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/atlas/call/meta.yml b/modules/nf-core/atlas/call/meta.yml
index 9b1142bdd94..a07bc6a7dd7 100644
--- a/modules/nf-core/atlas/call/meta.yml
+++ b/modules/nf-core/atlas/call/meta.yml
@@ -12,7 +12,7 @@ tools:
documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
tool_dev_url: "https://bitbucket.org/wegmannlab/atlas"
doi: "10.1101/105346"
- licence: "['GPL v3']"
+ licence: ["GPL v3"]
input:
- meta:
type: map
@@ -48,7 +48,7 @@ input:
description: Optional tab separated text file containing 1-based list of known alleles. See atlas call documentation.
pattern: "*.{txt.tsv}"
- method:
- type: character
+ type: string
description: Which variant calling algorithm to use. Some may require additional parameters supplied via ext.args. Check atlas documentation.
pattern: "MLE|Bayesian|allelePresence|randomBase|majorityBase"
output:
@@ -61,7 +61,7 @@ output:
type: file
description: File containing software versions
pattern: "versions.yml"
- - bam:
+ - vcf:
type: file
description: VCF file with variant calls
pattern: "*.vcf.gz"
diff --git a/modules/nf-core/atlas/call/tests/main.nf.test b/modules/nf-core/atlas/call/tests/main.nf.test
new file mode 100644
index 00000000000..dbd40640873
--- /dev/null
+++ b/modules/nf-core/atlas/call/tests/main.nf.test
@@ -0,0 +1,46 @@
+
+nextflow_process {
+
+ name "Test Process ATLAS_CALL"
+ script "../main.nf"
+ process "ATLAS_CALL"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "atlas"
+ tag "atlas/call"
+
+ test("test-atlas-call") {
+
+ 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] = 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] = []
+ input[4] = 'randomBase'
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.vcf[0][1]).vcf.summary,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/atlas/call/tests/main.nf.test.snap b/modules/nf-core/atlas/call/tests/main.nf.test.snap
new file mode 100644
index 00000000000..c5a406b2227
--- /dev/null
+++ b/modules/nf-core/atlas/call/tests/main.nf.test.snap
@@ -0,0 +1,15 @@
+{
+ "test-atlas-call": {
+ "content": [
+ "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=12674, phased=true, phasedAutodetect=true]",
+ [
+ "versions.yml:md5,abad4c906071792f8a5270fdb143fc4e"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T15:48:22.930389"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/atlas/pmd/meta.yml b/modules/nf-core/atlas/pmd/meta.yml
index 7b11d718e48..ed2ec3691ba 100644
--- a/modules/nf-core/atlas/pmd/meta.yml
+++ b/modules/nf-core/atlas/pmd/meta.yml
@@ -11,7 +11,7 @@ tools:
documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
tool_dev_url: "https://bitbucket.org/wegmannlab/atlas"
doi: "10.1101/105346"
- licence: "['GPL v3']"
+ licence: ["GPL v3"]
input:
- meta:
type: map
diff --git a/modules/nf-core/atlas/pmd/tests/main.nf.test b/modules/nf-core/atlas/pmd/tests/main.nf.test
new file mode 100644
index 00000000000..fc804e7b170
--- /dev/null
+++ b/modules/nf-core/atlas/pmd/tests/main.nf.test
@@ -0,0 +1,46 @@
+
+nextflow_process {
+
+ name "Test Process ATLAS_PMD"
+ script "../main.nf"
+ process "ATLAS_PMD"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "atlas"
+ tag "atlas/pmd"
+
+ test("test-atlas-pmd") {
+
+ 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)
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ file(process.out.empiric[0][1]).readLines()[0],
+ file(process.out.exponential[0][1]).readLines()[0][0..13],
+ file(process.out.counts[0][1]).readLines()[0],
+ file(process.out.table[0][1]).readLines()[0],
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/atlas/pmd/tests/main.nf.test.snap b/modules/nf-core/atlas/pmd/tests/main.nf.test.snap
new file mode 100644
index 00000000000..59f90a820f7
--- /dev/null
+++ b/modules/nf-core/atlas/pmd/tests/main.nf.test.snap
@@ -0,0 +1,18 @@
