATTAGAAAAATATATATATAGTCTTAAATCAGTATACAAATAATCTTTGCTAAACAATTTAAACACTCATTTTTGAAATCCAATAAATGTTACAATCATACTAATAATAACATTATTCAAAACCTGTAATTTAGAAGCAAAACCACCATGAGTTTCAGGTAGTTCCTGAATATGTGATTAAATAAACATCTAGTTTTTAGGTTTATTTCAACTAGTTTTCATTGACTAATCTCAGTACAAGATATAAAAGCATGAAAAAAGGAAATTGAGCACAAAAATAATCAAATGAAGAGGGAGGGAACAAAGCGCTCAGTGAATGCTGTTTGACTCTTCTGACACACGTCTACGCTTCTTGTTTTCAACTTAACTTCTGGGTTCCATTTTTAAATTTTAACACTTAAAATATCATATTAGATATAAATCTGTTTCTAAATTTATGAAAAGTTATATGGTTTATGACCTGTAACTTTTGAGTACTGCATATATCACATTCTACAAAACATTTTTTATTCTTAATTAGCTTGTTTTTCAGTAAGAACCACGGGAGTTTGACATTATTGTTCTGAATCTCAAGGTAAAACATTTTTTTTCTTTTTTTGGGGATATTTTAATCCATACACACAGTGAAACCTACAGCAATATTCATCTGGACCTAGAAAATTTTACTTAAGTAGAACAAAAATCTTTAAAAATATTTAAGCTCTCATTCATGACTGAAATTTAGTTTTGAATTTATTACTTTTTAAATTTCAAAGAGCAAAAGTTGAGAAGCTCATCACTGGTACAAAATAGTTTTAGTATGGAAAACTCTTCCAGCCAAACATAAACAAAAGTATATAAGTAATACATATTTATAAATCTATTAAGAAAGCAAGTAATATGTACCTTAAGAATTTAATGGGAAAATAATTAGACTTACTTTAAATGCCAAAAGAAAAAGTGCCCAATCCTTTGATTAGTCAATGCTTTCTTCAGTAAAAATCTCACAAGCAAGTTATCCAAATATTGTTCATATTTTAGGACCTAGGTGATTCAAAAAAAACAAATCAGGTTCAGTTTCTGCATGGCCGATCTAAAGAAAATTTTTTCAGAAAGAAAGTGGATATTACTG",
+ ">ENST00000472972",
+ "AACCTACTGAACACTGAACCATCAGCCTAACTCTATGCAATATAGTCATACTAAAATATTTCTCATAAAAAAGTTCTTAACAGTTCGTTCACTATATCTTTCACGCAGTTATTTTATAGAATAAGCAAAGTAGGGCATGTGAAACACTTTAGCTTAGCTTCTAGCATCCAGTAGCGGTGCTCAAAAATGTTAGATCATTTATGTAACAATCTGCTAGGTTATAACATTCAGTGAGCCTTGGTACTTTTCATTGAACAGCTGGTATAGAGGCTAGGGATAGGGAGCTGCAGTTCATTTTCCATGCCCC",
+ ">ENST00000359963 CDS=261-1934",
+ "TTTCTTTAAATAAAAACATGAAGGAACATAAAATTTCTTTTCATGCGCTTAGTTCCTTTCCAGTTCTCGACTTTTTTTGTTTTTTTTTTTTGAGAGACGGAGTCTTGCTCTGTTGCCCAGGCTGGTGTGCAGTGGCGTGATCTTGGCTCACTGCAACCTCCGCCTCCCAGGTTCAAGCGATTTTCCTGCCTCAGCCTCCTGAATAGCTGGGACTACAGGTGCGCGCCACCACGCCCAGCTATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATATTGACCAGGCTGGTCTCGAACTCCTGACCTCATGATCCTCCCGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGCGAGAGCCACTGTGCCCAGCCAGTTCTTGACCTTTTCATTTTGTGTTTCTATCAGATGCTCTTCCTTTCCTATGATAAGAGCAGGATTCAATTCTATTAAGATTTTTAAACTGAGTACCTATGTGGGCTTTGGGCGTGCAAAACACAGTGCAGCAATCTCTTCCCAACTATTTGAGCATTCCCTGCATGATATTCTGACATATATGGACTTATGTCTAGATGTCACTTTAGGAGTCTGAAAACATCAGTTGCAGCTTACAAGAGTGGTCAGTCCTTCCTGTTGTGGTTATTTGAAAAAAAAGAAGGGACTATCATCTTAAAGCACAGAGAGAGAGAGAGAGCAGGAGAAAGAGCTGCTGTGGTGGCAGGCAGAAATGTAACTTAAAAAGAAAAAAATCCTTGCCTGGCAAAGTGGCTCATGCCTATAATTCCTGCACTTTGGGAGGCTGAGACAGGAAGATCGCTTGAGTCCAGGAGTTCAAGACTAGCCTGGACAACATAGTGAGACCCTATCTCTACAAAAATAAAAATTAAAAAAAATTAGCCAGGCATGGGCCGGGCATGGTGGCTCAAGCCTTTAATCCCAGCACTTTGGGAGCCCAAGGTGGGTGGATCAGCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACGTGGAGAAACCCCATCTCTACTAAAAATACAAAACAGTAGCCGGATGTGATGGCACATGCCTGTAATCCCAGCTATTTGAGAGGCTGAGGCAGGAGAATTGCTTGAACCTGGGAGGCAGAGGTTGTGGTGAGCTGAGATGACACTATTGTACCCCAGCCTGGGCAACAAGAGCAAAACTCTGCCTCAAAAAAAAAAAAAAAAAAAAAAATTAGCCAGGCGTGGTGATGCATACCTGTAGTCCCAGCTACTCAGGAGGCTGAGTGGGGGGATCACTTAAGCCCAGGAGATCGAGGTTGCAGTGAGCTGTGATTGTGCCACTGCACTCCAGCCTAAGAGACAGAGCAAGACCCTGTCTCAACAAAACAAAACAAAACCAGCAAACATCCTTGGCATAGATAACAGAAGATAAGAACACATACTTTAGGACTATACTAAGGTTGCTGTGTAGGTGAGGAGAAAGCTGAGGGTAGGGGGAAGGGCTAGGATTGGACAACCTTGGGCATTAAAGAAGGGGTTTGAGCAGAGCTGAGTGGGTTTGGCACCTAATACGCAAAGCTTTTTCCACTTTTTTAACTTCCAAGTTACTCTAGGAAAAATCAGAACCTATGGGACAGAATCTAGGAGATGAGAAGGTACAATCTTTTAGAATCATAAAAATAAAAAAGCTTTAGGCATATGCAGAGAGAATGAGACTCAAGAAACCATTGTCTTATAGCACGCATATTAGCCGCAACACAGCAAAACAAAATTTTATTTATTTATTTATTTATTTTGAGACAGAGTCTTGCTCTGTCACCCAGGCATAGTGACTGGTGTGGCCCAGGCACCAGTGCAGCAGTGCAGTCTCAGCTCACTGCAACCTCTGCCTCCTGGGCTCAAATGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTACAGGTGTCCACCACCATGCCTGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCGCCATGTTGGTCAGGGTGGTCTCAAACTTTGGACCTCAGGTGATCCACCTGCCTCGGCCTCCCCAAATGCTGAGATTACAG"
+ ],
+ [
+ "",
+ ">tail_ENST00000472972",
+ "",
+ ">tail_ENST00000359963 CDS=261-1934",
+ ""
+ ],
+ [
+ "versions.yml:md5,dff6214a93a250748705dbd8ec455fec"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T10:44:18.309783"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gstama/polyacleanup/tests/nextflow.config b/modules/nf-core/gstama/polyacleanup/tests/nextflow.config
new file mode 100644
index 00000000000..0ffcbb55a35
--- /dev/null
+++ b/modules/nf-core/gstama/polyacleanup/tests/nextflow.config
@@ -0,0 +1,3 @@
+process {
+ ext.prefix = { "${meta.id}_tama" }
+}
diff --git a/modules/nf-core/happy/sompy/main.nf b/modules/nf-core/happy/sompy/main.nf
index e0c34e262de..ba23fd16765 100644
--- a/modules/nf-core/happy/sompy/main.nf
+++ b/modules/nf-core/happy/sompy/main.nf
@@ -54,7 +54,7 @@ process HAPPY_SOMPY {
"""
stub:
- def args = task.ext.args ?: ''
+ def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '0.3.14' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
touch ${prefix}.features.csv
diff --git a/modules/nf-core/happy/sompy/meta.yml b/modules/nf-core/happy/sompy/meta.yml
index 3dd2b911be8..8a04a601739 100644
--- a/modules/nf-core/happy/sompy/meta.yml
+++ b/modules/nf-core/happy/sompy/meta.yml
@@ -13,8 +13,7 @@ tools:
homepage: "https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html"
documentation: "https://github.com/Illumina/hap.py/blob/master/doc/sompy.md"
tool_dev_url: "https://github.com/Illumina/hap.py"
-
- licence: "['BSD-2-clause']"
+ licence: ["BSD-2-clause"]
input:
- meta:
@@ -22,6 +21,31 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
+ - meta2:
+ type: map
+ description: |
+ Groovy Map containing fasta file information
+ e.g. [ id:'test2']
+ - meta3:
+ type: map
+ description: |
+ Groovy Map containing fai file information
+ e.g. [ id:'test3']
+ - meta4:
+ type: map
+ description: |
+ Groovy Map containing false_positives_bed file information
+ e.g. [ id:'test4']
+ - meta5:
+ type: map
+ description: |
+ Groovy Map containing ambiguous_beds file information
+ e.g. [ id:'test5']
+ - meta6:
+ type: map
+ description: |
+ Groovy Map containing bam file information
+ e.g. [ id:'test6']
- query_vcf:
type: file
description: VCF/GVCF file to query
diff --git a/modules/nf-core/happy/sompy/tests/main.nf.test b/modules/nf-core/happy/sompy/tests/main.nf.test
new file mode 100644
index 00000000000..f4919c73f7b
--- /dev/null
+++ b/modules/nf-core/happy/sompy/tests/main.nf.test
@@ -0,0 +1,127 @@
+nextflow_process {
+
+ name "Test Process HAPPY_SOMPY"
+ script "../main.nf"
+ process "HAPPY_SOMPY"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "happy"
+ tag "happy/sompy"
+
+ test("homo_sapiens - vcf") {
+ config './nextflow.config'
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true),
+ []
+ ]
+ input[1] = [
+ [ id:'test2' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+ ]
+ input[2] = [
+ [ id:'test3' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+ ]
+ input[3] = [[],[]]
+ input[4] = [[],[]]
+ input[5] = [[],[]]
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out.stats,
+ process.out.versions,
+ file(process.out.metrics[0][1]).name,
+ file(process.out.features[0][1]).name).match()}
+ )
+ }
+
+ }
+ test("homo_sapiens - vcf - bam") {
+ config './nextflow.config'
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true),
+ []
+ ]
+ input[1] = [
+ [ id:'test2' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+ ]
+ input[2] = [
+ [ id:'test3' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+ ]
+ input[3] = [[],[]]
+ input[4] = [[],[]]
+ input[5] = [[ id:'test2' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true)]
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out.stats,
+ process.out.versions,
+ file(process.out.metrics[0][1]).name,
+ file(process.out.features[0][1]).name).match()}
+ )
+ }
+
+ }
+ test("homo_sapiens - vcf - stub") {
+
+ options "-stub"
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true),
+ []
+ ]
+ input[1] = [
+ [ id:'test2' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+ ]
+ input[2] = [
+ [ id:'test3' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+ ]
+ input[3] = [[],[]]
+ input[4] = [[],[]]
+ input[5] = [[],[]]
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+
+ }
+
+}
diff --git a/modules/nf-core/happy/sompy/tests/main.nf.test.snap b/modules/nf-core/happy/sompy/tests/main.nf.test.snap
new file mode 100644
index 00000000000..b6b25e6decf
--- /dev/null
+++ b/modules/nf-core/happy/sompy/tests/main.nf.test.snap
@@ -0,0 +1,111 @@
+{
+ "homo_sapiens - vcf": {
+ "content": [
+ [
+ [
+ {
+ "id": "test"
+ },
+ "test.stats.csv:md5,8b35dd00bf7b5bd697a05d73fb8c0816"
+ ]
+ ],
+ [
+ "versions.yml:md5,dda929752e25faa5e5dc8e82228980fc"
+ ],
+ "test.metrics.json",
+ "test.features.csv"
+ ],
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T08:56:57.589412212"
+ },
+ "homo_sapiens - vcf - bam": {
+ "content": [
+ [
+ [
+ {
+ "id": "test"
+ },
+ "test.stats.csv:md5,5e9aae3e92641f1934c10fe88f250e59"
+ ]
+ ],
+ [
+ "versions.yml:md5,dda929752e25faa5e5dc8e82228980fc"
+ ],
+ "test.metrics.json",
+ "test.features.csv"
+ ],
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T08:57:13.752402851"
+ },
+ "homo_sapiens - vcf - stub": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test"
+ },
+ "test.features.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ [
+ {
+ "id": "test"
+ },
+ "test.metrics.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "2": [
+ [
+ {
+ "id": "test"
+ },
+ "test.stats.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "3": [
+ "versions.yml:md5,dda929752e25faa5e5dc8e82228980fc"
+ ],
+ "features": [
+ [
+ {
+ "id": "test"
+ },
+ "test.features.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "metrics": [
+ [
+ {
+ "id": "test"
+ },
+ "test.metrics.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "stats": [
+ [
+ {
+ "id": "test"
+ },
+ "test.stats.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,dda929752e25faa5e5dc8e82228980fc"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-23T14:39:09.160343644"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/happy/sompy/tests/nextflow.config b/modules/nf-core/happy/sompy/tests/nextflow.config
new file mode 100644
index 00000000000..3a95dc4e6f3
--- /dev/null
+++ b/modules/nf-core/happy/sompy/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+ withName: HAPPY_SOMPY {
+ ext.args = '--feature-table hcc.mutect.snv'
+ }
+}
diff --git a/modules/nf-core/picard/bedtointervallist/tests/main.nf.test b/modules/nf-core/picard/bedtointervallist/tests/main.nf.test
new file mode 100644
index 00000000000..fd132089a41
--- /dev/null
+++ b/modules/nf-core/picard/bedtointervallist/tests/main.nf.test
@@ -0,0 +1,40 @@
+
+nextflow_process {
+
+ name "Test Process PICARD_BEDTOINTERVALLIST"
+ script "../main.nf"
+ process "PICARD_BEDTOINTERVALLIST"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "picard"
+ tag "picard/bedtointervallist"
+
+ test("test-picard-bedtointervallist") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test' ], // meta map
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ]
+ ]
+ input[1] = [
+ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
+ ]
+ input[2] = []
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/picard/bedtointervallist/tests/main.nf.test.snap b/modules/nf-core/picard/bedtointervallist/tests/main.nf.test.snap
new file mode 100644
index 00000000000..6abbf0e92f9
--- /dev/null
+++ b/modules/nf-core/picard/bedtointervallist/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+ "test-picard-bedtointervallist": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test"
+ },
+ "test.interval_list:md5,e51101c9357fb2d59fd30e370eefa39c"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,8d0ce8ecdf3bc716de22d75e61aaaf65"
+ ],
+ "interval_list": [
+ [
+ {
+ "id": "test"
+ },
+ "test.interval_list:md5,e51101c9357fb2d59fd30e370eefa39c"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,8d0ce8ecdf3bc716de22d75e61aaaf65"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T10:39:08.82372"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/picard/cleansam/meta.yml b/modules/nf-core/picard/cleansam/meta.yml
index ae98e2d2249..a74fe2e100d 100644
--- a/modules/nf-core/picard/cleansam/meta.yml
+++ b/modules/nf-core/picard/cleansam/meta.yml
@@ -21,7 +21,7 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- - sam:
+ - bam:
type: file
description: BAM file
pattern: "*.{bam}"
@@ -35,7 +35,7 @@ output:
type: file
description: File containing software versions
pattern: "versions.yml"
- - sam:
+ - bam:
type: file
description: Cleaned BAM file
pattern: "*.{bam}"
diff --git a/modules/nf-core/picard/cleansam/tests/main.nf.test b/modules/nf-core/picard/cleansam/tests/main.nf.test
new file mode 100644
index 00000000000..5d80739a472
--- /dev/null
+++ b/modules/nf-core/picard/cleansam/tests/main.nf.test
@@ -0,0 +1,40 @@
+
+nextflow_process {
+
+ name "Test Process PICARD_CLEANSAM"
+ script "../main.nf"
+ process "PICARD_CLEANSAM"
+ config "./nextflow.config"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "picard"
+ tag "picard/cleansam"
+
+ test("test-picard-cleansam") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:true ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ bam(process.out.bam[0][1]).getReadsMD5(),
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/picard/cleansam/tests/main.nf.test.snap b/modules/nf-core/picard/cleansam/tests/main.nf.test.snap
new file mode 100644
index 00000000000..63e2927e57a
--- /dev/null
+++ b/modules/nf-core/picard/cleansam/tests/main.nf.test.snap
@@ -0,0 +1,15 @@
+{
+ "test-picard-cleansam": {
+ "content": [
+ "798439cbd7fd81cbcc5078022dc5479d",
+ [
+ "versions.yml:md5,f99b648dc3d150a0561094e3a142ee22"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T10:36:05.525364"
+ }
+}
\ No newline at end of file
diff --git a/tests/modules/nf-core/picard/cleansam/nextflow.config b/modules/nf-core/picard/cleansam/tests/nextflow.config
similarity index 50%
rename from tests/modules/nf-core/picard/cleansam/nextflow.config
rename to modules/nf-core/picard/cleansam/tests/nextflow.config
index 7fbfaaa64f0..06a6daceb45 100644
--- a/tests/modules/nf-core/picard/cleansam/nextflow.config
+++ b/modules/nf-core/picard/cleansam/tests/nextflow.config
@@ -1,7 +1,4 @@
process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
withName: 'PICARD_CLEANSAM'{
ext.prefix = { "${meta.id}.cleaned"}
}
diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test
new file mode 100644
index 00000000000..5b67774f720
--- /dev/null
+++ b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test
@@ -0,0 +1,112 @@
+
+nextflow_process {
+
+ name "Test Process PICARD_COLLECTMULTIPLEMETRICS"
+ script "../main.nf"
+ process "PICARD_COLLECTMULTIPLEMETRICS"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "picard"
+ tag "picard/collectmultiplemetrics"
+
+ test("test-picard-collectmultiplemetrics") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+ ]
+ input[1] = [
+ [id:'genome'],
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+ ]
+ input[2] = [[id:'genome'],[]]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ process.out.metrics[0][1].collect { file(it).name }.toSorted(),
+ process.out.pdf[0][1].collect { file(it).name }.toSorted(),
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-picard-collectmultiplemetrics-nofasta") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+ ]
+ input[1] = [[id:'genome'],[]]
+ input[2] = [[id:'genome'],[]]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ process.out.metrics[0][1].collect { file(it).name }.toSorted(),
+ process.out.pdf[0][1].collect { file(it).name }.toSorted(),
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-picard-collectmultiplemetrics-cram") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+ ]
+ input[1] = [
+ [id:'genome'],
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+ ]
+ input[2] = [
+ [id:'genome'],
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ process.out.metrics[0][1].collect { file(it).name }.toSorted(),
+ process.out.pdf[0][1].collect { file(it).name }.toSorted(),
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap
new file mode 100644
index 00000000000..1859541b6dd
--- /dev/null
+++ b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap
@@ -0,0 +1,80 @@
+{
+ "test-picard-collectmultiplemetrics": {
+ "content": [
+ [
+ "test.CollectMultipleMetrics.alignment_summary_metrics",
+ "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+ "test.CollectMultipleMetrics.insert_size_metrics",
+ "test.CollectMultipleMetrics.quality_by_cycle_metrics",
+ "test.CollectMultipleMetrics.quality_distribution_metrics"
+ ],
+ [
+ "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+ "test.CollectMultipleMetrics.insert_size_histogram.pdf",
+ "test.CollectMultipleMetrics.quality_by_cycle.pdf",
+ "test.CollectMultipleMetrics.quality_distribution.pdf",
+ "test.CollectMultipleMetrics.read_length_histogram.pdf"
+ ],
+ [
+ "versions.yml:md5,b68b83e8dd0f9360453213acad639338"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T10:03:36.631174"
+ },
+ "test-picard-collectmultiplemetrics-cram": {
+ "content": [
+ [
+ "test.CollectMultipleMetrics.alignment_summary_metrics",
+ "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+ "test.CollectMultipleMetrics.insert_size_metrics",
+ "test.CollectMultipleMetrics.quality_by_cycle_metrics",
+ "test.CollectMultipleMetrics.quality_distribution_metrics"
+ ],
+ [
+ "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+ "test.CollectMultipleMetrics.insert_size_histogram.pdf",
+ "test.CollectMultipleMetrics.quality_by_cycle.pdf",
+ "test.CollectMultipleMetrics.quality_distribution.pdf",
+ "test.CollectMultipleMetrics.read_length_histogram.pdf"
+ ],
+ [
+ "versions.yml:md5,b68b83e8dd0f9360453213acad639338"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T10:04:13.955902"
+ },
+ "test-picard-collectmultiplemetrics-nofasta": {
+ "content": [
+ [
+ "test.CollectMultipleMetrics.alignment_summary_metrics",
+ "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+ "test.CollectMultipleMetrics.insert_size_metrics",
+ "test.CollectMultipleMetrics.quality_by_cycle_metrics",
+ "test.CollectMultipleMetrics.quality_distribution_metrics"
+ ],
+ [
+ "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+ "test.CollectMultipleMetrics.insert_size_histogram.pdf",
+ "test.CollectMultipleMetrics.quality_by_cycle.pdf",
+ "test.CollectMultipleMetrics.quality_distribution.pdf",
+ "test.CollectMultipleMetrics.read_length_histogram.pdf"
+ ],
+ [
+ "versions.yml:md5,b68b83e8dd0f9360453213acad639338"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T10:03:54.707587"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/picard/fastqtosam/tests/main.nf.test b/modules/nf-core/picard/fastqtosam/tests/main.nf.test
new file mode 100644
index 00000000000..ad3d52374a0
--- /dev/null
+++ b/modules/nf-core/picard/fastqtosam/tests/main.nf.test
@@ -0,0 +1,100 @@
+
+nextflow_process {
+
+ name "Test Process PICARD_FASTQTOSAM"
+ script "../main.nf"
+ process "PICARD_FASTQTOSAM"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "picard"
+ tag "picard/fastqtosam"
+
+ test("test-picard-fastqtosam-single") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:true ], // meta map
+ [
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+ ]
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ bam(process.out.bam[0][1]).getReadsMD5(),
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-picard-fastqtosam-paired") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+ ]
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ bam(process.out.bam[0][1]).getReadsMD5(),
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-picard-fastqtosam-paired-custom-samplename") {
+ config "./nextflow.config"
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+ ]
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ bam(process.out.bam[0][1]).getReadsMD5(),
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/picard/fastqtosam/tests/main.nf.test.snap b/modules/nf-core/picard/fastqtosam/tests/main.nf.test.snap
new file mode 100644
index 00000000000..2f999dcc9c9
--- /dev/null
+++ b/modules/nf-core/picard/fastqtosam/tests/main.nf.test.snap
@@ -0,0 +1,41 @@
+{
+ "test-picard-fastqtosam-paired-custom-samplename": {
+ "content": [
+ "e3cfa46b13cc4fc425cccae944f43b10",
+ [
+ "versions.yml:md5,24527dfda806cbcfd1609c4734f973f1"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T09:50:01.762254"
+ },
+ "test-picard-fastqtosam-single": {
+ "content": [
+ "e6a4aa204d980e177a0458596f0a70ac",
+ [
+ "versions.yml:md5,24527dfda806cbcfd1609c4734f973f1"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T09:49:32.460549"
+ },
+ "test-picard-fastqtosam-paired": {
+ "content": [
+ "e3cfa46b13cc4fc425cccae944f43b10",
+ [
+ "versions.yml:md5,24527dfda806cbcfd1609c4734f973f1"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T09:49:47.018269"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/picard/fastqtosam/tests/nextflow.config b/modules/nf-core/picard/fastqtosam/tests/nextflow.config
new file mode 100644
index 00000000000..22294c05eb3
--- /dev/null
+++ b/modules/nf-core/picard/fastqtosam/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+ withName: 'PICARD_FASTQTOSAM' {
+ ext.args = "--SAMPLE_NAME CustomSample"
+ }
+}
diff --git a/modules/nf-core/picard/fixmateinformation/tests/main.nf.test b/modules/nf-core/picard/fixmateinformation/tests/main.nf.test
new file mode 100644
index 00000000000..b45bdde582d
--- /dev/null
+++ b/modules/nf-core/picard/fixmateinformation/tests/main.nf.test
@@ -0,0 +1,40 @@
+
+nextflow_process {
+
+ name "Test Process PICARD_FIXMATEINFORMATION"
+ script "../main.nf"
+ process "PICARD_FIXMATEINFORMATION"
+ config "./nextflow.config"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "picard"
+ tag "picard/fixmateinformation"
+
+ test("test-picard-fixmateinformation") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ bam(process.out.bam[0][1]).getReadsMD5(),
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/picard/fixmateinformation/tests/main.nf.test.snap b/modules/nf-core/picard/fixmateinformation/tests/main.nf.test.snap
new file mode 100644
index 00000000000..799173a6f92
--- /dev/null
+++ b/modules/nf-core/picard/fixmateinformation/tests/main.nf.test.snap
@@ -0,0 +1,15 @@
+{
+ "test-picard-fixmateinformation": {
+ "content": [
+ "ddd0dc8f0cf1996d19dae51681187114",
+ [
+ "versions.yml:md5,36a59533c3e8578b046c4c2ec9caa8d4"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T09:45:26.092108"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/picard/fixmateinformation/tests/nextflow.config b/modules/nf-core/picard/fixmateinformation/tests/nextflow.config
new file mode 100644
index 00000000000..c6b0432e8a7
--- /dev/null
+++ b/modules/nf-core/picard/fixmateinformation/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+ withName: PICARD_FIXMATEINFORMATION {
+ ext.prefix = { "${meta.id}.fixed" }
+ }
+}
diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf
index e47b74f787e..a4b27c88e5f 100644
--- a/modules/nf-core/picard/liftovervcf/main.nf
+++ b/modules/nf-core/picard/liftovervcf/main.nf
@@ -50,8 +50,8 @@ process PICARD_LIFTOVERVCF {
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
- touch ${prefix}.lifted.vcf.gz
- touch ${prefix}.unlifted.vcf.gz
+ echo | gzip > ${prefix}.lifted.vcf.gz
+ echo | gzip > ${prefix}.unlifted.vcf.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
diff --git a/modules/nf-core/picard/liftovervcf/tests/main.nf.test b/modules/nf-core/picard/liftovervcf/tests/main.nf.test
new file mode 100644
index 00000000000..7b42102dec5
--- /dev/null
+++ b/modules/nf-core/picard/liftovervcf/tests/main.nf.test
@@ -0,0 +1,84 @@
+
+nextflow_process {
+
+ name "Test Process PICARD_LIFTOVERVCF"
+ script "../main.nf"
+ process "PICARD_LIFTOVERVCF"
+ config "./nextflow.config"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "picard"
+ tag "picard/liftovervcf"
+
+ test("test-picard-liftovervcf") {
+
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test' ],
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true)
+ ]
+ input[1] = [ [ id:'genome' ],
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+ ]
+ input[2] = [ [ id:'genome' ],
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+ ]
+ input[3] = [ [ id:'genome' ],
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.chain.gz', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.vcf_lifted[0][1]).vcf.summary,
+ path(process.out.vcf_unlifted[0][1]).vcf.variantsMD5,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-picard-liftovervcf-stubs") {
+ options '-stub'
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test' ],
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true)
+ ]
+ input[1] = [ [ id:'genome' ],
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+ ]
+ input[2] = [ [ id:'genome' ],
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+ ]
+ input[3] = [ [ id:'genome' ],
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.chain.gz', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ file(process.out.vcf_lifted[0][1]).name,
+ file(process.out.vcf_unlifted[0][1]).name,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap b/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap
new file mode 100644
index 00000000000..585ea369e8b
--- /dev/null
+++ b/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap
@@ -0,0 +1,30 @@
+{
+ "test-picard-liftovervcf-stubs": {
+ "content": [
+ "test.lifted.vcf.gz",
+ "test.unlifted.vcf.gz",
+ [
+ "versions.yml:md5,e1aaacb3c05a0d822f7abdcf3a55fa91"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T09:38:05.840798"
+ },
+ "test-picard-liftovervcf": {
+ "content": [
+ "VcfFile [chromosomes=[], sampleCount=1, variantCount=0, phased=true, phasedAutodetect=true]",
+ "39a9de5185d94289283bd27cfcdeba97",
+ [
+ "versions.yml:md5,e1aaacb3c05a0d822f7abdcf3a55fa91"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T09:41:33.022998"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/picard/liftovervcf/tests/nextflow.config b/modules/nf-core/picard/liftovervcf/tests/nextflow.config
new file mode 100644
index 00000000000..d89d78651b9
--- /dev/null
+++ b/modules/nf-core/picard/liftovervcf/tests/nextflow.config
@@ -0,0 +1,3 @@
+process {
+ ext.args = "--WARN_ON_MISSING_CONTIG true"
+}
diff --git a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test
new file mode 100644
index 00000000000..f755447ff4c
--- /dev/null
+++ b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test
@@ -0,0 +1,38 @@
+
+nextflow_process {
+
+ name "Test Process PICARD_RENAMESAMPLEINVCF"
+ script "../main.nf"
+ process "PICARD_RENAMESAMPLEINVCF"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "picard"
+ tag "picard/renamesampleinvcf"
+
+ test("test-picard-renamesampleinvcf") {
+
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test' ],
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.vcf[0][1]).vcf.variantsMD5,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap
new file mode 100644
index 00000000000..a9bf7b7bf04
--- /dev/null
+++ b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap
@@ -0,0 +1,15 @@
+{
+ "test-picard-renamesampleinvcf": {
+ "content": [
+ "e21a2349f41663d1fc38f47fbe65a6d5",
+ [
+ "versions.yml:md5,d4de734264e0c3b33d23e4a40de26a5f"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T09:32:02.18878"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/picard/sortsam/tests/main.nf.test b/modules/nf-core/picard/sortsam/tests/main.nf.test
new file mode 100644
index 00000000000..9d9af09ea77
--- /dev/null
+++ b/modules/nf-core/picard/sortsam/tests/main.nf.test
@@ -0,0 +1,40 @@
+
+nextflow_process {
+
+ name "Test Process PICARD_SORTSAM"
+ script "../main.nf"
+ process "PICARD_SORTSAM"
+ config "./nextflow.config"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "picard"
+ tag "picard/sortsam"
+
+ test("test-picard-sortsam") {
+
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
+ ]
+ input[1] = "queryname"
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ bam(process.out.bam[0][1]).getReadsMD5(),
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/picard/sortsam/tests/main.nf.test.snap b/modules/nf-core/picard/sortsam/tests/main.nf.test.snap
new file mode 100644
index 00000000000..bf447b8d135
--- /dev/null
+++ b/modules/nf-core/picard/sortsam/tests/main.nf.test.snap
@@ -0,0 +1,15 @@
+{
+ "test-picard-sortsam": {
+ "content": [
+ "b9847fed94d2b7286e18caaa099658ce",
+ [
+ "versions.yml:md5,f53876b7c58b5aa1564606f3c9c34108"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T09:23:48.485054"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/picard/sortsam/tests/nextflow.config b/modules/nf-core/picard/sortsam/tests/nextflow.config
new file mode 100644
index 00000000000..8512101e96f
--- /dev/null
+++ b/modules/nf-core/picard/sortsam/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+ withName: PICARD_SORTSAM {
+ ext.prefix = { "${meta.id}.sorted" }
+ }
+}
diff --git a/modules/nf-core/picard/sortvcf/tests/main.nf.test b/modules/nf-core/picard/sortvcf/tests/main.nf.test
new file mode 100644
index 00000000000..9df73ad430f
--- /dev/null
+++ b/modules/nf-core/picard/sortvcf/tests/main.nf.test
@@ -0,0 +1,44 @@
+
+nextflow_process {
+
+ name "Test Process PICARD_SORTVCF"
+ script "../main.nf"
+ process "PICARD_SORTVCF"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "picard"
+ tag "picard/sortvcf"
+
+ test("test-picard-sortvcf") {
+
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
+ ]
+ input[1] = [ [ id:'genome' ],
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+ ]
+ input[2] = [ [ id:'genome' ],
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.vcf[0][1]).linesGzip[3..7],
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap b/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap
new file mode 100644
index 00000000000..db80323bfe5
--- /dev/null
+++ b/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap
@@ -0,0 +1,21 @@
+{
+ "test-picard-sortvcf": {
+ "content": [
+ [
+ "##FILTER=",
+ "##FORMAT=",
+ "##FORMAT=",
+ "##INFO=",
+ "##INFO="
+ ],
+ [
+ "versions.yml:md5,11949a1af95080dcc5bd1c75d68dee71"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T09:20:13.124551"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/untarfiles/environment.yml b/modules/nf-core/untarfiles/environment.yml
index e479f80d548..be5a6da9d88 100644
--- a/modules/nf-core/untarfiles/environment.yml
+++ b/modules/nf-core/untarfiles/environment.yml
@@ -1,9 +1,11 @@
name: untarfiles
+
channels:
- conda-forge
- bioconda
- defaults
+
dependencies:
- - conda-forge::sed=4.7
- bioconda::grep=3.4
+ - conda-forge::sed=4.7
- conda-forge::tar=1.34
diff --git a/modules/nf-core/wittyer/Dockerfile b/modules/nf-core/wittyer/Dockerfile
index 3955699c92d..fae697ab9dc 100644
--- a/modules/nf-core/wittyer/Dockerfile
+++ b/modules/nf-core/wittyer/Dockerfile
@@ -1,11 +1,11 @@
-FROM mcr.microsoft.com/dotnet/sdk:6.0 as builder
+FROM mcr.microsoft.com/dotnet/sdk:6.0@sha256:6df1177e48b55272316d08f19cb383483af82aca5cdc67a76c414bc200847624 as builder
WORKDIR /src
COPY . /src
RUN cd Wittyer \
&& dotnet publish -f net6.0 -r linux-x64 -c Release -o /output \
&& chmod +x /output/Wittyer
-FROM mcr.microsoft.com/dotnet/runtime:6.0
+FROM mcr.microsoft.com/dotnet/runtime:6.0@sha256:437cda84bdce26ce074d88b63abeec567c7226d73e8b911605077468e1d5c8d5
LABEL git_repository=https://git.illumina.com/DASTE/Ilmn.Das.App.Wittyer.git
WORKDIR /opt/Wittyer
RUN apt-get -y update && apt-get -y install tabix libunwind8 openssl procps
diff --git a/subworkflows/nf-core/bcl_demultiplex/main.nf b/subworkflows/nf-core/bcl_demultiplex/main.nf
index 3816f310f9c..129b2f1b554 100644
--- a/subworkflows/nf-core/bcl_demultiplex/main.nf
+++ b/subworkflows/nf-core/bcl_demultiplex/main.nf
@@ -64,65 +64,67 @@ workflow BCL_DEMULTIPLEX {
}
// Generate meta for each fastq
- ch_fastq_with_meta = ch_fastq
- // reshapes the channel from a single emit of [meta, [fastq, fastq, fastq...]]
- // to emits per fastq file like [meta, fastq]
- .transpose()
- .map { fc_meta, fastq ->
- def meta = [:]
- meta.id = fastq.getSimpleName().toString() - ~/_R[0-9]_001.*$/
- meta.samplename = fastq.getSimpleName().toString() - ~/_S[0-9]+.*$/
- meta.fcid = fc_meta.id
- meta.lane = fc_meta.lane
- // The buffered input stream allows reading directly from cloud storage
- // It will not make a local copy of the file.
- fastq.withInputStream {
- InputStream gzipStream = new java.util.zip.GZIPInputStream(it)
- Reader decoder = new InputStreamReader(gzipStream, 'ASCII')
- BufferedReader buffered = new BufferedReader(decoder)
- line = buffered.readLine()
- buffered.close()
- }
- if ( line != null && line.startsWith('@') ) {
- line = line.substring(1)
- // expected format is like:
- // xx:yy:FLOWCELLID:LANE:... (seven fields)
- fields = line.split(':')
- // CASAVA 1.8+ format, from https://support.illumina.com/help/BaseSpace_OLH_009008/Content/Source/Informatics/BS/FileFormat_FASTQ-files_swBS.htm
- // "@::::::: :::"
- sequencer_serial = fields[0]
- run_nubmer = fields[1]
- fcid = fields[2]
- lane = fields[3]
- index = fields[-1] =~ /[GATC+-]/ ? fields[-1] : ""
- ID = [fcid, lane].join(".")
- PU = [fcid, lane, index].findAll().join(".")
- PL = "ILLUMINA"
- SM = fastq.getSimpleName().toString() - ~/_S[0-9]+.*$/
- meta.readgroup = [
- "ID": ID,
- "SM": SM,
- "PL": PL,
- "PU": PU
- ]
- meta.empty = false
- } else {
- println "No reads were found in FASTQ file: ${fastq}"
- meta.readgroup = [:]
- meta.empty = true
- }
- return [meta, fastq]
+ ch_fastq
+ // reshapes the channel from a single emit of [meta, [fastq, fastq, fastq...]]
+ // to emits per fastq file like [meta, fastq]
+ .transpose()
+ .map { fc_meta, fastq ->
+ def meta = [:]
+ meta.id = fastq.getSimpleName().toString() - ~/_R[0-9]_001.*$/
+ meta.samplename = fastq.getSimpleName().toString() - ~/_S[0-9]+.*$/
+ meta.fcid = fc_meta.id
+ meta.lane = fc_meta.lane
+ // The buffered input stream allows reading directly from cloud storage
+ // It will not make a local copy of the file.
+ def line = ""
+ fastq.withInputStream { fq ->
+ def gzipStream = new java.util.zip.GZIPInputStream(fq)
+ def decoder = new InputStreamReader(gzipStream, 'ASCII')
+ def buffered = new BufferedReader(decoder)
+ line = buffered.readLine()
+ buffered.close()
}
- // Group by the meta id so that we can find mate pairs if they exist
- .groupTuple(by: [0])
- .map { meta, fastq ->
- meta.single_end = fastq.size() == 1
- return [meta, fastq.flatten()]
- }
- .branch {
- fastq : it[0].empty == false
- empty_fastq : it[0].empty == true
+ if ( line != null && line.startsWith('@') ) {
+ line = line.substring(1)
+ // expected format is like:
+ // xx:yy:FLOWCELLID:LANE:... (seven fields)
+ fields = line.split(':')
+ // CASAVA 1.8+ format, from https://support.illumina.com/help/BaseSpace_OLH_009008/Content/Source/Informatics/BS/FileFormat_FASTQ-files_swBS.htm
+ // "@::::::: :::"
+ sequencer_serial = fields[0]
+ run_nubmer = fields[1]
+ fcid = fields[2]
+ lane = fields[3]
+ index = fields[-1] =~ /[GATC+-]/ ? fields[-1] : ""
+ ID = [fcid, lane].join(".")
+ PU = [fcid, lane, index].findAll().join(".")
+ PL = "ILLUMINA"
+ SM = fastq.getSimpleName().toString() - ~/_S[0-9]+.*$/
+ meta.readgroup = [
+ "ID": ID,
+ "SM": SM,
+ "PL": PL,
+ "PU": PU
+ ]
+ meta.empty = false
+ } else {
+ println "No reads were found in FASTQ file: ${fastq}"
+ meta.readgroup = [:]
+ meta.empty = true
}
+ return [meta, fastq]
+ }
+ // Group by the meta id so that we can find mate pairs if they exist
+ .groupTuple(by: [0])
+ .map { meta, fastq ->
+ meta.single_end = fastq.size() == 1
+ return [meta, fastq.flatten()]
+ }
+ .branch {
+ fastq : it[0].empty == false
+ empty_fastq : it[0].empty == true
+ }
+ .set{ch_fastq_with_meta}
emit:
fastq = ch_fastq_with_meta.fastq
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index e770d91b974..b54fc16c71a 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -2,10 +2,6 @@
// Subworkflow with functionality that may be useful for any Nextflow pipeline
//
-import org.yaml.snakeyaml.Yaml
-import groovy.json.JsonOutput
-import nextflow.extension.FilesEx
-
/*
========================================================================================
SUBWORKFLOW DEFINITION
@@ -58,7 +54,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
// Generate version string
//
def getWorkflowVersion() {
- String version_string = ""
+ def version_string = "" as String
if (workflow.manifest.version) {
def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
version_string += "${prefix_v}${workflow.manifest.version}"
@@ -79,10 +75,10 @@ def dumpParametersToJSON(outdir) {
def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
def filename = "params_${timestamp}.json"
def temp_pf = new File(workflow.launchDir.toString(), ".${filename}")
- def jsonStr = JsonOutput.toJson(params)
- temp_pf.text = JsonOutput.prettyPrint(jsonStr)
+ def jsonStr = groovy.json.JsonOutput.toJson(params)
+ temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr)
- FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
+ nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
temp_pf.delete()
}
@@ -90,7 +86,7 @@ def dumpParametersToJSON(outdir) {
// When running with -profile conda, warn if channels have not been set-up appropriately
//
def checkCondaChannels() {
- Yaml parser = new Yaml()
+ def parser = new org.yaml.snakeyaml.Yaml()
def channels = []
try {
def config = parser.load("conda config --show channels".execute().text)
@@ -102,14 +98,16 @@ def checkCondaChannels() {
// Check that all channels are present
// This channel list is ordered by required channel priority.