+{
+ "test-atlas-pmd": {
+ "content": [
+ "1\tCT\tEmpiric[0.000831,0.000000,0.001339,0.001350,0.001437,0.000000,0.002210,0.001314,0.001466,0.000000,0.001395,0.001403,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.001362,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000794,0.000000,0.000000,0.000000,0.001297,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000]",
+ "1\tExponential[",
+ "1\tforward\tA->A\t2050\t2033\t2081\t2078\t2138\t2119\t2038\t2007\t2035\t2113\t2049\t2048\t1974\t2012\t2066\t2093\t2110\t1971\t1976\t1906\t1968\t1951\t1917\t1912\t1955\t1956\t1933\t1872\t1922\t1933\t1974\t1840\t1963\t1897\t1870\t1823\t1923\t1908\t1902\t1883\t1973\t1899\t1908\t1912\t1972\t1913\t1922\t1959\t1995\t2039",
+ "1\tforward\tA->A\t0.998539\t0.997547\t0.997603\t1\t0.998133\t0.998586\t0.99902\t0.998507\t0.998038\t0.999527\t0.997566\t0.997565\t0.998988\t0.998016\t0.99855\t0.999522\t0.996223\t0.99848\t0.999494\t0.998952\t0.999492\t0.997444\t0.998958\t0.997912\t0.997958\t0.997959\t0.997935\t0.998933\t0.996888\t0.999483\t0.998988\t0.999457\t0.998474\t0.998947\t0.998398\t0.998357\t0.997924\t0.999476\t0.999475\t1\t0.998987\t0.998423\t0.999476\t1\t1\t0.998956\t0.998442\t0.997454\t0.9975\t0.99951",
+ [
+ "versions.yml:md5,abec49256c52cb677fa0dad3473ed5a6"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T16:01:09.837624"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/atlas/recal/meta.yml b/modules/nf-core/atlas/recal/meta.yml
index 886e93cb4e6..47b9c9afe6d 100644
--- a/modules/nf-core/atlas/recal/meta.yml
+++ b/modules/nf-core/atlas/recal/meta.yml
@@ -1,15 +1,16 @@
name: "atlas_recal"
-description: gives an estimation of the sequencing bias based on known invariant sites
+description: Gives an estimation of the sequencing bias based on known invariant sites
keywords:
- sequencing_bias
- ATLAS
+ - bias
tools:
- "atlas":
description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity"
homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
doi: "10.1101/105346"
- licence: "['GPL v3']"
+ licence: ["GPL v3"]
input:
- meta:
type: map
diff --git a/modules/nf-core/atlas/recal/tests/main.nf.test b/modules/nf-core/atlas/recal/tests/main.nf.test
new file mode 100644
index 00000000000..e03c6208b36
--- /dev/null
+++ b/modules/nf-core/atlas/recal/tests/main.nf.test
@@ -0,0 +1,44 @@
+
+nextflow_process {
+
+ name "Test Process ATLAS_RECAL"
+ script "../main.nf"
+ process "ATLAS_RECAL"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "atlas"
+ tag "atlas/recal"
+
+ test("test-atlas-recal") {
+
+ 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] = []
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ file(process.out.recal_patterns[0][1]).readLines()[0],
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/atlas/recal/tests/main.nf.test.snap b/modules/nf-core/atlas/recal/tests/main.nf.test.snap
new file mode 100644
index 00000000000..a780f7c9b17
--- /dev/null
+++ b/modules/nf-core/atlas/recal/tests/main.nf.test.snap
@@ -0,0 +1,15 @@
+{
+ "test-atlas-recal": {
+ "content": [
+ "readGroup\tmate\tmodel\tquality\tposition\tcontext",
+ [
+ "versions.yml:md5,69864cf23ffc5b0559af20e0675c4290"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T15:57:16.06295"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/atlas/splitmerge/main.nf b/modules/nf-core/atlas/splitmerge/main.nf
index 1a4725cf1ec..222b55af7eb 100644
--- a/modules/nf-core/atlas/splitmerge/main.nf
+++ b/modules/nf-core/atlas/splitmerge/main.nf
@@ -11,7 +11,8 @@ process ATLAS_SPLITMERGE {
tuple val(meta), path(bam), path(bai), path(read_group_settings), path(blacklist)
output:
- tuple val(meta), path("*_mergedReads.bam"), path("*.txt.gz"), emit: data
+ tuple val(meta), path("*_mergedReads.bam") , emit: bam
+ tuple val(meta), path("*.txt.gz") , emit: txt
path "versions.yml", emit: versions