- def required_channels_in_order = ['conda-forge', 'bioconda']
+ def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
// Check that they are in the right order
def channel_priority_violation = false
- def n = required_channels_in_order.size()
- for (int i = 0; i < n - 1; i++) {
- channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
+
+ required_channels_in_order.eachWithIndex { channel, index ->
+ if (index < required_channels_in_order.size() - 1) {
+ channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1]))
+ }
}
if (channels_missing | channel_priority_violation) {
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
index d0a926bf6dd..a09572e5bbf 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -3,7 +3,7 @@ manifest {
author = """nf-core"""
homePage = 'https://127.0.0.1'
description = """Dummy pipeline"""
- nextflowVersion = '!>=23.04.0'
+ nextflowVersion = '!>=23.04.0'
version = '9.9.9'
doi = 'https://doi.org/10.5281/zenodo.5070524'
}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 14558c39278..cbd8495bb60 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -2,9 +2,6 @@
// Subworkflow with utility functions specific to the nf-core pipeline template
//
-import org.yaml.snakeyaml.Yaml
-import nextflow.extension.FilesEx
-
/*
========================================================================================
SUBWORKFLOW DEFINITION
@@ -34,7 +31,7 @@ workflow UTILS_NFCORE_PIPELINE {
// Warn if a -profile or Nextflow config has not been provided to run the pipeline
//
def checkConfigProvided() {
- valid_config = true
+ def valid_config = true as Boolean
if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
"This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
@@ -66,11 +63,13 @@ def checkProfileProvided(nextflow_cli_args) {
//
def workflowCitation() {
def temp_doi_ref = ""
- String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+ def manifest_doi = workflow.manifest.doi.tokenize(",")
// Using a loop to handle multiple DOIs
// Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
// Removing ` ` since the manifest.doi is a string and not a proper list
- for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+ manifest_doi.each { doi_ref ->
+ temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+ }
return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
"* The pipeline\n" +
temp_doi_ref + "\n" +
@@ -84,7 +83,7 @@ def workflowCitation() {
// Generate workflow version string
//
def getWorkflowVersion() {
- String version_string = ""
+ def version_string = "" as String
if (workflow.manifest.version) {
def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
version_string += "${prefix_v}${workflow.manifest.version}"
@@ -102,8 +101,8 @@ def getWorkflowVersion() {
// Get software versions for pipeline
//
def processVersionsFromYAML(yaml_file) {
- Yaml yaml = new Yaml()
- versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
+ def yaml = new org.yaml.snakeyaml.Yaml()
+ def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
return yaml.dumpAsMap(versions).trim()
}
@@ -124,7 +123,7 @@ def workflowVersionToYAML() {
def softwareVersionsToYAML(ch_versions) {
return ch_versions
.unique()
- .map { processVersionsFromYAML(it) }
+ .map { version -> processVersionsFromYAML(version) }
.unique()
.mix(Channel.of(workflowVersionToYAML()))
}
@@ -134,19 +133,19 @@ def softwareVersionsToYAML(ch_versions) {
//
def paramsSummaryMultiqc(summary_params) {
def summary_section = ''
- for (group in summary_params.keySet()) {
+ summary_params.keySet().each { group ->
def group_params = summary_params.get(group) // This gets the parameters of that particular group
if (group_params) {
summary_section += " $group
\n"
summary_section += " \n"
- for (param in group_params.keySet()) {
+ group_params.keySet().sort().each { param ->
summary_section += " - $param
- ${group_params.get(param) ?: 'N/A'}
\n"
}
summary_section += "
\n"
}
}
- String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
+ def yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String
yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n"
yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
@@ -161,7 +160,7 @@ def paramsSummaryMultiqc(summary_params) {
// nf-core logo
//
def nfCoreLogo(monochrome_logs=true) {
- Map colors = logColours(monochrome_logs)
+ def colors = logColours(monochrome_logs) as Map
String.format(
"""\n
${dashedLine(monochrome_logs)}
@@ -180,7 +179,7 @@ def nfCoreLogo(monochrome_logs=true) {
// Return dashed line
//
def dashedLine(monochrome_logs=true) {
- Map colors = logColours(monochrome_logs)
+ def colors = logColours(monochrome_logs) as Map
return "-${colors.dim}----------------------------------------------------${colors.reset}-"
}
@@ -188,7 +187,7 @@ def dashedLine(monochrome_logs=true) {
// ANSII colours used for terminal logging
//
def logColours(monochrome_logs=true) {
- Map colorcodes = [:]
+ def colorcodes = [:] as Map
// Reset / Meta
colorcodes['reset'] = monochrome_logs ? '' : "\033[0m"
@@ -287,7 +286,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
}
def summary = [:]
- for (group in summary_params.keySet()) {
+ summary_params.keySet().sort().each { group ->
summary << summary_params[group]
}
@@ -344,10 +343,10 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
def sendmail_html = sendmail_template.toString()
// Send the HTML e-mail
- Map colors = logColours(monochrome_logs)
+ def colors = logColours(monochrome_logs) as Map
if (email_address) {
try {
- if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+ if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') }
// Try to send HTML e-mail using sendmail
def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
sendmail_tf.withWriter { w -> w << sendmail_html }
@@ -364,13 +363,13 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
// Write summary e-mail HTML to a file
def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
output_hf.withWriter { w -> w << email_html }
- FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
+ nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
output_hf.delete()
// Write summary e-mail TXT to a file
def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
output_tf.withWriter { w -> w << email_txt }
- FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
+ nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
output_tf.delete()
}
@@ -378,7 +377,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
// Print pipeline summary on completion
//
def completionSummary(monochrome_logs=true) {
- Map colors = logColours(monochrome_logs)
+ def colors = logColours(monochrome_logs) as Map
if (workflow.success) {
if (workflow.stats.ignoredCount == 0) {
log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
@@ -395,7 +394,7 @@ def completionSummary(monochrome_logs=true) {
//
def imNotification(summary_params, hook_url) {
def summary = [:]
- for (group in summary_params.keySet()) {
+ summary_params.keySet().sort().each { group ->
summary << summary_params[group]
}
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
new file mode 100644
index 00000000000..4994303ea0b
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -0,0 +1,46 @@
+//
+// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary
+//
+
+include { paramsSummaryLog } from 'plugin/nf-schema'
+include { validateParameters } from 'plugin/nf-schema'
+
+workflow UTILS_NFSCHEMA_PLUGIN {
+
+ take:
+ input_workflow // workflow: the workflow object used by nf-schema to get metadata from the workflow
+ validate_params // boolean: validate the parameters
+ parameters_schema // string: path to the parameters JSON schema.
+ // this has to be the same as the schema given to `validation.parametersSchema`
+ // when this input is empty it will automatically use the configured schema or
+ // "${projectDir}/nextflow_schema.json" as default. This input should not be empty
+ // for meta pipelines
+
+ main:
+
+ //
+ // Print parameter summary to stdout. This will display the parameters
+ // that differ from the default given in the JSON schema
+ //
+ if(parameters_schema) {
+ log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema)
+ } else {
+ log.info paramsSummaryLog(input_workflow)
+ }
+
+ //
+ // Validate the parameters using nextflow_schema.json or the schema
+ // given via the validation.parametersSchema configuration option
+ //
+ if(validate_params) {
+ if(parameters_schema) {
+ validateParameters(parameters_schema:parameters_schema)
+ } else {
+ validateParameters()
+ }
+ }
+
+ emit:
+ dummy_emit = true
+}
+
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
new file mode 100644
index 00000000000..f7d9f028850
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
@@ -0,0 +1,35 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "utils_nfschema_plugin"
+description: Run nf-schema to validate parameters and create a summary of changed parameters
+keywords:
+ - validation
+ - JSON schema
+ - plugin
+ - parameters
+ - summary
+components: []
+input:
+ - input_workflow:
+ type: object
+ description: |
+ The workflow object of the used pipeline.
+ This object contains meta data used to create the params summary log
+ - validate_params:
+ type: boolean
+ description: Validate the parameters and error if invalid.
+ - parameters_schema:
+ type: string
+ description: |
+ Path to the parameters JSON schema.
+ This has to be the same as the schema given to the `validation.parametersSchema` config
+ option. When this input is empty it will automatically use the configured schema or
+ "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way
+ for meta pipelines.
+output:
+ - dummy_emit:
+ type: boolean
+ description: Dummy emit to make nf-core subworkflows lint happy
+authors:
+ - "@nvnieuwk"
+maintainers:
+ - "@nvnieuwk"
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
new file mode 100644
index 00000000000..842dc432af7
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -0,0 +1,117 @@
+nextflow_workflow {
+
+ name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN"
+ script "../main.nf"
+ workflow "UTILS_NFSCHEMA_PLUGIN"
+
+ tag "subworkflows"
+ tag "subworkflows_nfcore"
+ tag "subworkflows/utils_nfschema_plugin"
+ tag "plugin/nf-schema"
+
+ config "./nextflow.config"
+
+ test("Should run nothing") {
+
+ when {
+
+ params {
+ test_data = ''
+ }
+
+ workflow {
+ """
+ validate_params = false
+ input[0] = workflow
+ input[1] = validate_params
+ input[2] = ""
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert workflow.success }
+ )
+ }
+ }
+
+ test("Should validate params") {
+
+ when {
+
+ params {
+ test_data = ''
+ outdir = 1
+ }
+
+ workflow {
+ """
+ validate_params = true
+ input[0] = workflow
+ input[1] = validate_params
+ input[2] = ""
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert workflow.failed },
+ { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
+ )
+ }
+ }
+
+ test("Should run nothing - custom schema") {
+
+ when {
+
+ params {
+ test_data = ''
+ }
+
+ workflow {
+ """
+ validate_params = false
+ input[0] = workflow
+ input[1] = validate_params
+ input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert workflow.success }
+ )
+ }
+ }
+
+ test("Should validate params - custom schema") {
+
+ when {
+
+ params {
+ test_data = ''
+ outdir = 1
+ }
+
+ workflow {
+ """
+ validate_params = true
+ input[0] = workflow
+ input[1] = validate_params
+ input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert workflow.failed },
+ { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
+ )
+ }
+ }
+}
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
new file mode 100644
index 00000000000..0907ac58f00
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -0,0 +1,8 @@
+plugins {
+ id "nf-schema@2.1.0"
+}
+
+validation {
+ parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+ monochromeLogs = true
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
new file mode 100644
index 00000000000..331e0d2f443
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
@@ -0,0 +1,96 @@
+{
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
+ "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
+ "title": ". pipeline parameters",
+ "description": "",
+ "type": "object",
+ "$defs": {
+ "input_output_options": {
+ "title": "Input/output options",
+ "type": "object",
+ "fa_icon": "fas fa-terminal",
+ "description": "Define where the pipeline should find input data and save output data.",
+ "required": ["outdir"],
+ "properties": {
+ "validate_params": {
+ "type": "boolean",
+ "description": "Validate parameters?",
+ "default": true,
+ "hidden": true
+ },
+ "outdir": {
+ "type": "string",
+ "format": "directory-path",
+ "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
+ "fa_icon": "fas fa-folder-open"
+ },
+ "test_data_base": {
+ "type": "string",
+ "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules",
+ "description": "Base for test data directory",
+ "hidden": true
+ },
+ "test_data": {
+ "type": "string",
+ "description": "Fake test data param",
+ "hidden": true
+ }
+ }
+ },
+ "generic_options": {
+ "title": "Generic options",
+ "type": "object",
+ "fa_icon": "fas fa-file-import",
+ "description": "Less common options for the pipeline, typically set in a config file.",
+ "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
+ "properties": {
+ "help": {
+ "type": "boolean",
+ "description": "Display help text.",
+ "fa_icon": "fas fa-question-circle",
+ "hidden": true
+ },
+ "version": {
+ "type": "boolean",
+ "description": "Display version and exit.",
+ "fa_icon": "fas fa-question-circle",
+ "hidden": true
+ },
+ "logo": {
+ "type": "boolean",
+ "default": true,
+ "description": "Display nf-core logo in console output.",
+ "fa_icon": "fas fa-image",
+ "hidden": true
+ },
+ "singularity_pull_docker_container": {
+ "type": "boolean",
+ "description": "Pull Singularity container from Docker?",
+ "hidden": true
+ },
+ "publish_dir_mode": {
+ "type": "string",
+ "default": "copy",
+ "description": "Method used to save pipeline results to output directory.",
+ "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
+ "fa_icon": "fas fa-copy",
+ "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
+ "hidden": true
+ },
+ "monochrome_logs": {
+ "type": "boolean",
+ "description": "Use monochrome_logs",
+ "hidden": true
+ }
+ }
+ }
+ },
+ "allOf": [
+ {
+ "$ref": "#/$defs/input_output_options"
+ },
+ {
+ "$ref": "#/$defs/generic_options"
+ }
+ ]
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index e6efda55068..19e00530590 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -34,69 +34,21 @@ bamtools/convert:
bamtools/split:
- modules/nf-core/bamtools/split/**
- tests/modules/nf-core/bamtools/split/**
-bandage/image:
- - modules/nf-core/bandage/image/**
- - tests/modules/nf-core/bandage/image/**
basicpy:
- modules/nf-core/basicpy/**
- tests/modules/nf-core/basicpy/**
bbmap/align:
- modules/nf-core/bbmap/align/**
- tests/modules/nf-core/bbmap/align/**
-bbmap/bbnorm:
- - modules/nf-core/bbmap/bbnorm/**
- - tests/modules/nf-core/bbmap/bbnorm/**
-bbmap/index:
- - modules/nf-core/bbmap/index/**
- - tests/modules/nf-core/bbmap/index/**
-bbmap/pileup:
- - modules/nf-core/bbmap/pileup/**
- - tests/modules/nf-core/bbmap/pileup/**
bcftools/convert:
- modules/nf-core/bcftools/convert/**
- tests/modules/nf-core/bcftools/convert/**
bcftools/merge:
- modules/nf-core/bcftools/merge/**
- tests/modules/nf-core/bcftools/merge/**
-bcftools/roh:
- - modules/nf-core/bcftools/roh/**
- - tests/modules/nf-core/bcftools/roh/**
-bcftools/split:
- - modules/nf-core/bcftools/split/**
- - tests/modules/nf-core/bcftools/split/**
-beagle5/beagle:
- - modules/nf-core/beagle5/beagle/**
- - tests/modules/nf-core/beagle5/beagle/**
-bedtools/groupby:
- - modules/nf-core/bedtools/groupby/**
- - tests/modules/nf-core/bedtools/groupby/**
bedtools/intersect:
- modules/nf-core/bedtools/intersect/**
- tests/modules/nf-core/bedtools/intersect/**
-bedtools/jaccard:
- - modules/nf-core/bedtools/jaccard/**
- - tests/modules/nf-core/bedtools/jaccard/**
-bedtools/makewindows:
- - modules/nf-core/bedtools/makewindows/**
- - tests/modules/nf-core/bedtools/makewindows/**
-bedtools/maskfasta:
- - modules/nf-core/bedtools/maskfasta/**
- - tests/modules/nf-core/bedtools/maskfasta/**
-bedtools/multiinter:
- - modules/nf-core/bedtools/multiinter/**
- - tests/modules/nf-core/bedtools/multiinter/**
-bedtools/shift:
- - modules/nf-core/bedtools/shift/**
- - tests/modules/nf-core/bedtools/shift/**
-bedtools/slop:
- - modules/nf-core/bedtools/slop/**
- - tests/modules/nf-core/bedtools/slop/**
-bedtools/split:
- - modules/nf-core/bedtools/split/**
- - tests/modules/nf-core/bedtools/split/**
-bedtools/subtract:
- - modules/nf-core/bedtools/subtract/**
- - tests/modules/nf-core/bedtools/subtract/**
bedtools/unionbedg:
- modules/nf-core/bedtools/unionbedg/**
- tests/modules/nf-core/bedtools/unionbedg/**
@@ -407,27 +359,9 @@ gappa/examineheattree:
gatk/indelrealigner:
- modules/nf-core/gatk/indelrealigner/**
- tests/modules/nf-core/gatk/indelrealigner/**
-gatk/unifiedgenotyper:
- - modules/nf-core/gatk/unifiedgenotyper/**
- - tests/modules/nf-core/gatk/unifiedgenotyper/**
-gatk4/calibratedragstrmodel:
- - modules/nf-core/gatk4/calibratedragstrmodel/**
- - tests/modules/nf-core/gatk4/calibratedragstrmodel/**
gatk4/cnnscorevariants:
- modules/nf-core/gatk4/cnnscorevariants/**
- tests/modules/nf-core/gatk4/cnnscorevariants/**
-gatk4/collectreadcounts:
- - modules/nf-core/gatk4/collectreadcounts/**
- - tests/modules/nf-core/gatk4/collectreadcounts/**
-gatk4/collectsvevidence:
- - modules/nf-core/gatk4/collectsvevidence/**
- - tests/modules/nf-core/gatk4/collectsvevidence/**
-gatk4/composestrtablefile:
- - modules/nf-core/gatk4/composestrtablefile/**
- - tests/modules/nf-core/gatk4/composestrtablefile/**
-gatk4/condensedepthevidence:
- - modules/nf-core/gatk4/condensedepthevidence/**
- - tests/modules/nf-core/gatk4/condensedepthevidence/**
gatk4/createreadcountpanelofnormals:
- modules/nf-core/gatk4/createreadcountpanelofnormals/**
- tests/modules/nf-core/gatk4/createreadcountpanelofnormals/**
@@ -437,21 +371,9 @@ gatk4/createsomaticpanelofnormals:
gatk4/determinegermlinecontigploidy:
- modules/nf-core/gatk4/determinegermlinecontigploidy/**
- tests/modules/nf-core/gatk4/determinegermlinecontigploidy/**
-gatk4/fastqtosam:
- - modules/nf-core/gatk4/fastqtosam/**
- - tests/modules/nf-core/gatk4/fastqtosam/**
-gatk4/filterintervals:
- - modules/nf-core/gatk4/filterintervals/**
- - tests/modules/nf-core/gatk4/filterintervals/**
gatk4/filtervarianttranches:
- modules/nf-core/gatk4/filtervarianttranches/**
- tests/modules/nf-core/gatk4/filtervarianttranches/**
-gatk4/gatherbqsrreports:
- - modules/nf-core/gatk4/gatherbqsrreports/**
- - tests/modules/nf-core/gatk4/gatherbqsrreports/**
-gatk4/gatherpileupsummaries:
- - modules/nf-core/gatk4/gatherpileupsummaries/**
- - tests/modules/nf-core/gatk4/gatherpileupsummaries/**
gatk4/genotypegvcfs:
- modules/nf-core/gatk4/genotypegvcfs/**
- tests/modules/nf-core/gatk4/genotypegvcfs/**
@@ -461,39 +383,15 @@ gatk4/germlinecnvcaller:
gatk4/intervallisttobed:
- modules/nf-core/gatk4/intervallisttobed/**
- tests/modules/nf-core/gatk4/intervallisttobed/**
-gatk4/learnreadorientationmodel:
- - modules/nf-core/gatk4/learnreadorientationmodel/**
- - tests/modules/nf-core/gatk4/learnreadorientationmodel/**
-gatk4/leftalignandtrimvariants:
- - modules/nf-core/gatk4/leftalignandtrimvariants/**
- - tests/modules/nf-core/gatk4/leftalignandtrimvariants/**
-gatk4/mergebamalignment:
- - modules/nf-core/gatk4/mergebamalignment/**
- - tests/modules/nf-core/gatk4/mergebamalignment/**
gatk4/postprocessgermlinecnvcalls:
- modules/nf-core/gatk4/postprocessgermlinecnvcalls/**
- tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/**
-gatk4/preprocessintervals:
- - modules/nf-core/gatk4/preprocessintervals/**
- - tests/modules/nf-core/gatk4/preprocessintervals/**
-gatk4/printreads:
- - modules/nf-core/gatk4/printreads/**
- - tests/modules/nf-core/gatk4/printreads/**
gatk4/printsvevidence:
- modules/nf-core/gatk4/printsvevidence/**
- tests/modules/nf-core/gatk4/printsvevidence/**
-gatk4/revertsam:
- - modules/nf-core/gatk4/revertsam/**
- - tests/modules/nf-core/gatk4/revertsam/**
-gatk4/samtofastq:
- - modules/nf-core/gatk4/samtofastq/**
- - tests/modules/nf-core/gatk4/samtofastq/**
gatk4/selectsamples:
- modules/nf-core/gatk4/selectsamples/**
- tests/modules/nf-core/gatk4/selectsamples/**
-gatk4/shiftfasta:
- - modules/nf-core/gatk4/shiftfasta/**
- - tests/modules/nf-core/gatk4/shiftfasta/**
gatk4/sitedepthtobaf:
- modules/nf-core/gatk4/sitedepthtobaf/**
- tests/modules/nf-core/gatk4/sitedepthtobaf/**
@@ -590,15 +488,6 @@ gridss/gridssgenerateponbedpe:
gsea/gsea:
- modules/nf-core/gsea/gsea/**
- tests/modules/nf-core/gsea/gsea/**
-gstama/collapse:
- - modules/nf-core/gstama/collapse/**
- - tests/modules/nf-core/gstama/collapse/**
-gstama/merge:
- - modules/nf-core/gstama/merge/**
- - tests/modules/nf-core/gstama/merge/**
-gstama/polyacleanup:
- - modules/nf-core/gstama/polyacleanup/**
- - tests/modules/nf-core/gstama/polyacleanup/**
gubbins:
- modules/nf-core/gubbins/**
- tests/modules/nf-core/gubbins/**
@@ -623,9 +512,6 @@ haplocheck:
haplogrep2/classify:
- modules/nf-core/haplogrep2/classify/**
- tests/modules/nf-core/haplogrep2/classify/**
-happy/sompy:
- - modules/nf-core/happy/sompy/**
- - tests/modules/nf-core/happy/sompy/**
hicap:
- modules/nf-core/hicap/**
- tests/modules/nf-core/hicap/**
@@ -1013,42 +899,15 @@ peka:
phyloflash:
- modules/nf-core/phyloflash/**
- tests/modules/nf-core/phyloflash/**
-picard/bedtointervallist:
- - modules/nf-core/picard/bedtointervallist/**
- - tests/modules/nf-core/picard/bedtointervallist/**
-picard/cleansam:
- - modules/nf-core/picard/cleansam/**
- - tests/modules/nf-core/picard/cleansam/**
picard/collectinsertsizemetrics:
- modules/nf-core/picard/collectinsertsizemetrics/**
- tests/modules/nf-core/picard/collectinsertsizemetrics/**
-picard/collectmultiplemetrics:
- - modules/nf-core/picard/collectmultiplemetrics/**
- - tests/modules/nf-core/picard/collectmultiplemetrics/**
picard/collectrnaseqmetrics:
- modules/nf-core/picard/collectrnaseqmetrics/**
- tests/modules/nf-core/picard/collectrnaseqmetrics/**
-picard/fastqtosam:
- - modules/nf-core/picard/fastqtosam/**
- - tests/modules/nf-core/picard/fastqtosam/**
picard/filtersamreads:
- modules/nf-core/picard/filtersamreads/**
- tests/modules/nf-core/picard/filtersamreads/**
-picard/fixmateinformation:
- - modules/nf-core/picard/fixmateinformation/**
- - tests/modules/nf-core/picard/fixmateinformation/**
-picard/liftovervcf:
- - modules/nf-core/picard/liftovervcf/**
- - tests/modules/nf-core/picard/liftovervcf/**
-picard/renamesampleinvcf:
- - modules/nf-core/picard/renamesampleinvcf/**
- - tests/modules/nf-core/picard/renamesampleinvcf/**
-picard/sortsam:
- - modules/nf-core/picard/sortsam/**
- - tests/modules/nf-core/picard/sortsam/**
-picard/sortvcf:
- - modules/nf-core/picard/sortvcf/**
- - tests/modules/nf-core/picard/sortvcf/**
pindel/pindel:
- modules/nf-core/pindel/pindel/**
- tests/modules/nf-core/pindel/pindel/**
diff --git a/tests/modules/nf-core/bandage/image/main.nf b/tests/modules/nf-core/bandage/image/main.nf
deleted file mode 100644
index 3da08d40bc0..00000000000
--- a/tests/modules/nf-core/bandage/image/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BANDAGE_IMAGE } from '../../../../../modules/nf-core/bandage/image/main.nf'
-
-workflow test_bandage_image {
- input = [
- [ id:'B-3106' ], // meta map
- file( params.test_data['sarscov2']['illumina']['assembly_gfa'], checkIfExists: true)
- ]
-
- BANDAGE_IMAGE ( input )
-}
diff --git a/tests/modules/nf-core/bandage/image/nextflow.config b/tests/modules/nf-core/bandage/image/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/bandage/image/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/bandage/image/test.yml b/tests/modules/nf-core/bandage/image/test.yml
deleted file mode 100644
index 07949fcd17c..00000000000
--- a/tests/modules/nf-core/bandage/image/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bandage image
- command: nextflow run ./tests/modules/nf-core/bandage/image -entry test_bandage_image -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bandage/image/nextflow.config
- tags:
- - bandage
- - bandage/image
- files:
- - path: output/bandage/B-3106.png
- - path: output/bandage/B-3106.svg
diff --git a/tests/modules/nf-core/bbmap/bbnorm/main.nf b/tests/modules/nf-core/bbmap/bbnorm/main.nf
deleted file mode 100644
index d0f65273280..00000000000
--- a/tests/modules/nf-core/bbmap/bbnorm/main.nf
+++ /dev/null
@@ -1,50 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BBMAP_BBNORM } from '../../../../../modules/nf-core/bbmap/bbnorm/main.nf'
-
-workflow test_bbmap_bbnorm_se {
-
- input = [
- [ id:'test', single_end:true ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
- ]
-
- BBMAP_BBNORM ( input )
-}
-
-workflow test_bbmap_bbnorm_pe {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- [
- file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
- ]
- ]
-
- BBMAP_BBNORM ( input )
-}
-
-workflow test_bbmap_bbnorm_interleaved {
-
- input = [
- [id:'test', single_end:true ],
- [ file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true)]
- ]
-
- BBMAP_BBNORM ( input )
-}
-
- workflow test_bbmap_bbnorm_multiple_input {
- input = [
- [id:'test', single_end:true ],
- [
- file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
- ]
- ]
-
- BBMAP_BBNORM ( input )
-}
diff --git a/tests/modules/nf-core/bbmap/bbnorm/nextflow.config b/tests/modules/nf-core/bbmap/bbnorm/nextflow.config
deleted file mode 100644
index 40716de692c..00000000000
--- a/tests/modules/nf-core/bbmap/bbnorm/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
- ext.args = 'target=100 min=5'
-}
diff --git a/tests/modules/nf-core/bbmap/bbnorm/test.yml b/tests/modules/nf-core/bbmap/bbnorm/test.yml
deleted file mode 100644
index c5c15edc783..00000000000
--- a/tests/modules/nf-core/bbmap/bbnorm/test.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-- name: bbmap bbnorm test_bbmap_bbnorm_se
- command: nextflow run ./tests/modules/nf-core/bbmap/bbnorm -entry test_bbmap_bbnorm_se -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/bbnorm/nextflow.config
- tags:
- - bbmap/bbnorm
- - bbmap
- files:
- - path: output/bbmap/test.bbnorm.log
- - path: output/bbmap/test.fastq.gz
- - path: output/bbmap/versions.yml
-
-- name: bbmap bbnorm test_bbmap_bbnorm_pe
- command: nextflow run ./tests/modules/nf-core/bbmap/bbnorm -entry test_bbmap_bbnorm_pe -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/bbnorm/nextflow.config
- tags:
- - bbmap/bbnorm
- - bbmap
- files:
- - path: output/bbmap/test.bbnorm.log
- - path: output/bbmap/test_1.nm.fastq.gz
- - path: output/bbmap/test_2.nm.fastq.gz
- - path: output/bbmap/versions.yml
-
-- name: bbmap bbnorm test_bbmap_bbnorm_interleaved
- command: nextflow run ./tests/modules/nf-core/bbmap/bbnorm -entry test_bbmap_bbnorm_interleaved -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/bbnorm/nextflow.config
- tags:
- - bbmap/bbnorm
- - bbmap
- files:
- - path: output/bbmap/test.bbnorm.log
- - path: output/bbmap/test.fastq.gz
- - path: output/bbmap/versions.yml
diff --git a/tests/modules/nf-core/bbmap/index/main.nf b/tests/modules/nf-core/bbmap/index/main.nf
deleted file mode 100644
index 1c1ad0f422e..00000000000
--- a/tests/modules/nf-core/bbmap/index/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BBMAP_INDEX } from '../../../../../modules/nf-core/bbmap/index/main.nf'
-
-workflow test_bbmap_index {
-
- input = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
- BBMAP_INDEX ( input )
-}
diff --git a/tests/modules/nf-core/bbmap/index/nextflow.config b/tests/modules/nf-core/bbmap/index/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/bbmap/index/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/bbmap/index/test.yml b/tests/modules/nf-core/bbmap/index/test.yml
deleted file mode 100644
index d9956fabca4..00000000000
--- a/tests/modules/nf-core/bbmap/index/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: bbmap index
- command: nextflow run ./tests/modules/nf-core/bbmap/index -entry test_bbmap_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/index/nextflow.config
- tags:
- - bbmap
- - bbmap/index
- files:
- - path: output/bbmap/ref/genome/1/chr1.chrom.gz
- - path: output/bbmap/ref/index/1/chr1_index_k13_c15_b1.block
- md5sum: 9f0d9a7413c1d2c16cc24555b2381163
diff --git a/tests/modules/nf-core/bbmap/pileup/main.nf b/tests/modules/nf-core/bbmap/pileup/main.nf
deleted file mode 100644
index beb482abfce..00000000000
--- a/tests/modules/nf-core/bbmap/pileup/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BBMAP_PILEUP } from '../../../../../modules/nf-core/bbmap/pileup/main.nf'
-
-workflow test_bbmap_pileup {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
- ]
-
- BBMAP_PILEUP ( input )
-}
diff --git a/tests/modules/nf-core/bbmap/pileup/nextflow.config b/tests/modules/nf-core/bbmap/pileup/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/bbmap/pileup/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/bbmap/pileup/test.yml b/tests/modules/nf-core/bbmap/pileup/test.yml
deleted file mode 100644
index befee77155f..00000000000
--- a/tests/modules/nf-core/bbmap/pileup/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: "bbmap pileup"
- command: nextflow run ./tests/modules/nf-core/bbmap/pileup -entry test_bbmap_pileup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/pileup/nextflow.config
- tags:
- - "bbmap"
- - "bbmap/pileup"
- files:
- - path: "output/bbmap/test.coverage.stats.txt"
- md5sum: c3fc9d0681589b69e3301ca3cb27b7a4
- - path: "output/bbmap/test.coverage.hist.txt"
- md5sum: 96915920ef42ddc9483457dd4585a088
- - path: output/bbmap/versions.yml
- md5sum: 20fc1f456119714e10196c62f6d04be4
diff --git a/tests/modules/nf-core/bcftools/roh/main.nf b/tests/modules/nf-core/bcftools/roh/main.nf
deleted file mode 100644
index d18a0aecefc..00000000000
--- a/tests/modules/nf-core/bcftools/roh/main.nf
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_ROH } from '../../../../../modules/nf-core/bcftools/roh/main.nf'
-
-workflow test_bcftools_roh {
-
- input = [ [ id:'test' ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
-
- af_file = [[],[]]
- gen_map = []
- regions = []
- targets = []
- samples = []
-
- BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets )
-}
-
-workflow test_bcftools_roh_stub {
-
- input = [ [ id:'test' ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
-
- af_file = [[],[]]
- gen_map = []
- regions = []
- targets = []
- samples = []
-
- BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets )
-}
diff --git a/tests/modules/nf-core/bcftools/roh/nextflow.config b/tests/modules/nf-core/bcftools/roh/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/bcftools/roh/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/bcftools/roh/test.yml b/tests/modules/nf-core/bcftools/roh/test.yml
deleted file mode 100644
index 3ea272dd53a..00000000000
--- a/tests/modules/nf-core/bcftools/roh/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: "bcftools roh"
- command: nextflow run ./tests/modules/nf-core/bcftools/roh -entry test_bcftools_roh -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/roh/nextflow.config
- tags:
- - "bcftools"
- - "bcftools/roh"
- files:
- - path: "output/bcftools/test.roh"
- - path: "output/bcftools/versions.yml"
-
-- name: "bcftools roh stub"
- command: nextflow run ./tests/modules/nf-core/bcftools/roh -entry test_bcftools_roh_stub -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/roh/nextflow.config
- tags:
- - "bcftools"
- - "bcftools/roh"
- files:
- - path: "output/bcftools/test.roh"
- - path: "output/bcftools/versions.yml"
diff --git a/tests/modules/nf-core/bcftools/split/main.nf b/tests/modules/nf-core/bcftools/split/main.nf
deleted file mode 100644
index 6304841ca82..00000000000
--- a/tests/modules/nf-core/bcftools/split/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_SPLIT } from '../../../../../modules/nf-core/bcftools/split/main.nf'
-
-workflow test_bcftools_split {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true)
- ]
-
- BCFTOOLS_SPLIT ( input )
-}
diff --git a/tests/modules/nf-core/bcftools/split/nextflow.config b/tests/modules/nf-core/bcftools/split/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/bcftools/split/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/bcftools/split/test.yml b/tests/modules/nf-core/bcftools/split/test.yml
deleted file mode 100644
index d4178a52b41..00000000000
--- a/tests/modules/nf-core/bcftools/split/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bcftools split test_bcftools_split
- command: nextflow run ./tests/modules/nf-core/bcftools/split -entry test_bcftools_split -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/split/nextflow.config
- tags:
- - bcftools
- - bcftools/split
- files:
- - path: output/bcftools/test.chr22.vcf.gz
- - path: output/bcftools/versions.yml
diff --git a/tests/modules/nf-core/beagle5/beagle/main.nf b/tests/modules/nf-core/beagle5/beagle/main.nf
deleted file mode 100644
index b54d2b13e02..00000000000
--- a/tests/modules/nf-core/beagle5/beagle/main.nf
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEAGLE5_BEAGLE } from '../../../../../modules/nf-core/beagle5/beagle/main.nf'
-
-workflow test_beagle5_beagle {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/target.22Jul22.46e.vcf.gz", checkIfExists: true)
- ]
- refpanel = []
- genmap = []
- exclsamples = []
- exclmarkers = []
-
- BEAGLE5_BEAGLE ( input, refpanel, genmap, exclsamples, exclmarkers )
-}
-
-workflow test_beagle5_beagle_ref {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/target.22Jul22.46e.vcf.gz", checkIfExists: true)
- ]
- refpanel = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/ref.22Jul22.46e.vcf.gz", checkIfExists: true)
- genmap = []
- exclsamples = []
- exclmarkers = []
-
- BEAGLE5_BEAGLE ( input, refpanel, genmap, exclsamples, exclmarkers )
-}
-
-workflow test_beagle5_beagle_ref_map {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/target.22Jul22.46e.vcf.gz", checkIfExists: true)
- ]
- refpanel = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/ref.22Jul22.46e.vcf.gz", checkIfExists: true)
- genmap = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/beagle/plink.chr22.GRCh38.map", checkIfExists: true)
- exclsamples = []
- exclmarkers = []
-
- BEAGLE5_BEAGLE ( input, refpanel, genmap, exclsamples, exclmarkers )
-}
diff --git a/tests/modules/nf-core/beagle5/beagle/nextflow.config b/tests/modules/nf-core/beagle5/beagle/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/beagle5/beagle/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/beagle5/beagle/test.yml b/tests/modules/nf-core/beagle5/beagle/test.yml
deleted file mode 100644
index 4d7831c3558..00000000000
--- a/tests/modules/nf-core/beagle5/beagle/test.yml
+++ /dev/null
@@ -1,32 +0,0 @@
-- name: beagle5 beagle test_beagle5_beagle
- command: nextflow run ./tests/modules/nf-core/beagle5/beagle -entry test_beagle5_beagle -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/beagle5/beagle/nextflow.config
- tags:
- - beagle5
- - beagle5/beagle
- files:
- - path: output/beagle5/test.bglout.log
- contains: ["Brian L. Browning"]
- - path: output/beagle5/test.bglout.vcf.gz
- md5sum: 14e622330da1749c77d5b488b76842cc
-
-- name: beagle5 beagle test_beagle5_beagle_ref
- command: nextflow run ./tests/modules/nf-core/beagle5/beagle -entry test_beagle5_beagle_ref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/beagle5/beagle/nextflow.config
- tags:
- - beagle5
- - beagle5/beagle
- files:
- - path: output/beagle5/test.bglout.log
- contains: ["Brian L. Browning"]
- - path: output/beagle5/test.bglout.vcf.gz
- md5sum: 1c2dbf11ede60ac2f2e16b02e5351f3d
-
-- name: beagle5 beagle test_beagle5_beagle_ref_map
- command: nextflow run ./tests/modules/nf-core/beagle5/beagle -entry test_beagle5_beagle_ref_map -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/beagle5/beagle/nextflow.config
- tags:
- - beagle5
- - beagle5/beagle
- files:
- - path: output/beagle5/test.bglout.log
- contains: ["Brian L. Browning"]
- - path: output/beagle5/test.bglout.vcf.gz
- md5sum: 1c9f97b269542c0e632c47d854a74457
diff --git a/tests/modules/nf-core/bedtools/groupby/main.nf b/tests/modules/nf-core/bedtools/groupby/main.nf
deleted file mode 100644
index f76256c4b19..00000000000
--- a/tests/modules/nf-core/bedtools/groupby/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_GROUPBY } from '../../../../../modules/nf-core/bedtools/groupby/main.nf'
-
-workflow test_bedtools_groupby {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
- ]
- BEDTOOLS_GROUPBY ( input, 5 )
-}
diff --git a/tests/modules/nf-core/bedtools/groupby/nextflow.config b/tests/modules/nf-core/bedtools/groupby/nextflow.config
deleted file mode 100644
index 97db8a6c3f0..00000000000
--- a/tests/modules/nf-core/bedtools/groupby/nextflow.config
+++ /dev/null
@@ -1,10 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-
- withName: BEDTOOLS_GROUPBY {
- ext.args = "-g 1"
- }
-
-}
diff --git a/tests/modules/nf-core/bedtools/groupby/test.yml b/tests/modules/nf-core/bedtools/groupby/test.yml
deleted file mode 100644
index ab0f437dcac..00000000000
--- a/tests/modules/nf-core/bedtools/groupby/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: bedtools groupby test_bedtools_groupby
- command: nextflow run ./tests/modules/nf-core/bedtools/groupby -entry test_bedtools_groupby -c ./tests/config/nextflow.config
- tags:
- - bedtools
- - bedtools/groupby
- files:
- - path: output/bedtools/test.grouped.bed
- md5sum: ba080b3d282f206f6312122c71a66745
- - path: output/bedtools/versions.yml
diff --git a/tests/modules/nf-core/bedtools/jaccard/main.nf b/tests/modules/nf-core/bedtools/jaccard/main.nf
deleted file mode 100644
index 97823041cc3..00000000000
--- a/tests/modules/nf-core/bedtools/jaccard/main.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_JACCARD } from '../../../../../modules/nf-core/bedtools/jaccard/main.nf'
-
-workflow test_bedtools_jaccard {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true)
- ]
-
- BEDTOOLS_JACCARD ( input, [[],[]] )
-}
-
-workflow test_bedtools_jaccard_genome {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true)
- ]
-
- genome = [
- [ id:'genome' ],
- file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
- ]
-
- BEDTOOLS_JACCARD ( input, genome )
-}
diff --git a/tests/modules/nf-core/bedtools/jaccard/nextflow.config b/tests/modules/nf-core/bedtools/jaccard/nextflow.config
deleted file mode 100644
index 499fa9974b3..00000000000
--- a/tests/modules/nf-core/bedtools/jaccard/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
- withName: "test_bedtools_jaccard_genome:BEDTOOLS_JACCARD" {
- ext.args = "-sorted"
- }
-
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/bedtools/jaccard/test.yml b/tests/modules/nf-core/bedtools/jaccard/test.yml
deleted file mode 100644
index 0368fc92217..00000000000
--- a/tests/modules/nf-core/bedtools/jaccard/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: bedtools jaccard test_bedtools_jaccard
- command: nextflow run ./tests/modules/nf-core/bedtools/jaccard -entry test_bedtools_jaccard -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/jaccard/nextflow.config
- tags:
- - bedtools/jaccard
- - bedtools
- files:
- - path: output/bedtools/test.tsv
- md5sum: b737742026a3b512a494f3aa7935fded
- - path: output/bedtools/versions.yml
-
-- name: bedtools jaccard test_bedtools_jaccard_genome
- command: nextflow run ./tests/modules/nf-core/bedtools/jaccard -entry test_bedtools_jaccard_genome -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/jaccard/nextflow.config
- tags:
- - bedtools/jaccard
- - bedtools
- files:
- - path: output/bedtools/test.tsv
- md5sum: b737742026a3b512a494f3aa7935fded
- - path: output/bedtools/versions.yml
diff --git a/tests/modules/nf-core/bedtools/makewindows/main.nf b/tests/modules/nf-core/bedtools/makewindows/main.nf
deleted file mode 100644
index 13b59ea54e1..00000000000
--- a/tests/modules/nf-core/bedtools/makewindows/main.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_MAKEWINDOWS } from '../../../../../modules/nf-core/bedtools/makewindows/main.nf'
-
-workflow test_bedtools_makewindows_bed {
-
- input = [
- [ id:'test2'],
- file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
- ]
-
- BEDTOOLS_MAKEWINDOWS ( input )
-}
-
-workflow test_bedtools_makewindows_fai {
-
- input = [
- [ id:'test2'],
- file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
- ]
-
- BEDTOOLS_MAKEWINDOWS ( input )
-}
diff --git a/tests/modules/nf-core/bedtools/makewindows/nextflow.config b/tests/modules/nf-core/bedtools/makewindows/nextflow.config
deleted file mode 100644
index e8b8c3eae29..00000000000
--- a/tests/modules/nf-core/bedtools/makewindows/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
- withName: BEDTOOLS_MAKEWINDOWS {
- ext.args = '-w 50 '
- }
-
-}
diff --git a/tests/modules/nf-core/bedtools/makewindows/test.yml b/tests/modules/nf-core/bedtools/makewindows/test.yml
deleted file mode 100644
index f286c65abaa..00000000000
--- a/tests/modules/nf-core/bedtools/makewindows/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: bedtools makewindows test_bedtools_makewindows_bed