when:
diff --git a/modules/nf-core/atlas/splitmerge/meta.yml b/modules/nf-core/atlas/splitmerge/meta.yml
index fc6289c78da..24621b1901b 100644
--- a/modules/nf-core/atlas/splitmerge/meta.yml
+++ b/modules/nf-core/atlas/splitmerge/meta.yml
@@ -12,7 +12,7 @@ tools:
documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
tool_dev_url: "https://bitbucket.org/wegmannlab/atlas"
doi: "10.1101/105346"
- licence: "['GPL v3']"
+ licence: ["GPL v3"]
input:
- meta:
type: map
@@ -27,7 +27,7 @@ input:
type: file
description: The BAI file for the input BAM file
pattern: "*.bai"
- - read_group_setting:
+ - read_group_settings:
type: file
description: |
TXT file containing the split and merge settings for
@@ -55,7 +55,7 @@ output:
type: file
description: A BAM file with suffix_mergedReads.bam
pattern: "*_mergedReads.bam"
- - filelist:
+ - txt:
type: file
description: A file listing all reads that were filtered out in the merging process with suffix_ignoredReads.txt.gz
pattern: "*.txt.gz"
diff --git a/modules/nf-core/atlas/splitmerge/tests/main.nf.test b/modules/nf-core/atlas/splitmerge/tests/main.nf.test
new file mode 100644
index 00000000000..9d7d1884b97
--- /dev/null
+++ b/modules/nf-core/atlas/splitmerge/tests/main.nf.test
@@ -0,0 +1,43 @@
+
+nextflow_process {
+
+ name "Test Process ATLAS_SPLITMERGE"
+ script "../main.nf"
+ process "ATLAS_SPLITMERGE"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "atlas"
+ tag "atlas/splitmerge"
+
+ test("test-atlas-splitmerge") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ],
+ 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/bam/read_group_settings.txt', checkIfExists: true),
+ []
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ path(process.out.txt[0][1]).linesGzip[3..7],
+ bam(process.out.bam[0][1]).getReadsMD5(),
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/atlas/splitmerge/tests/main.nf.test.snap b/modules/nf-core/atlas/splitmerge/tests/main.nf.test.snap
new file mode 100644
index 00000000000..dfb38da0af1
--- /dev/null
+++ b/modules/nf-core/atlas/splitmerge/tests/main.nf.test.snap
@@ -0,0 +1,22 @@
+{
+ "test-atlas-splitmerge": {
+ "content": [
+ [
+ "Read testN:1, rev : not a proper pair (orphan)",
+ "Read testN:99, rev : longer than insert size (TLEN)",
+ "Read testN:99, rev : not a proper pair (orphan)",
+ "Read testN:830, rev : longer than insert size (TLEN)",
+ "Read testN:830, fwd : longer than insert size (TLEN)"
+ ],
+ "66f5f17da47cc4dced99bd17d739b536",
+ [
+ "versions.yml:md5,208f6ef7923cec00ddbcd5825f84a4fa"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T15:33:41.150912"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test b/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test
new file mode 100644
index 00000000000..0d4f80ae699
--- /dev/null
+++ b/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test
@@ -0,0 +1,37 @@
+
+nextflow_process {
+
+ name "Test Process BAM2FASTX_BAM2FASTQ"
+ script "../main.nf"
+ process "BAM2FASTX_BAM2FASTQ"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "bam2fastx"
+ tag "bam2fastx/bam2fastq"
+
+ test("test-bam2fastx-bam2fastq") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam.pbi', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test.snap b/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test.snap
new file mode 100644
index 00000000000..342241ef940
--- /dev/null
+++ b/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+ "test-bam2fastx-bam2fastq": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test"
+ },
+ "test.fastq.gz:md5,8abf16176fd1625998ee28590e1039b1"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,1b954947255d9b2ad16d2c523258cceb"
+ ],
+ "fastq": [
+ [
+ {
+ "id": "test"
+ },