- command: nextflow run ./tests/modules/nf-core/bedtools/makewindows -entry test_bedtools_makewindows_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/makewindows/nextflow.config
- tags:
- - bedtools/makewindows
- - bedtools
- files:
- - path: output/bedtools/test2.bed
- md5sum: 0cf6ed2b6f470cd44a247da74ca4fe4e
- - path: output/bedtools/versions.yml
-
-- name: bedtools makewindows test_bedtools_makewindows_fai
- command: nextflow run ./tests/modules/nf-core/bedtools/makewindows -entry test_bedtools_makewindows_fai -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/makewindows/nextflow.config
- tags:
- - bedtools/makewindows
- - bedtools
- files:
- - path: output/bedtools/test2.bed
- md5sum: 622d1f62786fe4239b76c53168f21c54
- - path: output/bedtools/versions.yml
diff --git a/tests/modules/nf-core/bedtools/maskfasta/main.nf b/tests/modules/nf-core/bedtools/maskfasta/main.nf
deleted file mode 100644
index 115a44e6b6e..00000000000
--- a/tests/modules/nf-core/bedtools/maskfasta/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_MASKFASTA } from '../../../../../modules/nf-core/bedtools/maskfasta/main.nf'
-
-workflow test_bedtools_maskfasta {
- bed = [ [ id:'test'],
- file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
- ]
- fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
- BEDTOOLS_MASKFASTA ( bed, fasta )
-}
diff --git a/tests/modules/nf-core/bedtools/maskfasta/nextflow.config b/tests/modules/nf-core/bedtools/maskfasta/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/bedtools/maskfasta/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/bedtools/maskfasta/test.yml b/tests/modules/nf-core/bedtools/maskfasta/test.yml
deleted file mode 100644
index 62c834a8c09..00000000000
--- a/tests/modules/nf-core/bedtools/maskfasta/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bedtools maskfasta
- command: nextflow run ./tests/modules/nf-core/bedtools/maskfasta -entry test_bedtools_maskfasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/maskfasta/nextflow.config
- tags:
- - bedtools
- - bedtools/maskfasta
- files:
- - path: ./output/bedtools/test.fa
- md5sum: f4f6749698f11074228d2c79338e3b9c
diff --git a/tests/modules/nf-core/bedtools/multiinter/main.nf b/tests/modules/nf-core/bedtools/multiinter/main.nf
deleted file mode 100644
index b453116857c..00000000000
--- a/tests/modules/nf-core/bedtools/multiinter/main.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_MULTIINTER } from '../../../../../modules/nf-core/bedtools/multiinter/main.nf'
-
-workflow test_bedtools_multiinter {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- [
- file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
- file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)
- ]
- ]
-
- BEDTOOLS_MULTIINTER ( input, [] )
-}
-
-workflow test_bedtools_multiinter_genome {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- [
- file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
- file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)
- ]
- ]
- sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
-
- BEDTOOLS_MULTIINTER ( input, sizes )
-}
diff --git a/tests/modules/nf-core/bedtools/multiinter/nextflow.config b/tests/modules/nf-core/bedtools/multiinter/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/bedtools/multiinter/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/bedtools/multiinter/test.yml b/tests/modules/nf-core/bedtools/multiinter/test.yml
deleted file mode 100644
index 16e7bca6636..00000000000
--- a/tests/modules/nf-core/bedtools/multiinter/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: bedtools multiinter test_bedtools_multiinter
- command: nextflow run ./tests/modules/nf-core/bedtools/multiinter -entry test_bedtools_multiinter -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/multiinter/nextflow.config
- tags:
- - bedtools/multiinter
- - bedtools
- files:
- - path: output/bedtools/test.bed
- md5sum: 03d8d889a19cf26e038868775bbcbaa7
- - path: output/bedtools/versions.yml
-
-- name: bedtools multiinter test_bedtools_multiinter_genome
- command: nextflow run ./tests/modules/nf-core/bedtools/multiinter -entry test_bedtools_multiinter_genome -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/multiinter/nextflow.config
- tags:
- - bedtools/multiinter
- - bedtools
- files:
- - path: output/bedtools/test.bed
- md5sum: 03d8d889a19cf26e038868775bbcbaa7
- - path: output/bedtools/versions.yml
diff --git a/tests/modules/nf-core/bedtools/shift/main.nf b/tests/modules/nf-core/bedtools/shift/main.nf
deleted file mode 100644
index e4453c85367..00000000000
--- a/tests/modules/nf-core/bedtools/shift/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_SHIFT } from '../../../../../modules/nf-core/bedtools/shift/main.nf'
-
-workflow test_bedtools_shift {
- input = [ [ id:'test'],
- file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
- ]
- sizes = [[id:'sizes'],file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)]
- BEDTOOLS_SHIFT ( input, sizes )
-}
diff --git a/tests/modules/nf-core/bedtools/shift/test.yml b/tests/modules/nf-core/bedtools/shift/test.yml
deleted file mode 100644
index 820eb95a042..00000000000
--- a/tests/modules/nf-core/bedtools/shift/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bedtools shift
- command: nextflow run ./tests/modules/nf-core/bedtools/shift -entry test_bedtools_shift -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/shift/nextflow.config
- tags:
- - bedtools
- - bedtools/shift
- files:
- - path: ./output/bedtools/test_out.bed
- md5sum: fdfa2c33084f1f8e42505076a449afdc
diff --git a/tests/modules/nf-core/bedtools/slop/main.nf b/tests/modules/nf-core/bedtools/slop/main.nf
deleted file mode 100644
index 40531695034..00000000000
--- a/tests/modules/nf-core/bedtools/slop/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_SLOP } from '../../../../../modules/nf-core/bedtools/slop/main.nf'
-
-workflow test_bedtools_slop {
- input = [ [ id:'test'],
- file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
- ]
- sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
-
- BEDTOOLS_SLOP ( input, sizes )
-}
-
diff --git a/tests/modules/nf-core/bedtools/slop/test.yml b/tests/modules/nf-core/bedtools/slop/test.yml
deleted file mode 100644
index a69dedb6317..00000000000
--- a/tests/modules/nf-core/bedtools/slop/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bedtools slop
- command: nextflow run ./tests/modules/nf-core/bedtools/slop -entry test_bedtools_slop -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/slop/nextflow.config
- tags:
- - bedtools
- - bedtools/slop
- files:
- - path: ./output/bedtools/test_out.bed
- md5sum: 4f1d8924925fe5d205c9e1981fe290a4
diff --git a/tests/modules/nf-core/bedtools/split/main.nf b/tests/modules/nf-core/bedtools/split/main.nf
deleted file mode 100644
index 686d251cc96..00000000000
--- a/tests/modules/nf-core/bedtools/split/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_SPLIT } from '../../../../../modules/nf-core/bedtools/split/main.nf'
-
-workflow test_bedtools_split {
-
- input = [
- [ id:'test' ], // meta map
- file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true),
- 2
- ]
-
- BEDTOOLS_SPLIT ( input )
-}
diff --git a/tests/modules/nf-core/bedtools/split/nextflow.config b/tests/modules/nf-core/bedtools/split/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/bedtools/split/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/bedtools/split/test.yml b/tests/modules/nf-core/bedtools/split/test.yml
deleted file mode 100644
index efb7065ba9b..00000000000
--- a/tests/modules/nf-core/bedtools/split/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: bedtools split test_bedtools_split
- command: nextflow run ./tests/modules/nf-core/bedtools/split -entry test_bedtools_split -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/split/nextflow.config
- tags:
- - bedtools/split
- - bedtools
- files:
- - path: output/bedtools/test.00001.bed
- - path: output/bedtools/test.00002.bed
- - path: output/bedtools/versions.yml
diff --git a/tests/modules/nf-core/bedtools/subtract/main.nf b/tests/modules/nf-core/bedtools/subtract/main.nf
deleted file mode 100644
index a86c81a1870..00000000000
--- a/tests/modules/nf-core/bedtools/subtract/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_SUBTRACT } from '../../../../../modules/nf-core/bedtools/subtract/main.nf'
-
-workflow test_bedtools_subtract {
- input = [
- [ id:'test_subtract' ],
- file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true),
- file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
- ]
-
- BEDTOOLS_SUBTRACT ( input )
-}
diff --git a/tests/modules/nf-core/bedtools/subtract/nextflow.config b/tests/modules/nf-core/bedtools/subtract/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/bedtools/subtract/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/bedtools/subtract/test.yml b/tests/modules/nf-core/bedtools/subtract/test.yml
deleted file mode 100644
index efb1863cbaa..00000000000
--- a/tests/modules/nf-core/bedtools/subtract/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bedtools subtract
- command: nextflow run ./tests/modules/nf-core/bedtools/subtract -entry test_bedtools_subtract -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/subtract/nextflow.config
- tags:
- - bedtools
- - bedtools/subtract
- files:
- - path: output/bedtools/test_subtract.bed
- md5sum: 63513c4dc69e8b481ce3b4b2a9f24259
diff --git a/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf b/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf
deleted file mode 100644
index b308871657b..00000000000
--- a/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK_UNIFIEDGENOTYPER } from '../../../../../modules/nf-core/gatk/unifiedgenotyper/main.nf'
-
-workflow test_gatk_unifiedgenotyper {
-
- input = [
- [ id:'test' ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
- ]
- fasta = [
- [id: 'test'],
- file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
- ]
- fai = [
- [id: 'test'],
- file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
- ]
- dict = [
- [id: 'test'],
- file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
- ]
-
- GATK_UNIFIEDGENOTYPER ( input, fasta, fai, dict, [[],[]], [[],[]], [[],[]], [[],[]])
-}
diff --git a/tests/modules/nf-core/gatk/unifiedgenotyper/nextflow.config b/tests/modules/nf-core/gatk/unifiedgenotyper/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/gatk/unifiedgenotyper/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/gatk/unifiedgenotyper/test.yml b/tests/modules/nf-core/gatk/unifiedgenotyper/test.yml
deleted file mode 100644
index 9350e5a6af6..00000000000
--- a/tests/modules/nf-core/gatk/unifiedgenotyper/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: gatk unifiedgenotyper test_gatk_unifiedgenotyper
- command: nextflow run ./tests/modules/nf-core/gatk/unifiedgenotyper -entry test_gatk_unifiedgenotyper -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk/unifiedgenotyper/nextflow.config
- tags:
- - gatk
- - gatk/unifiedgenotyper
- files:
- - path: output/gatk/test.vcf.gz
- contains:
- - "#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test"
diff --git a/tests/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/tests/modules/nf-core/gatk4/calibratedragstrmodel/main.nf
deleted file mode 100644
index 29b149b2cd9..00000000000
--- a/tests/modules/nf-core/gatk4/calibratedragstrmodel/main.nf
+++ /dev/null
@@ -1,82 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_CALIBRATEDRAGSTRMODEL } from '../../../../../modules/nf-core/gatk4/calibratedragstrmodel/main.nf'
-
-workflow test_gatk4_calibratedragstrmodel_bam {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
- ]
-
- fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
- fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
- dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
- strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true)
-
- GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile )
-}
-
-workflow test_gatk4_calibratedragstrmodel_cram {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
- ]
-
- fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
- fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
- dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
- strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true)
-
- GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile )
-}
-
-workflow test_gatk4_calibratedragstrmodel_beds {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
- ]
-
- fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
- fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
- dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
- strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true)
-
- GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile )
-}
-
-workflow test_gatk4_calibratedragstrmodel_gzipped_beds {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
- ]
-
- fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
- fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
- dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
- strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true)
-
- GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile )
-}
-
diff --git a/tests/modules/nf-core/gatk4/calibratedragstrmodel/nextflow.config b/tests/modules/nf-core/gatk4/calibratedragstrmodel/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/gatk4/calibratedragstrmodel/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/gatk4/calibratedragstrmodel/test.yml b/tests/modules/nf-core/gatk4/calibratedragstrmodel/test.yml
deleted file mode 100644
index 60a33dc1c92..00000000000
--- a/tests/modules/nf-core/gatk4/calibratedragstrmodel/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_bam
- command: nextflow run ./tests/modules/nf-core/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/calibratedragstrmodel/nextflow.config
- tags:
- - gatk4/calibratedragstrmodel
- - gatk4
- files:
- - path: output/gatk4/test.txt
- md5sum: e16fa32906c74bb18b93e98a86718ff1
- - path: output/gatk4/versions.yml
-
-- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_cram
- command: nextflow run ./tests/modules/nf-core/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/calibratedragstrmodel/nextflow.config
- tags:
- - gatk4/calibratedragstrmodel
- - gatk4
- files:
- - path: output/gatk4/test.txt
- md5sum: 81c7bf338886cb4d5c2cc07fc56afe44
- - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/collectreadcounts/main.nf b/tests/modules/nf-core/gatk4/collectreadcounts/main.nf
deleted file mode 100644
index 2ddc184a236..00000000000
--- a/tests/modules/nf-core/gatk4/collectreadcounts/main.nf
+++ /dev/null
@@ -1,54 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_COLLECTREADCOUNTS } from '../../../../../modules/nf-core/gatk4/collectreadcounts/main.nf'
-
-workflow test_gatk4_collectreadcounts_hdf5 {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
- ]
-
- fasta = [[],[]]
- fai = [[],[]]
- dict = [[],[]]
-
- GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict )
-}
-
-workflow test_gatk4_collectreadcounts_tsv {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
- ]
-
- fasta = [[],[]]
- fai = [[],[]]
- dict = [[],[]]
-
- GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict )
-}
-
-workflow test_gatk4_collectreadcounts_cram {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
- ]
-
- fasta = [[id:'test'], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)]
- fai = [[id:'test'], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)]
- dict = [[id:'test'], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)]
-
- GATK4_COLLECTREADCOUNTS ( input, fasta, fai, dict )
-}
-
diff --git a/tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config b/tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config
deleted file mode 100644
index 3863bf92946..00000000000
--- a/tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config
+++ /dev/null
@@ -1,17 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
- withName: 'test_gatk4_collectreadcounts_hdf5:GATK4_COLLECTREADCOUNTS'{
- ext.args = "--interval-merging-rule OVERLAPPING_ONLY"
- }
-
- withName: 'test_gatk4_collectreadcounts_tsv:GATK4_COLLECTREADCOUNTS' {
- ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY"
- }
-
- withName: 'test_gatk4_collectreadcounts_cram:GATK4_COLLECTREADCOUNTS' {
- ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY"
- }
-
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/gatk4/collectreadcounts/test.yml b/tests/modules/nf-core/gatk4/collectreadcounts/test.yml
deleted file mode 100644
index cc0f2106d3c..00000000000
--- a/tests/modules/nf-core/gatk4/collectreadcounts/test.yml
+++ /dev/null
@@ -1,54 +0,0 @@
-- name: gatk4 collectreadcounts test_gatk4_collectreadcounts_hdf5
- command: nextflow run ./tests/modules/nf-core/gatk4/collectreadcounts -entry test_gatk4_collectreadcounts_hdf5 -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config
- tags:
- - gatk4/collectreadcounts
- - gatk4
- files:
- - path: output/gatk4/test.hdf5
- - path: output/gatk4/versions.yml
-
-- name: gatk4 collectreadcounts test_gatk4_collectreadcounts_tsv
- command: nextflow run ./tests/modules/nf-core/gatk4/collectreadcounts -entry test_gatk4_collectreadcounts_tsv -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config
- tags:
- - gatk4/collectreadcounts
- - gatk4
- files:
- - path: output/gatk4/test.tsv
- md5sum: 8e45a6164916c303387f39f02ce45841
- - path: output/gatk4/versions.yml
-
-- name: gatk4 collectreadcounts test_gatk4_collectreadcounts_cram
- command: nextflow run ./tests/modules/nf-core/gatk4/collectreadcounts -entry test_gatk4_collectreadcounts_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config
- tags:
- - gatk4/collectreadcounts
- - gatk4
- files:
- - path: output/gatk4/test.tsv
- - path: output/gatk4/versions.yml
-
-- name: gatk4 collectreadcounts test_gatk4_collectreadcounts_hdf5_stub
- command: nextflow run ./tests/modules/nf-core/gatk4/collectreadcounts -entry test_gatk4_collectreadcounts_hdf5 -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config -stub
- tags:
- - gatk4/collectreadcounts
- - gatk4
- files:
- - path: output/gatk4/test.hdf5
- - path: output/gatk4/versions.yml
-
-- name: gatk4 collectreadcounts test_gatk4_collectreadcounts_tsv_stub
- command: nextflow run ./tests/modules/nf-core/gatk4/collectreadcounts -entry test_gatk4_collectreadcounts_tsv -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config -stub
- tags:
- - gatk4/collectreadcounts
- - gatk4
- files:
- - path: output/gatk4/test.tsv
- - path: output/gatk4/versions.yml
-
-- name: gatk4 collectreadcounts test_gatk4_collectreadcounts_cram_stub
- command: nextflow run ./tests/modules/nf-core/gatk4/collectreadcounts -entry test_gatk4_collectreadcounts_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/collectreadcounts/nextflow.config -stub
- tags:
- - gatk4/collectreadcounts
- - gatk4
- files:
- - path: output/gatk4/test.tsv
- - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/collectsvevidence/main.nf b/tests/modules/nf-core/gatk4/collectsvevidence/main.nf
deleted file mode 100644
index 68f406bd560..00000000000
--- a/tests/modules/nf-core/gatk4/collectsvevidence/main.nf
+++ /dev/null
@@ -1,56 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_COLLECTSVEVIDENCE } from '../../../../../modules/nf-core/gatk4/collectsvevidence/main.nf'
-
-workflow test_gatk4_collectsvevidence_cram {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
- [],
- []
- ]
-
- fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
- fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
- dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
- GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict )
-}
-
-workflow test_gatk4_collectsvevidence_bam {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
- [],
- []
- ]
-
- fasta = []
- fasta_fai = []
- dict = []
-
- GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict )
-}
-
-workflow test_gatk4_collectsvevidence_allele_count {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true)
- ]
-
- fasta = []
- fasta_fai = []
- dict = []
-
- GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict )
-}
diff --git a/tests/modules/nf-core/gatk4/collectsvevidence/nextflow.config b/tests/modules/nf-core/gatk4/collectsvevidence/nextflow.config
deleted file mode 100644
index 08bbbe32685..00000000000
--- a/tests/modules/nf-core/gatk4/collectsvevidence/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
- withName: GATK4_COLLECTSVEVIDENCE {
- ext.args = "--sample-name normal"
- }
-
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/gatk4/collectsvevidence/test.yml b/tests/modules/nf-core/gatk4/collectsvevidence/test.yml
deleted file mode 100644
index 9032e7f0cf3..00000000000
--- a/tests/modules/nf-core/gatk4/collectsvevidence/test.yml
+++ /dev/null
@@ -1,51 +0,0 @@
-- name: gatk4 collectsvevidence test_gatk4_collectsvevidence_cram
- command: nextflow run ./tests/modules/nf-core/gatk4/collectsvevidence -entry test_gatk4_collectsvevidence_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/collectsvevidence/nextflow.config
- tags:
- - gatk4/collectsvevidence
- - gatk4
- files:
- - path: output/gatk4/test.pe.txt.gz
- md5sum: 19f13dd0408204590b40239d14acbdde
- - path: output/gatk4/test.pe.txt.gz.tbi
- md5sum: a41bb7768ba058a95c67b69bad9e096d
- - path: output/gatk4/test.sr.txt.gz
- md5sum: fb9ce52193a0db3a084890bd6bbf6a64
- - path: output/gatk4/test.sr.txt.gz.tbi
- md5sum: 33b3a9ff444eb0e0fc3016239651f05f
- - path: output/gatk4/versions.yml
-
-- name: gatk4 collectsvevidence test_gatk4_collectsvevidence_bam
- command: nextflow run ./tests/modules/nf-core/gatk4/collectsvevidence -entry test_gatk4_collectsvevidence_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/collectsvevidence/nextflow.config
- tags:
- - gatk4/collectsvevidence
- - gatk4
- files:
- - path: output/gatk4/test.pe.txt.gz
- md5sum: 19f13dd0408204590b40239d14acbdde
- - path: output/gatk4/test.pe.txt.gz.tbi
- md5sum: a41bb7768ba058a95c67b69bad9e096d
- - path: output/gatk4/test.sr.txt.gz
- md5sum: fb9ce52193a0db3a084890bd6bbf6a64
- - path: output/gatk4/test.sr.txt.gz.tbi
- md5sum: 33b3a9ff444eb0e0fc3016239651f05f
- - path: output/gatk4/versions.yml
-
-- name: gatk4 collectsvevidence test_gatk4_collectsvevidence_allele_count
- command: nextflow run ./tests/modules/nf-core/gatk4/collectsvevidence -entry test_gatk4_collectsvevidence_allele_count -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/collectsvevidence/nextflow.config
- tags:
- - gatk4/collectsvevidence
- - gatk4
- files:
- - path: output/gatk4/test.pe.txt.gz
- md5sum: 19f13dd0408204590b40239d14acbdde
- - path: output/gatk4/test.pe.txt.gz.tbi
- md5sum: a41bb7768ba058a95c67b69bad9e096d
- - path: output/gatk4/test.sd.txt.gz
- md5sum: 1d1f4e95ee036020a0e5d41dbf114cd7
- - path: output/gatk4/test.sd.txt.gz.tbi
- md5sum: 2eafe78041c60b0d6b9b077dd88eb3ee
- - path: output/gatk4/test.sr.txt.gz
- md5sum: fb9ce52193a0db3a084890bd6bbf6a64
- - path: output/gatk4/test.sr.txt.gz.tbi
- md5sum: 33b3a9ff444eb0e0fc3016239651f05f
- - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/composestrtablefile/main.nf b/tests/modules/nf-core/gatk4/composestrtablefile/main.nf
deleted file mode 100644
index 4c62f05de88..00000000000
--- a/tests/modules/nf-core/gatk4/composestrtablefile/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_COMPOSESTRTABLEFILE } from '../../../../../modules/nf-core/gatk4/composestrtablefile/main.nf'
-
-workflow test_gatk4_composestrtablefile {
-
- fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-
- fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
- dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
- GATK4_COMPOSESTRTABLEFILE ( fasta, fasta_fai, dict )
-}
diff --git a/tests/modules/nf-core/gatk4/composestrtablefile/nextflow.config b/tests/modules/nf-core/gatk4/composestrtablefile/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/gatk4/composestrtablefile/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/gatk4/composestrtablefile/test.yml b/tests/modules/nf-core/gatk4/composestrtablefile/test.yml
deleted file mode 100644
index 9af011197f5..00000000000
--- a/tests/modules/nf-core/gatk4/composestrtablefile/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: gatk4 composestrtablefile test_gatk4_composestrtablefile
- command: nextflow run ./tests/modules/nf-core/gatk4/composestrtablefile -entry test_gatk4_composestrtablefile -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/composestrtablefile/nextflow.config
- tags:
- - gatk4/composestrtablefile
- - gatk4
- files:
- - path: output/gatk4/genome.zip
- - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/condensedepthevidence/main.nf b/tests/modules/nf-core/gatk4/condensedepthevidence/main.nf
deleted file mode 100644
index dc3c89640f7..00000000000
--- a/tests/modules/nf-core/gatk4/condensedepthevidence/main.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_CONDENSEDEPTHEVIDENCE } from '../../../../../modules/nf-core/gatk4/condensedepthevidence/main.nf'
-
-workflow test_gatk4_condensdepthevidence {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/condensedepthevidence/testN.rd.txt.gz", checkIfExists: true),
- file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/condensedepthevidence/testN.rd.txt.gz.tbi", checkIfExists: true)
- ]
-
- fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
- fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
- dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
- GATK4_CONDENSEDEPTHEVIDENCE (
- input,
- fasta,
- fasta_fai,
- dict
- )
-}
diff --git a/tests/modules/nf-core/gatk4/condensedepthevidence/nextflow.config b/tests/modules/nf-core/gatk4/condensedepthevidence/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/gatk4/condensedepthevidence/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/gatk4/condensedepthevidence/test.yml b/tests/modules/nf-core/gatk4/condensedepthevidence/test.yml
deleted file mode 100644
index 671d81dcab0..00000000000
--- a/tests/modules/nf-core/gatk4/condensedepthevidence/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: gatk4 condensedepthevidence test_gatk4_condensdepthevidence
- command: nextflow run ./tests/modules/nf-core/gatk4/condensedepthevidence -entry test_gatk4_condensdepthevidence -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/condensedepthevidence/nextflow.config
- tags:
- - gatk4
- - gatk4/condensedepthevidence
- files:
- - path: output/gatk4/test.rd.txt.gz
- md5sum: c6c04b78f2aa40744f267518b3cb21b8
- - path: output/gatk4/test.rd.txt.gz.tbi
- md5sum: c30d5548ad94063b105e227483b68779
- - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/fastqtosam/main.nf b/tests/modules/nf-core/gatk4/fastqtosam/main.nf
deleted file mode 100644
index 0a3aef644d4..00000000000
--- a/tests/modules/nf-core/gatk4/fastqtosam/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_FASTQTOSAM } from '../../../../../modules/nf-core/gatk4/fastqtosam/main.nf'
-
-workflow test_gatk4_fastqtosam_single_end {
- input = [ [ id:'test', single_end:true ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
- ]
-
- GATK4_FASTQTOSAM ( input )
-}
-
-workflow test_gatk4_fastqtosam_paired_end {
- input = [ [ id:'test', single_end:false ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
- ]
-
- GATK4_FASTQTOSAM ( input )
-}
diff --git a/tests/modules/nf-core/gatk4/fastqtosam/nextflow.config b/tests/modules/nf-core/gatk4/fastqtosam/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/gatk4/fastqtosam/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/gatk4/fastqtosam/test.yml b/tests/modules/nf-core/gatk4/fastqtosam/test.yml
deleted file mode 100644
index 482284d5956..00000000000
--- a/tests/modules/nf-core/gatk4/fastqtosam/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: gatk4 fastqtosam test_gatk4_fastqtosam_single_end
- command: nextflow run ./tests/modules/nf-core/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/fastqtosam/nextflow.config
- tags:
- - gatk4
- - gatk4/fastqtosam
- files:
- - path: output/gatk4/test.bam
-
-- name: gatk4 fastqtosam test_gatk4_fastqtosam_paired_end
- command: nextflow run ./tests/modules/nf-core/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/fastqtosam/nextflow.config
- tags:
- - gatk4
- - gatk4/fastqtosam
- files:
- - path: output/gatk4/test.bam
- - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/filterintervals/main.nf b/tests/modules/nf-core/gatk4/filterintervals/main.nf
deleted file mode 100644
index 9b45cf5925b..00000000000
--- a/tests/modules/nf-core/gatk4/filterintervals/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_FILTERINTERVALS } from '../../../../../modules/nf-core/gatk4/filterintervals/main.nf'
-
-workflow test_gatk4_filterintervals {
-
- intervals = [
- [ id:'test' ], // meta map
- file(params.test_data['homo_sapiens']['genome']['genome_preprocessed_interval_list'], checkIfExists: true)
- ]
- read_counts = [[:],[file(params.test_data['homo_sapiens']['genome']['genome_preprocessed_count_tsv'], checkIfExists: true)]]
- annotated_intervals = [[:],file(params.test_data['homo_sapiens']['genome']['genome_annotated_interval_tsv'], checkIfExists: true)]
-
- GATK4_FILTERINTERVALS ( intervals, read_counts, annotated_intervals )
-}
diff --git a/tests/modules/nf-core/gatk4/filterintervals/test.yml b/tests/modules/nf-core/gatk4/filterintervals/test.yml
deleted file mode 100644
index 792e07d2426..00000000000
--- a/tests/modules/nf-core/gatk4/filterintervals/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: gatk4 filterintervals test_gatk4_filterintervals
- command: nextflow run ./tests/modules/nf-core/gatk4/filterintervals -entry test_gatk4_filterintervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/filterintervals/nextflow.config
- tags:
- - gatk4/filterintervals
- - gatk4
- files:
- - path: output/gatk4/test.interval_list
- md5sum: 67b15dff732693db3542e6b1dc30a5da
-
-- name: gatk4 filterintervals test_gatk4_filterintervals_stub
- command: nextflow run ./tests/modules/nf-core/gatk4/filterintervals -entry test_gatk4_filterintervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/filterintervals/nextflow.config -stub
- tags:
- - gatk4/filterintervals
- - gatk4
- files:
- - path: output/gatk4/test.interval_list
diff --git a/tests/modules/nf-core/gatk4/gatherbqsrreports/main.nf b/tests/modules/nf-core/gatk4/gatherbqsrreports/main.nf
deleted file mode 100644
index 150c958c682..00000000000
--- a/tests/modules/nf-core/gatk4/gatherbqsrreports/main.nf
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_GATHERBQSRREPORTS } from '../../../../../modules/nf-core/gatk4/gatherbqsrreports/main.nf'
-
-workflow test_gatk4_gatherbqsrreports {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true)
- ]
-
- GATK4_GATHERBQSRREPORTS ( input )
-}
-
-workflow test_gatk4_gatherbqsrreports_multiple {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- [file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test2_baserecalibrator_table'], checkIfExists: true)
- ]
- ]
-
- GATK4_GATHERBQSRREPORTS ( input )
-}
diff --git a/tests/modules/nf-core/gatk4/gatherbqsrreports/nextflow.config b/tests/modules/nf-core/gatk4/gatherbqsrreports/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/gatk4/gatherbqsrreports/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/gatk4/gatherbqsrreports/test.yml b/tests/modules/nf-core/gatk4/gatherbqsrreports/test.yml
deleted file mode 100644
index e70c49eaa86..00000000000
--- a/tests/modules/nf-core/gatk4/gatherbqsrreports/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: gatk4 gatherbqsrreports test_gatk4_gatherbqsrreports
- command: nextflow run ./tests/modules/nf-core/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports -c ./tests/config/nextflow.config
- tags:
- - gatk4
- - gatk4/gatherbqsrreports
- files:
- - path: output/gatk4/test.table
- md5sum: 9603b69fdc3b5090de2e0dd78bfcc4bf
- - path: output/gatk4/versions.yml
-
-- name: gatk4 gatherbqsrreports test_gatk4_gatherbqsrreports_multiple
- command: nextflow run ./tests/modules/nf-core/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports_multiple -c ./tests/config/nextflow.config
- tags:
- - gatk4
- - gatk4/gatherbqsrreports
- files:
- - path: output/gatk4/test.table
- md5sum: 0c1257eececf95db8ca378272d0f21f9
- - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/tests/modules/nf-core/gatk4/gatherpileupsummaries/main.nf
deleted file mode 100644
index a30364439f5..00000000000
--- a/tests/modules/nf-core/gatk4/gatherpileupsummaries/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_GATHERPILEUPSUMMARIES } from '../../../../../modules/nf-core/gatk4/gatherpileupsummaries/main.nf'
-
-workflow test_gatk4_gatherpileupsummaries {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- [file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true)]
- //file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true)]
- ]
-
- dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-
- GATK4_GATHERPILEUPSUMMARIES ( input, dict )
-}
diff --git a/tests/modules/nf-core/gatk4/gatherpileupsummaries/test.yml b/tests/modules/nf-core/gatk4/gatherpileupsummaries/test.yml
deleted file mode 100644
index 835d20d2d7d..00000000000
--- a/tests/modules/nf-core/gatk4/gatherpileupsummaries/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: gatk4 gatherpileupsummaries
- command: nextflow run ./tests/modules/nf-core/gatk4/gatherpileupsummaries -entry test_gatk4_gatherpileupsummaries -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/gatherpileupsummaries/nextflow.config
- tags:
- - gatk4
- - gatk4/gatherpileupsummaries
- files:
- - path: output/gatk4/test.out.pileups.table
- md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
- - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/learnreadorientationmodel/main.nf b/tests/modules/nf-core/gatk4/learnreadorientationmodel/main.nf
deleted file mode 100644
index 5960a568964..00000000000
--- a/tests/modules/nf-core/gatk4/learnreadorientationmodel/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_LEARNREADORIENTATIONMODEL } from '../../../../../modules/nf-core/gatk4/learnreadorientationmodel/main.nf'
-
-workflow test_gatk4_learnreadorientationmodel {
-
- input = [ [ id:'test' ], // meta map
- [file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_f1r2_tar_gz'], checkIfExists: true)] ]
-
- GATK4_LEARNREADORIENTATIONMODEL ( input )
-}
diff --git a/tests/modules/nf-core/gatk4/learnreadorientationmodel/test.yml b/tests/modules/nf-core/gatk4/learnreadorientationmodel/test.yml
deleted file mode 100644
index fff1b387ac4..00000000000
--- a/tests/modules/nf-core/gatk4/learnreadorientationmodel/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: gatk4 learnreadorientationmodel test_gatk4_learnreadorientationmodel
- command: nextflow run ./tests/modules/nf-core/gatk4/learnreadorientationmodel -entry test_gatk4_learnreadorientationmodel -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/learnreadorientationmodel/nextflow.config
- tags:
- - gatk4
- - gatk4/learnreadorientationmodel
- files:
- - path: output/gatk4/test.artifact-prior.tar.gz
- - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf b/tests/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf
deleted file mode 100644
index 8028168f366..00000000000
--- a/tests/modules/nf-core/gatk4/leftalignandtrimvariants/main.nf
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_LEFTALIGNANDTRIMVARIANTS } from '../../../../../modules/nf-core/gatk4/leftalignandtrimvariants/main.nf'
-
-workflow test_gatk4_leftalignandtrimvariants_interval {
-
- input = [ [ id:'test' ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
- file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
- ]
-
- fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
- fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
- dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
- GATK4_LEFTALIGNANDTRIMVARIANTS ( input, fasta, fai, dict )
-}
-
-workflow test_gatk4_leftalignandtrimvariants_no_interval {
-
- input = [ [ id:'test' ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
- []
- ]
-
- fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
- fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
- dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
-
- GATK4_LEFTALIGNANDTRIMVARIANTS ( input, fasta, fai, dict )
-}
diff --git a/tests/modules/nf-core/gatk4/leftalignandtrimvariants/test.yml b/tests/modules/nf-core/gatk4/leftalignandtrimvariants/test.yml
deleted file mode 100644
index 97afa0fa6f2..00000000000
--- a/tests/modules/nf-core/gatk4/leftalignandtrimvariants/test.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-- name: gatk4 leftalignandtrimvariants test_gatk4_leftalignandtrimvariants_interval
- command: nextflow run ./tests/modules/nf-core/gatk4/leftalignandtrimvariants -entry test_gatk4_leftalignandtrimvariants_interval -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/leftalignandtrimvariants/nextflow.config
- tags:
- - gatk4
- - gatk4/leftalignandtrimvariants
- files:
- - path: output/gatk4/test.normalised.vcf.gz
- contains:
- - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
- - path: output/gatk4/test.normalised.vcf.gz.tbi
-
-- name: gatk4 leftalignandtrimvariants test_gatk4_leftalignandtrimvariants_no_interval
- command: nextflow run ./tests/modules/nf-core/gatk4/leftalignandtrimvariants -entry test_gatk4_leftalignandtrimvariants_no_interval -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/leftalignandtrimvariants/nextflow.config
- tags:
- - gatk4
- - gatk4/leftalignandtrimvariants
- files:
- - path: output/gatk4/test.normalised.vcf.gz
- contains:
- - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
- - "MT192765.1\t10502\t.\tTAGATTATGACTGTGTCTCTTTTTGTTACATGCACCA\tTAGAT"
- - path: output/gatk4/test.normalised.vcf.gz.tbi
- - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/mergebamalignment/main.nf b/tests/modules/nf-core/gatk4/mergebamalignment/main.nf
deleted file mode 100644
index 90497e51b1a..00000000000
--- a/tests/modules/nf-core/gatk4/mergebamalignment/main.nf
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_MERGEBAMALIGNMENT } from '../../../../../modules/nf-core/gatk4/mergebamalignment/main.nf'
-
-workflow test_gatk4_mergebamalignment {
- input = [ [ id:'test' ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
- ]
- fasta = [ [ id:'genome' ], // meta map
- file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
- ]
- dict = [ [ id:'genome' ], // meta map
- file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
- ]
-
- GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
-}
-
-workflow test_gatk4_mergebamalignment_stubs {
- input = [ [ id:'test' ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
- ]
- fasta = [ [ id:'genome' ], // meta map
- file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
- ]
- dict = [ [ id:'genome' ], // meta map
- file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
- ]
-
- GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
-}
diff --git a/tests/modules/nf-core/gatk4/mergebamalignment/nextflow.config b/tests/modules/nf-core/gatk4/mergebamalignment/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/gatk4/mergebamalignment/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/gatk4/mergebamalignment/test.yml b/tests/modules/nf-core/gatk4/mergebamalignment/test.yml
deleted file mode 100644
index c918d6297c1..00000000000
--- a/tests/modules/nf-core/gatk4/mergebamalignment/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: gatk4 mergebamalignment test_gatk4_mergebamalignment
- command: nextflow run ./tests/modules/nf-core/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/mergebamalignment/nextflow.config
- tags:
- - gatk4
- - gatk4/mergebamalignment
- files:
- - path: output/gatk4/test.bam
- md5sum: e6f1b343700b7ccb94e81ae127433988
- - path: output/gatk4/versions.yml
-
-- name: gatk4 mergebamalignment test_gatk4_mergebamalignment_stubs
- command: nextflow run ./tests/modules/nf-core/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment_stubs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/mergebamalignment/nextflow.config -stub-run
- tags:
- - gatk4
- - gatk4/mergebamalignment
- files:
- - path: output/gatk4/test.bam
- - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/preprocessintervals/main.nf b/tests/modules/nf-core/gatk4/preprocessintervals/main.nf
deleted file mode 100644
index 4bebde64956..00000000000
--- a/tests/modules/nf-core/gatk4/preprocessintervals/main.nf
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_PREPROCESSINTERVALS } from '../../../../../modules/nf-core/gatk4/preprocessintervals/main.nf'
-
-workflow test_gatk4_preprocessintervals {
-
- fasta = [
- [ id:'test' ], // meta map
- file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
- ]
- fai = [
- [ id:'test' ], // meta map
- file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
- ]
- dict = [
- [ id:'test' ], // meta map
- file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
- ]
- exc_inter = [
- [ id:'test' ], // meta map
- file(params.test_data['homo_sapiens']['genome']['genome_blacklist_interval_bed'], checkIfExists: true)
- ]
-
- GATK4_PREPROCESSINTERVALS ( fasta, fai, dict, [[],[]], exc_inter )
-}
diff --git a/tests/modules/nf-core/gatk4/preprocessintervals/test.yml b/tests/modules/nf-core/gatk4/preprocessintervals/test.yml
deleted file mode 100644
index 7fc0b075c47..00000000000
--- a/tests/modules/nf-core/gatk4/preprocessintervals/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: gatk4 preprocessintervals test_gatk4_preprocessintervals
- command: nextflow run ./tests/modules/nf-core/gatk4/preprocessintervals -entry test_gatk4_preprocessintervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/preprocessintervals/nextflow.config
- tags:
- - gatk4/preprocessintervals
- - gatk4
- files:
- - path: output/gatk4/test.interval_list
- md5sum: ce14b8fb47a60483fe44473ba40e1583
-
-- name: gatk4 preprocessintervals test_gatk4_preprocessintervals_stub
- command: nextflow run ./tests/modules/nf-core/gatk4/preprocessintervals -entry test_gatk4_preprocessintervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/preprocessintervals/nextflow.config -stub
- tags:
- - gatk4/preprocessintervals
- - gatk4
- files:
- - path: output/gatk4/test.interval_list
diff --git a/tests/modules/nf-core/gatk4/printreads/main.nf b/tests/modules/nf-core/gatk4/printreads/main.nf
deleted file mode 100644
index 4107651e8fc..00000000000
--- a/tests/modules/nf-core/gatk4/printreads/main.nf
+++ /dev/null
@@ -1,49 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_PRINTREADS } from '../../../../../modules/nf-core/gatk4/printreads/main.nf'
-
-workflow test_gatk4_printreads_bam {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-
- ]
-
- fasta = [ [ id:'genome' ], // meta map
- file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
- ]
- fai = [ [ id:'genome' ], // meta map
- file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
- ]
- dict = [ [ id:'genome' ], // meta map
- file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
- ]
-
- GATK4_PRINTREADS ( input, fasta, fai, dict )
-}
-
-workflow test_gatk4_printreads_cram {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
-
- ]
-
- fasta = [ [ id:'genome' ], // meta map
- file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
- ]
- fai = [ [ id:'genome' ], // meta map
- file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
- ]
- dict = [ [ id:'genome' ], // meta map
- file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
- ]
-
- GATK4_PRINTREADS ( input, fasta, fai, dict )
-}
diff --git a/tests/modules/nf-core/gatk4/printreads/nextflow.config b/tests/modules/nf-core/gatk4/printreads/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/gatk4/printreads/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/gatk4/printreads/test.yml b/tests/modules/nf-core/gatk4/printreads/test.yml
deleted file mode 100644
index c42c20e58e7..00000000000
--- a/tests/modules/nf-core/gatk4/printreads/test.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: "gatk4 printreads bam"
- command: nextflow run ./tests/modules/nf-core/gatk4/printreads -entry test_gatk4_printreads_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/printreads/nextflow.config
- tags:
- - "gatk4"
- - "gatk4/printreads"
- files:
- - path: "output/gatk4/test.bam"
- - path: "output/gatk4/versions.yml"
-
-- name: "gatk4 printreads cram"
- command: nextflow run ./tests/modules/nf-core/gatk4/printreads -entry test_gatk4_printreads_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/printreads/nextflow.config
- tags:
- - "gatk4"
- - "gatk4/printreads"
- files:
- - path: "output/gatk4/test.cram"
- - path: "output/gatk4/versions.yml"
-
-- name: "gatk4 printreads stub"
- command: nextflow run ./tests/modules/nf-core/gatk4/printreads -entry test_gatk4_printreads_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/printreads/nextflow.config -stub
- tags:
- - "gatk4"
- - "gatk4/printreads"
- files:
- - path: "output/gatk4/test.bam"
- - path: "output/gatk4/versions.yml"
diff --git a/tests/modules/nf-core/gatk4/revertsam/main.nf b/tests/modules/nf-core/gatk4/revertsam/main.nf
deleted file mode 100644
index 2f4c153be69..00000000000
--- a/tests/modules/nf-core/gatk4/revertsam/main.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_REVERTSAM } from '../../../../../modules/nf-core/gatk4/revertsam/main.nf'
-
-workflow test_gatk4_revertsam {
- input = [ [ id:'test' ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
- ]
-
- GATK4_REVERTSAM ( input )
-}
-
-workflow test_gatk4_revertsam_stubs {
- input = [ [ id:'test' ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
- ]
-
- GATK4_REVERTSAM ( input )
-}
diff --git a/tests/modules/nf-core/gatk4/revertsam/nextflow.config b/tests/modules/nf-core/gatk4/revertsam/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/gatk4/revertsam/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/gatk4/revertsam/test.yml b/tests/modules/nf-core/gatk4/revertsam/test.yml
deleted file mode 100644
index 9666fd19a40..00000000000
--- a/tests/modules/nf-core/gatk4/revertsam/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: gatk4 revertsam test_gatk4_revertsam
- command: nextflow run ./tests/modules/nf-core/gatk4/revertsam -entry test_gatk4_revertsam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/revertsam/nextflow.config
- tags:
- - gatk4
- - gatk4/revertsam
- files:
- - path: output/gatk4/test.reverted.bam
- md5sum: f783a88deb45c3a2c20ca12cbe1c5652
- - path: output/gatk4/versions.yml
-
-- name: gatk4 revertsam test_gatk4_revertsam_stubs
- command: nextflow run ./tests/modules/nf-core/gatk4/revertsam -entry test_gatk4_revertsam_stubs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/revertsam/nextflow.config -stub-run
- tags:
- - gatk4
- - gatk4/revertsam
- files:
- - path: output/gatk4/test.reverted.bam
- - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/samtofastq/main.nf b/tests/modules/nf-core/gatk4/samtofastq/main.nf
deleted file mode 100644
index 35f1f9d36c9..00000000000
--- a/tests/modules/nf-core/gatk4/samtofastq/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_SAMTOFASTQ } from '../../../../../modules/nf-core/gatk4/samtofastq/main.nf'
-
-workflow test_gatk4_samtofastq_single_end {
- input = [ [ id:'test', single_end: true ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
- ]
-
- GATK4_SAMTOFASTQ ( input )
-}
-
-workflow test_gatk4_samtofastq_paired_end {
- input = [ [ id:'test', single_end: false ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
- ]
-
- GATK4_SAMTOFASTQ ( input )
-}
-
-workflow test_gatk4_samtofastq_paired_end_stubs {
- input = [ [ id:'test', single_end: true ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
- ]
-
- GATK4_SAMTOFASTQ ( input )
-}
diff --git a/tests/modules/nf-core/gatk4/samtofastq/nextflow.config b/tests/modules/nf-core/gatk4/samtofastq/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/gatk4/samtofastq/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/gatk4/samtofastq/test.yml b/tests/modules/nf-core/gatk4/samtofastq/test.yml
deleted file mode 100644
index eb179abba4e..00000000000
--- a/tests/modules/nf-core/gatk4/samtofastq/test.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-- name: gatk4 samtofastq test_gatk4_samtofastq_single_end
- command: nextflow run ./tests/modules/nf-core/gatk4/samtofastq -entry test_gatk4_samtofastq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/samtofastq/nextflow.config
- tags:
- - gatk4
- - gatk4/samtofastq
- files:
- - path: output/gatk4/test.fastq.gz
- md5sum: 370979e8ecb385d0e91968c4124c08bd
- - path: output/gatk4/versions.yml
-
-- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end
- command: nextflow run ./tests/modules/nf-core/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/samtofastq/nextflow.config
- tags:
- - gatk4
- - gatk4/samtofastq
- files:
- - path: output/gatk4/test_1.fastq.gz
- md5sum: 8b74ed77c5afdec6e10a0839931be7f4
- - path: output/gatk4/test_2.fastq.gz
- md5sum: ec085c1af75d08205d209a6d6d5e0111
- - path: output/gatk4/versions.yml
-
-- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end_stubs
- command: nextflow run ./tests/modules/nf-core/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end_stubs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/samtofastq/nextflow.config -stub-run
- tags:
- - gatk4
- - gatk4/samtofastq
- files:
- - path: output/gatk4/test_1.fastq.gz
- - path: output/gatk4/test_2.fastq.gz
- - path: output/gatk4/versions.yml
diff --git a/tests/modules/nf-core/gatk4/shiftfasta/main.nf b/tests/modules/nf-core/gatk4/shiftfasta/main.nf
deleted file mode 100644
index 75e0e7f7879..00000000000
--- a/tests/modules/nf-core/gatk4/shiftfasta/main.nf
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_SHIFTFASTA } from '../../../../../modules/nf-core/gatk4/shiftfasta/main.nf'
-
-workflow test_gatk4_shiftfasta {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
- ]
- index = [
- [ id:'genome' ], // meta map
- file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
- ]
- dict = [
- [ id:'genome' ], // meta map
- file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
- ]
-
- GATK4_SHIFTFASTA ( input, index, dict )
-}
diff --git a/tests/modules/nf-core/gatk4/shiftfasta/test.yml b/tests/modules/nf-core/gatk4/shiftfasta/test.yml
deleted file mode 100644
index 9d8c564fe7f..00000000000
--- a/tests/modules/nf-core/gatk4/shiftfasta/test.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-- name: "gatk4 shiftfasta"
- command: nextflow run ./tests/modules/nf-core/gatk4/shiftfasta -entry test_gatk4_shiftfasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/shiftfasta/nextflow.config
- tags:
- - "gatk4"
- - "gatk4/shiftfasta"
- files:
- - path: "output/gatk4/test_shift.back_chain"
- - path: "output/gatk4/test_shift.dict"
- - path: "output/gatk4/test_shift.fasta"
- - path: "output/gatk4/test_shift.fasta.fai"
- - path: "output/gatk4/test.intervals"
- - path: "output/gatk4/test.shifted.intervals"
- - path: "output/gatk4/test_shift.fasta.fai"
- - path: "output/gatk4/versions.yml"
-
-- name: "gatk4 shiftfasta stub"
- command: nextflow run ./tests/modules/nf-core/gatk4/shiftfasta -entry test_gatk4_shiftfasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/shiftfasta/nextflow.config -stub
- tags:
- - "gatk4"
- - "gatk4/shiftfasta"
- files:
- - path: "output/gatk4/test_shift.back_chain"
- - path: "output/gatk4/test_shift.dict"
- - path: "output/gatk4/test_shift.fasta"
- - path: "output/gatk4/test_shift.fasta.fai"
- - path: "output/gatk4/test.intervals"
- - path: "output/gatk4/test.shifted.intervals"
- - path: "output/gatk4/test_shift.fasta.fai"
- - path: "output/gatk4/versions.yml"
diff --git a/tests/modules/nf-core/gstama/collapse/main.nf b/tests/modules/nf-core/gstama/collapse/main.nf
deleted file mode 100644
index 20c3ff74ccf..00000000000
--- a/tests/modules/nf-core/gstama/collapse/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GSTAMA_COLLAPSE } from '../../../../../modules/nf-core/gstama/collapse/main.nf'
-
-workflow test_gstama_collapse {
-
- input = [
- [ id:'test' ], // meta map
- file(params.test_data['homo_sapiens']['pacbio']['aligned'], checkIfExists: true)
- ]
- genome = file(params.test_data['homo_sapiens']['genome']['genome2_fasta'], checkIfExists: true)
-
- GSTAMA_COLLAPSE ( input, genome )
-}
diff --git a/tests/modules/nf-core/gstama/collapse/test.yml b/tests/modules/nf-core/gstama/collapse/test.yml
deleted file mode 100644
index 484fe1db4d9..00000000000
--- a/tests/modules/nf-core/gstama/collapse/test.yml
+++ /dev/null
@@ -1,24 +0,0 @@
-- name: gstama collapse test_gstama_collapse
- command: nextflow run ./tests/modules/nf-core/gstama/collapse -entry test_gstama_collapse -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gstama/collapse/nextflow.config
- tags:
- - gstama
- - gstama/collapse
- files:
- - path: output/gstama/test_tc_collapsed.bed
- md5sum: e5105198ed970a33ae0ecaa7bff421d9
- - path: output/gstama/test_tc_local_density_error.txt
- md5sum: b917ac1f14eccd590b6881a686f324d5
- - path: output/gstama/test_tc_polya.txt
- md5sum: 628ea62b918fc4f31e109f724d714a66
- - path: output/gstama/test_tc_read.txt
- md5sum: d2685d7f24cd1611e0770a5ce25422fe
- - path: output/gstama/test_tc_strand_check.txt
- md5sum: 42cc52b2660b1e0b84e1c9ab37a965ec
- - path: output/gstama/test_tc_trans_read.bed
- md5sum: 0ca1a32f33ef05242d897d913802554b
- - path: output/gstama/test_tc_trans_report.txt
- md5sum: 33a86c15ca2acce36b2a5962f4c1adc4
- - path: output/gstama/test_tc_varcov.txt
- md5sum: 587fd899ff658eb66b1770a35283bfcb
- - path: output/gstama/test_tc_variants.txt
- md5sum: 5b1165e9f33faba4f7207013fc27257e
diff --git a/tests/modules/nf-core/gstama/merge/main.nf b/tests/modules/nf-core/gstama/merge/main.nf
deleted file mode 100644
index dad081f557b..00000000000
--- a/tests/modules/nf-core/gstama/merge/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GSTAMA_MERGE } from '../../../../../modules/nf-core/gstama/merge/main'
-
-workflow test_gstama_merge {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- [
- file(params.test_data['homo_sapiens']['pacbio']['genemodel1'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['pacbio']['genemodel2'], checkIfExists: true)
- ]
- ]
- filelist = file(params.test_data['homo_sapiens']['pacbio']['filelist'], checkIfExists: true)
-
- GSTAMA_MERGE ( input, filelist )
-}
diff --git a/tests/modules/nf-core/gstama/merge/nextflow.config b/tests/modules/nf-core/gstama/merge/nextflow.config
deleted file mode 100644
index e0d7c8ef185..00000000000
--- a/tests/modules/nf-core/gstama/merge/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
- withName: GSTAMA_MERGE {
- ext.prefix = { "${meta.id}_merged" }
- }
-
-}
diff --git a/tests/modules/nf-core/gstama/merge/test.yml b/tests/modules/nf-core/gstama/merge/test.yml
deleted file mode 100644
index b0a81a3f1bc..00000000000
--- a/tests/modules/nf-core/gstama/merge/test.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-- name: gstama merge test_gstama_merge
- command: nextflow run ./tests/modules/nf-core/gstama/merge -entry test_gstama_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gstama/merge/nextflow.config
- tags:
- - gstama
- - gstama/merge
- files:
- - path: output/gstama/test_merged.bed
- md5sum: 60ec34e1ff9655d4ce2e83d3f4bbf448
- - path: output/gstama/test_merged_gene_report.txt
- md5sum: 7029fd183dfd905a233403cfbe44722a
- - path: output/gstama/test_merged_merge.txt
- md5sum: 4279e59ed5739ce4f2f811568962893f
- - path: output/gstama/test_merged_trans_report.txt
- md5sum: 97d8346d9eb9da140941656c3a3325cd
diff --git a/tests/modules/nf-core/gstama/polyacleanup/main.nf b/tests/modules/nf-core/gstama/polyacleanup/main.nf
deleted file mode 100644
index e1ed59663f9..00000000000
--- a/tests/modules/nf-core/gstama/polyacleanup/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GSTAMA_POLYACLEANUP } from '../../../../../modules/nf-core/gstama/polyacleanup/main.nf'
-
-workflow test_gstama_polyacleanup {
-
- input = [
- [ id:'test' ], // meta map
- file(params.test_data['homo_sapiens']['genome']['transcriptome_fasta'], checkIfExists: true)
- ]
-
- GSTAMA_POLYACLEANUP ( input )
-}
diff --git a/tests/modules/nf-core/gstama/polyacleanup/nextflow.config b/tests/modules/nf-core/gstama/polyacleanup/nextflow.config
deleted file mode 100644
index ff4077028bf..00000000000
--- a/tests/modules/nf-core/gstama/polyacleanup/nextflow.config
+++ /dev/null
@@ -1,6 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
- ext.prefix = { "${meta.id}_tama" }
-
-}
diff --git a/tests/modules/nf-core/gstama/polyacleanup/test.yml b/tests/modules/nf-core/gstama/polyacleanup/test.yml
deleted file mode 100644
index 6a1ed064c0e..00000000000
--- a/tests/modules/nf-core/gstama/polyacleanup/test.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-- name: gstama polyacleanup test_gstama_polyacleanup
- command: nextflow run ./tests/modules/nf-core/gstama/polyacleanup -entry test_gstama_polyacleanup -c ./tests/config/nextflow.config
- tags:
- - gstama
- - gstama/polyacleanup
- files:
- - path: output/gstama/test_tama.fa.gz
- md5sum: 9c768387478e5f966a42c369c0270b09
- - path: output/gstama/test_tama_polya_flnc_report.txt.gz
- md5sum: fe3606979ed11538aacd83159f4cff03
- - path: output/gstama/test_tama_tails.fa.gz
- md5sum: ba21256c0afe0bda71b3ee66b4c761bf
- - path: output/gstama/versions.yml
- md5sum: 07ebb812ae13a350d955fab7600b2542
diff --git a/tests/modules/nf-core/happy/sompy/main.nf b/tests/modules/nf-core/happy/sompy/main.nf
deleted file mode 100644
index bec0ada84ba..00000000000
--- a/tests/modules/nf-core/happy/sompy/main.nf
+++ /dev/null
@@ -1,67 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HAPPY_SOMPY } from '../../../../../modules/nf-core/happy/sompy/main.nf'
-
-workflow test_sompy {
-
- input = [
- [ id:'test' ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true),
- [],
- []
- ]
-
- fasta = [
- [ id:'test1' ],
- file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
- ]
- fasta_fai = [
- [ id:'test1' ],
- file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
- ]
-
- HAPPY_SOMPY (
- input,
- fasta,
- fasta_fai,
- [[],[]],
- [[],[]],
- [[],[]]
- )
-}
-workflow test_sompy_bam {
-
- input = [
- [ id:'test' ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true),
- [],
- []
- ]
-
- fasta = [
- [ id:'test1' ],
- file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
- ]
- fasta_fai = [
- [ id:'test1' ],
- file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
- ]
-
- bam = [
- [id:'test2'],
- file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists:true)
- ]
-
- HAPPY_SOMPY (
- input,
- fasta,
- fasta_fai,
- [[],[]],
- [[],[]],
- bam
- )
-}
diff --git a/tests/modules/nf-core/happy/sompy/nextflow.config b/tests/modules/nf-core/happy/sompy/nextflow.config
deleted file mode 100644
index 32d6b83227b..00000000000
--- a/tests/modules/nf-core/happy/sompy/nextflow.config
+++ /dev/null
@@ -1,8 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
- withName: HAPPY_SOMPY {
- ext.args = '--feature-table hcc.mutect.snv'
- }
-}
diff --git a/tests/modules/nf-core/happy/sompy/test.yml b/tests/modules/nf-core/happy/sompy/test.yml
deleted file mode 100644
index 6bde5712fb9..00000000000
--- a/tests/modules/nf-core/happy/sompy/test.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-- name: happy sompy test_sompy
- command: nextflow run ./tests/modules/nf-core/happy/sompy -entry test_sompy -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/happy/sompy/nextflow.config
- tags:
- - happy
- - happy/sompy
- files:
- - path: output/happy/test.features.csv
- md5sum: 34a8239e739edd5ea89be78b86262d4e
- - path: output/happy/test.metrics.json
- - path: output/happy/test.stats.csv
- md5sum: 402dc827ee8ec5e155fc7ea47232963e
- - path: output/happy/versions.yml
-
-- name: happy sompy test_sompy_bam
- command: nextflow run ./tests/modules/nf-core/happy/sompy -entry test_sompy_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/happy/sompy/nextflow.config
- tags:
- - happy
- - happy/sompy
- files:
- - path: output/happy/test.features.csv
- md5sum: 34a8239e739edd5ea89be78b86262d4e
- - path: output/happy/test.metrics.json
- - path: output/happy/test.stats.csv
- md5sum: 72653d4fa9150f54395c37e2220b2468
- - path: output/happy/versions.yml
diff --git a/tests/modules/nf-core/picard/bedtointervallist/main.nf b/tests/modules/nf-core/picard/bedtointervallist/main.nf
deleted file mode 100644
index 55a40a25ab7..00000000000
--- a/tests/modules/nf-core/picard/bedtointervallist/main.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_BEDTOINTERVALLIST } from '../../../../../modules/nf-core/picard/bedtointervallist/main.nf'
-
-workflow test_picard_bedtointervallist {
- input = [
- [ id:'test' ], // meta map
- [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
- ]
- dict = [
- [ id:'test' ], // meta map
- file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
- ]
-
- PICARD_BEDTOINTERVALLIST ( input, dict, [] )
-}
diff --git a/tests/modules/nf-core/picard/bedtointervallist/nextflow.config b/tests/modules/nf-core/picard/bedtointervallist/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/picard/bedtointervallist/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/picard/bedtointervallist/test.yml b/tests/modules/nf-core/picard/bedtointervallist/test.yml
deleted file mode 100644
index 51c9dfba79f..00000000000
--- a/tests/modules/nf-core/picard/bedtointervallist/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: picard bedtointervallist test_picard_bedtointervallist
- command: nextflow run ./tests/modules/nf-core/picard/bedtointervallist -entry test_picard_bedtointervallist -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/bedtointervallist/nextflow.config
- tags:
- - picard/bedtointervallist
- - picard
- files:
- - path: output/picard/test.interval_list
- md5sum: e51101c9357fb2d59fd30e370eefa39c
diff --git a/tests/modules/nf-core/picard/cleansam/main.nf b/tests/modules/nf-core/picard/cleansam/main.nf
deleted file mode 100644
index d337aca51ee..00000000000
--- a/tests/modules/nf-core/picard/cleansam/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_CLEANSAM } from '../../../../../modules/nf-core/picard/cleansam/main.nf'
-
-workflow test_picard_cleansam {
-
- input = [
- [ id:'test', single_end:true ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
- ]
-
- PICARD_CLEANSAM ( input )
-}
diff --git a/tests/modules/nf-core/picard/cleansam/test.yml b/tests/modules/nf-core/picard/cleansam/test.yml
deleted file mode 100644
index fd80f244cae..00000000000
--- a/tests/modules/nf-core/picard/cleansam/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: picard cleansam test_picard_cleansam
- command: nextflow run ./tests/modules/nf-core/picard/cleansam -entry test_picard_cleansam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/cleansam/nextflow.config
- tags:
- - picard/cleansam
- - picard
- files:
- - path: output/picard/test.cleaned.bam
- md5sum: a48f8e77a1480445efc57570c3a38a68
- - path: output/picard/versions.yml
-
-- name: picard cleansam test_picard_cleansam stub
- command: nextflow run ./tests/modules/nf-core/picard/cleansam -entry test_picard_cleansam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/cleansam/nextflow.config -stub-run
- tags:
- - picard/cleansam
- - picard
- files:
- - path: output/picard/test.cleaned.bam
- - path: output/picard/versions.yml
diff --git a/tests/modules/nf-core/picard/collectmultiplemetrics/main.nf b/tests/modules/nf-core/picard/collectmultiplemetrics/main.nf
deleted file mode 100644
index 12ea0022356..00000000000
--- a/tests/modules/nf-core/picard/collectmultiplemetrics/main.nf
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../../modules/nf-core/picard/collectmultiplemetrics/main.nf'
-
-workflow test_picard_collectmultiplemetrics {
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
- ]
- fasta = [
- [id:'genome'],
- file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
- ]
- fai = [[id:'genome'],[]]
-
- PICARD_COLLECTMULTIPLEMETRICS ( input, fasta, fai )
-}
-
-workflow test_picard_collectmultiplemetrics_nofasta {
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
- ]
-
- PICARD_COLLECTMULTIPLEMETRICS ( input, [[id:'genome'],[]], [[id:'genome'],[]] )
-}
-
-workflow test_picard_collectmultiplemetrics_cram {
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
- ]
- fasta = [
- [id:'genome'],
- file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
- ]
- fai = [
- [id:'genome'],
- file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
- ]
-
- PICARD_COLLECTMULTIPLEMETRICS ( input, fasta, fai )
-}
diff --git a/tests/modules/nf-core/picard/collectmultiplemetrics/nextflow.config b/tests/modules/nf-core/picard/collectmultiplemetrics/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/picard/collectmultiplemetrics/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/picard/collectmultiplemetrics/test.yml b/tests/modules/nf-core/picard/collectmultiplemetrics/test.yml
deleted file mode 100644
index c8e987d9d28..00000000000
--- a/tests/modules/nf-core/picard/collectmultiplemetrics/test.yml
+++ /dev/null
@@ -1,93 +0,0 @@
-- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics
- command: nextflow run ./tests/modules/nf-core/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/collectmultiplemetrics/nextflow.config
- tags:
- - picard/collectmultiplemetrics
- - picard
- files:
- - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
- contains:
- - "## METRICS CLASS\tpicard.analysis.AlignmentSummaryMetrics"
- - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
- - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
- contains:
- - "READ_END\tCYCLE\tPCT_A\tPCT_C\tPCT_G\tPCT_T\tPCT_N"
- - "1\t1\t20\t26\t32\t22\t0"
- - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
- - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
- contains:
- - "MEDIAN_INSERT_SIZE\tMODE_INSERT_SIZE\tMEDIAN_ABSOLUTE_DEVIATION\tMIN_INSERT_SIZE\tMAX_INSERT_SIZE\tMEAN_INSERT_SIZE\tSTANDARD_DEVIATION\tREAD_PAIRS\tPAIR_ORIENTATION\tWIDTH_OF_10_PERCENT\tWIDTH_OF_20_PERCENT\tWIDTH_OF_30_PERCENT\tWIDTH_OF_40_PERCENT\tWIDTH_OF_50_PERCENT\tWIDTH_OF_60_PERCENT\tWIDTH_OF_70_PERCENT\tWIDTH_OF_80_PERCENT\tWIDTH_OF_90_PERCENT\tWIDTH_OF_95_PERCENT\tWIDTH_OF_99_PERCENT\tSAMPLE\tLIBRARY\tREAD_GROUP"
- - "209\t159\t46\t77\t364\t207.659794\t66.769018\t97\tFR\t25\t49\t59\t77\t93\t123\t145\t183\t223\t255\t311"
- - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
- - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
- contains:
- - "CYCLE\tMEAN_QUALITY"
- - "1\t32"
- - "2\t31.35"
- - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
- - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
- contains:
- - "QUALITY\tCOUNT_OF_Q"
- - "14\t1926"
- - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
- - path: output/picard/versions.yml
-
-- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics_nofasta
- command: nextflow run ./tests/modules/nf-core/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics_nofasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/collectmultiplemetrics/nextflow.config
- tags:
- - picard/collectmultiplemetrics
- - picard
- files:
- - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
- contains:
- - "## METRICS CLASS\tpicard.analysis.AlignmentSummaryMetrics"
- - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
- - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
- contains:
- - "READ_END\tCYCLE\tPCT_A\tPCT_C\tPCT_G\tPCT_T\tPCT_N"
- - "1\t1\t20\t26\t32\t22\t0"
- - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
- - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
- contains:
- - "MEDIAN_INSERT_SIZE\tMODE_INSERT_SIZE\tMEDIAN_ABSOLUTE_DEVIATION\tMIN_INSERT_SIZE\tMAX_INSERT_SIZE\tMEAN_INSERT_SIZE\tSTANDARD_DEVIATION\tREAD_PAIRS\tPAIR_ORIENTATION\tWIDTH_OF_10_PERCENT\tWIDTH_OF_20_PERCENT\tWIDTH_OF_30_PERCENT\tWIDTH_OF_40_PERCENT\tWIDTH_OF_50_PERCENT\tWIDTH_OF_60_PERCENT\tWIDTH_OF_70_PERCENT\tWIDTH_OF_80_PERCENT\tWIDTH_OF_90_PERCENT\tWIDTH_OF_95_PERCENT\tWIDTH_OF_99_PERCENT\tSAMPLE\tLIBRARY\tREAD_GROUP"
- - "209\t159\t46\t77\t364\t207.659794\t66.769018\t97\tFR\t25\t49\t59\t77\t93\t123\t145\t183\t223\t255\t311"
- - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
- - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
- contains:
- - "CYCLE\tMEAN_QUALITY"
- - "1\t32"
- - "2\t31.35"
- - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
- - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
- contains:
- - "QUALITY\tCOUNT_OF_Q"
- - "14\t1926"
- - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
- - path: output/picard/versions.yml
-
-- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics_cram
- command: nextflow run ./tests/modules/nf-core/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/collectmultiplemetrics/nextflow.config
- tags:
- - picard/collectmultiplemetrics
- - picard
- files:
- - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
- contains:
- - "## METRICS CLASS\tpicard.analysis.AlignmentSummaryMetrics"
- - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
- - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
- contains:
- - "READ_END\tCYCLE\tPCT_A\tPCT_C\tPCT_G\tPCT_T\tPCT_N"
- - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
- - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
- contains:
- - "MEDIAN_INSERT_SIZE\tMODE_INSERT_SIZE\tMEDIAN_ABSOLUTE_DEVIATION\tMIN_INSERT_SIZE\tMAX_INSERT_SIZE\tMEAN_INSERT_SIZE\tSTANDARD_DEVIATION\tREAD_PAIRS\tPAIR_ORIENTATION\tWIDTH_OF_10_PERCENT\tWIDTH_OF_20_PERCENT\tWIDTH_OF_30_PERCENT\tWIDTH_OF_40_PERCENT\tWIDTH_OF_50_PERCENT\tWIDTH_OF_60_PERCENT\tWIDTH_OF_70_PERCENT\tWIDTH_OF_80_PERCENT\tWIDTH_OF_90_PERCENT\tWIDTH_OF_95_PERCENT\tWIDTH_OF_99_PERCENT\tSAMPLE\tLIBRARY\tREAD_GROUP"
- - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
- - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
- contains:
- - "CYCLE\tMEAN_QUALITY"
- - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
- - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
- contains:
- - "QUALITY\tCOUNT_OF_Q"
- - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
- - path: output/picard/versions.yml
diff --git a/tests/modules/nf-core/picard/fastqtosam/main.nf b/tests/modules/nf-core/picard/fastqtosam/main.nf
deleted file mode 100644
index 5b1af7ea9fc..00000000000
--- a/tests/modules/nf-core/picard/fastqtosam/main.nf
+++ /dev/null
@@ -1,43 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_FASTQTOSAM } from '../../../../../modules/nf-core/picard/fastqtosam/main.nf'
-
-workflow test_picard_fastqtosam_single {
-
- input = [
- [ id:'test', single_end:true ], // meta map
- [
- file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
- ]
- ]
-
- PICARD_FASTQTOSAM ( input )
-}
-
-workflow test_picard_fastqtosam_paired {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- [
- file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
- ]
- ]
-
- PICARD_FASTQTOSAM ( input )
-}
-
-workflow test_picard_fastqtosam_paired_custom_samplename {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- [
- file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
- ]
- ]
-
- PICARD_FASTQTOSAM ( input )
-}
diff --git a/tests/modules/nf-core/picard/fastqtosam/nextflow.config b/tests/modules/nf-core/picard/fastqtosam/nextflow.config
deleted file mode 100644
index 25c849c9e85..00000000000
--- a/tests/modules/nf-core/picard/fastqtosam/nextflow.config
+++ /dev/null
@@ -1,7 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
- withName: "test_picard_fastqtosam_paired_custom_samplename:PICARD_FASTQTOSAM" {
- ext.args = "--SAMPLE_NAME CustomSample"
- }
-}
diff --git a/tests/modules/nf-core/picard/fastqtosam/test.yml b/tests/modules/nf-core/picard/fastqtosam/test.yml
deleted file mode 100644
index 348337c46b9..00000000000
--- a/tests/modules/nf-core/picard/fastqtosam/test.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-- name: picard fastqtosam test_picard_fastqtosam_single
- command: nextflow run ./tests/modules/nf-core/picard/fastqtosam -entry test_picard_fastqtosam_single -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/fastqtosam/nextflow.config
- tags:
- - picard
- - picard/fastqtosam
- files:
- - path: output/picard/test.bam
- md5sum: fe2882efe8f13a8da20fcc63469ed0aa
-
-- name: picard fastqtosam test_picard_fastqtosam_paired
- command: nextflow run ./tests/modules/nf-core/picard/fastqtosam -entry test_picard_fastqtosam_paired -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/fastqtosam/nextflow.config
- tags:
- - picard
- - picard/fastqtosam
- files:
- - path: output/picard/test.bam
- md5sum: 90e4f59f9d942f96c3f3c41160f3fd5d
-
-- name: picard fastqtosam test_picard_fastqtosam_paired_custom_samplename
- command: nextflow run ./tests/modules/nf-core/picard/fastqtosam -entry test_picard_fastqtosam_paired_custom_samplename -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/fastqtosam/nextflow.config
- tags:
- - picard
- - picard/fastqtosam
- files:
- - path: output/picard/test.bam
- md5sum: 69d35ee2b5dc263d022eaf59a9e383d3
diff --git a/tests/modules/nf-core/picard/fixmateinformation/main.nf b/tests/modules/nf-core/picard/fixmateinformation/main.nf
deleted file mode 100644
index 92277611f29..00000000000
--- a/tests/modules/nf-core/picard/fixmateinformation/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_FIXMATEINFORMATION } from '../../../../../modules/nf-core/picard/fixmateinformation/main.nf'
-
-workflow test_picard_fixmateinformation {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
- ]
-
- PICARD_FIXMATEINFORMATION ( input )
-}
diff --git a/tests/modules/nf-core/picard/fixmateinformation/nextflow.config b/tests/modules/nf-core/picard/fixmateinformation/nextflow.config
deleted file mode 100644
index 431e8c71024..00000000000
--- a/tests/modules/nf-core/picard/fixmateinformation/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-
- withName: PICARD_FIXMATEINFORMATION {
- ext.prefix = { "${meta.id}.fixed" }
- }
-}
diff --git a/tests/modules/nf-core/picard/fixmateinformation/test.yml b/tests/modules/nf-core/picard/fixmateinformation/test.yml
deleted file mode 100644
index e62e9250b28..00000000000
--- a/tests/modules/nf-core/picard/fixmateinformation/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: picard fixmateinformation test_picard_fixmateinformation
- command: nextflow run ./tests/modules/nf-core/picard/fixmateinformation -entry test_picard_fixmateinformation -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/fixmateinformation/nextflow.config
- tags:
- - picard/fixmateinformation
- - picard
- files:
- - path: output/picard/test.fixed.bam
- md5sum: 746102e8c242c0ef42e045c49d320030
- - path: output/picard/versions.yml
-
-- name: picard fixmateinformation test_picard_fixmateinformation stub
- command: nextflow run ./tests/modules/nf-core/picard/fixmateinformation -entry test_picard_fixmateinformation -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/fixmateinformation/nextflow.config -stub-run
- tags:
- - picard/fixmateinformation
- - picard
- files:
- - path: output/picard/test.fixed.bam
- - path: output/picard/versions.yml
diff --git a/tests/modules/nf-core/picard/liftovervcf/main.nf b/tests/modules/nf-core/picard/liftovervcf/main.nf
deleted file mode 100644
index 1cecc56e643..00000000000
--- a/tests/modules/nf-core/picard/liftovervcf/main.nf
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_LIFTOVERVCF } from '../../../../../modules/nf-core/picard/liftovervcf/main.nf'
-
-workflow test_picard_liftovervcf {
-
- input_vcf = [ [ id:'test' ],
- file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
- ]
- dict = [ [ id:'genome' ],
- file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
- ]
- chain = [ [ id:'genome' ],
- file(params.test_data['homo_sapiens']['genome']['genome_chain_gz'], checkIfExists: true)
- ]
- fasta = [ [ id:'genome' ],
- file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
- ]
- PICARD_LIFTOVERVCF ( input_vcf, dict, fasta, chain )
-}
-
-workflow test_picard_liftovervcf_stubs {
-
- input_vcf = [ [ id:'test' ],
- file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
- ]
- dict = [ [ id:'genome' ],
- file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
- ]
- chain = [ [ id:'genome' ],
- file(params.test_data['homo_sapiens']['genome']['genome_chain_gz'], checkIfExists: true)
- ]
- fasta = [ [ id:'genome' ],
- file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
- ]
-
- PICARD_LIFTOVERVCF ( input_vcf, dict, fasta, chain )
-}
diff --git a/tests/modules/nf-core/picard/liftovervcf/nextflow.config b/tests/modules/nf-core/picard/liftovervcf/nextflow.config
deleted file mode 100644
index f69fc351ad6..00000000000
--- a/tests/modules/nf-core/picard/liftovervcf/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
- ext.args = "--WARN_ON_MISSING_CONTIG true"
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/picard/liftovervcf/test.yml b/tests/modules/nf-core/picard/liftovervcf/test.yml
deleted file mode 100644
index 09bd2dd14c2..00000000000
--- a/tests/modules/nf-core/picard/liftovervcf/test.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-- name: picard liftovervcf test_picard_liftovervcf
- command: nextflow run ./tests/modules/nf-core/picard/liftovervcf -entry test_picard_liftovervcf -c ./tests/config/nextflow.config
- tags:
- - picard/liftovervcf
- - picard
- files:
- - path: output/picard/test.lifted.vcf.gz
- contains:
- - "chr22"
- - path: output/picard/test.unlifted.vcf.gz
- - path: output/picard/versions.yml
-
-- name: picard liftovervcf test_picard_liftovervcf_stubs
- command: nextflow run ./tests/modules/nf-core/picard/liftovervcf -entry test_picard_liftovervcf_stubs -c ./tests/config/nextflow.config -stub-run
- tags:
- - picard/liftovervcf
- - picard
- files:
- - path: output/picard/test.lifted.vcf.gz
- - path: output/picard/test.unlifted.vcf.gz
- - path: output/picard/versions.yml
diff --git a/tests/modules/nf-core/picard/renamesampleinvcf/main.nf b/tests/modules/nf-core/picard/renamesampleinvcf/main.nf
deleted file mode 100644
index a17975be5fb..00000000000
--- a/tests/modules/nf-core/picard/renamesampleinvcf/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_RENAMESAMPLEINVCF } from '../../../../../modules/nf-core/picard/renamesampleinvcf/main.nf'
-
-workflow test_picard_renamesampleinvcf {
-
- input = [ [ id:'test' ],
- file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
- ]
-
- PICARD_RENAMESAMPLEINVCF ( input )
-}
diff --git a/tests/modules/nf-core/picard/renamesampleinvcf/nextflow.config b/tests/modules/nf-core/picard/renamesampleinvcf/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/picard/renamesampleinvcf/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/picard/renamesampleinvcf/test.yml b/tests/modules/nf-core/picard/renamesampleinvcf/test.yml
deleted file mode 100644
index 3b2f8e06299..00000000000
--- a/tests/modules/nf-core/picard/renamesampleinvcf/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: picard renamesampleinvcf test_picard_renamesampleinvcf
- command: nextflow run ./tests/modules/nf-core/picard/renamesampleinvcf -entry test_picard_renamesampleinvcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/renamesampleinvcf/nextflow.config
- tags:
- - picard
- - picard/renamesampleinvcf
- files:
- - path: output/picard/test_renam.vcf.gz
- md5sum: 6664b59319777b3152fcccc79c35fdb8
- - path: output/picard/versions.yml
-
-- name: picard renamesampleinvcf test_picard_renamesampleinvcf_stub
- command: nextflow run ./tests/modules/nf-core/picard/renamesampleinvcf -entry test_picard_renamesampleinvcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/renamesampleinvcf/nextflow.config -stub-run
- tags:
- - picard
- - picard/renamesampleinvcf
- files:
- - path: output/picard/test_renam.vcf.gz
diff --git a/tests/modules/nf-core/picard/sortsam/main.nf b/tests/modules/nf-core/picard/sortsam/main.nf
deleted file mode 100644
index 4b4e801355a..00000000000
--- a/tests/modules/nf-core/picard/sortsam/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_SORTSAM } from '../../../../../modules/nf-core/picard/sortsam/main.nf'
-
-workflow test_picard_sortsam {
-
- input = [ [ id:'test', single_end:false ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
- sort_order = "queryname"
-
- PICARD_SORTSAM ( input, sort_order )
-}
diff --git a/tests/modules/nf-core/picard/sortsam/nextflow.config b/tests/modules/nf-core/picard/sortsam/nextflow.config
deleted file mode 100644
index ca572c2f41c..00000000000
--- a/tests/modules/nf-core/picard/sortsam/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
- withName: PICARD_SORTSAM {
- ext.prefix = { "${meta.id}.sorted" }
- }
-
-}
diff --git a/tests/modules/nf-core/picard/sortsam/test.yml b/tests/modules/nf-core/picard/sortsam/test.yml
deleted file mode 100644
index 9322ed77b5b..00000000000
--- a/tests/modules/nf-core/picard/sortsam/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: picard sortsam test_picard_sortsam
- command: nextflow run ./tests/modules/nf-core/picard/sortsam -entry test_picard_sortsam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/sortsam/nextflow.config
- tags:
- - picard
- - picard/sortsam
- files:
- - path: output/picard/test.sorted.bam
- md5sum: b44a6ca04811a9470c7813c3c9465fd5
- - path: output/picard/versions.yml
diff --git a/tests/modules/nf-core/picard/sortvcf/main.nf b/tests/modules/nf-core/picard/sortvcf/main.nf
deleted file mode 100644
index c374b5b575c..00000000000
--- a/tests/modules/nf-core/picard/sortvcf/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_SORTVCF } from '../../../../../modules/nf-core/picard/sortvcf/main.nf'
-
-workflow test_picard_sortvcf {
-
- input = [ [ id:'test' ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
- ]
-
- fasta = [ [ id:'genome' ],
- file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
- ]
-
- dict = [ [ id:'genome' ],
- file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
- ]
-
- PICARD_SORTVCF ( input, fasta, dict )
-}
diff --git a/tests/modules/nf-core/picard/sortvcf/nextflow.config b/tests/modules/nf-core/picard/sortvcf/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/picard/sortvcf/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/picard/sortvcf/test.yml b/tests/modules/nf-core/picard/sortvcf/test.yml
deleted file mode 100644
index 67458bdf65a..00000000000
--- a/tests/modules/nf-core/picard/sortvcf/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: picard sortvcf
- command: nextflow run ./tests/modules/nf-core/picard/sortvcf -entry test_picard_sortvcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/sortvcf/nextflow.config
- tags:
- - picard
- - picard/sortvcf
- files:
- - path: output/picard/test_sorted.vcf.gz