+ "test.fastq.gz:md5,8abf16176fd1625998ee28590e1039b1"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,1b954947255d9b2ad16d2c523258cceb"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T06:30:10.25178642"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bamtools/stats/tests/main.nf.test b/modules/nf-core/bamtools/stats/tests/main.nf.test
new file mode 100644
index 00000000000..478a6f0e84d
--- /dev/null
+++ b/modules/nf-core/bamtools/stats/tests/main.nf.test
@@ -0,0 +1,35 @@
+
+nextflow_process {
+
+ name "Test Process BAMTOOLS_STATS"
+ script "../main.nf"
+ process "BAMTOOLS_STATS"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "bamtools"
+ tag "bamtools/stats"
+
+ test("test-bamtools-stats") {
+
+ 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/bamtools/stats/tests/main.nf.test.snap b/modules/nf-core/bamtools/stats/tests/main.nf.test.snap
new file mode 100644
index 00000000000..c12ce29e5fb
--- /dev/null
+++ b/modules/nf-core/bamtools/stats/tests/main.nf.test.snap
@@ -0,0 +1,37 @@
+{
+ "test-bamtools-stats": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.bam.stats:md5,b7c3f01682673a652d664a2889b15b66"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,cdecc135c35467721cc72a58b542323b"
+ ],
+ "stats": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.bam.stats:md5,b7c3f01682673a652d664a2889b15b66"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,cdecc135c35467721cc72a58b542323b"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T15:23:51.167984"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bamutil/trimbam/tests/main.nf.test b/modules/nf-core/bamutil/trimbam/tests/main.nf.test
new file mode 100644
index 00000000000..6ce0bbdd2aa
--- /dev/null
+++ b/modules/nf-core/bamutil/trimbam/tests/main.nf.test
@@ -0,0 +1,41 @@
+
+nextflow_process {
+
+ name "Test Process BAMUTIL_TRIMBAM"
+ script "../main.nf"
+ process "BAMUTIL_TRIMBAM"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "bamutil"
+ tag "bamutil/trimbam"
+
+ test("test-bamutil-trimbam") {
+
+ 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),
+ 2,
+ 2
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ bam(process.out.bam[0][1]).getReadsMD5(),
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/bamutil/trimbam/tests/main.nf.test.snap b/modules/nf-core/bamutil/trimbam/tests/main.nf.test.snap
new file mode 100644
index 00000000000..bebeabd6f8f
--- /dev/null
+++ b/modules/nf-core/bamutil/trimbam/tests/main.nf.test.snap
@@ -0,0 +1,15 @@
+{
+ "test-bamutil-trimbam": {
+ "content": [
+ "483cb3b74b338dcc04ea6ae53e86e179",
+ [
+ "versions.yml:md5,db7889ac58ea4eeb68ceb652de159cc4"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T15:21:23.796158"
+ }
+}
\ No newline at end of file
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/clumpify/tests/main.nf.test b/modules/nf-core/bbmap/clumpify/tests/main.nf.test
new file mode 100644
index 00000000000..f43b8767964
--- /dev/null
+++ b/modules/nf-core/bbmap/clumpify/tests/main.nf.test
@@ -0,0 +1,72 @@
+
+nextflow_process {
+
+ name "Test Process BBMAP_CLUMPIFY"
+ script "../main.nf"
+ process "BBMAP_CLUMPIFY"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "bbmap"
+ tag "bbmap/clumpify"
+
+ test("test-bbmap-clumpify-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(
+ process.out.reads,
+ file(process.out.log[0][1]).name,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-bbmap-clumpify-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(
+ process.out.reads,
+ file(process.out.log[0][1]).name,
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/bbmap/clumpify/tests/main.nf.test.snap b/modules/nf-core/bbmap/clumpify/tests/main.nf.test.snap
new file mode 100644
index 00000000000..d2fa37f18c5
--- /dev/null
+++ b/modules/nf-core/bbmap/clumpify/tests/main.nf.test.snap
@@ -0,0 +1,49 @@
+{
+ "test-bbmap-clumpify-paired-end": {
+ "content": [
+ [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ [
+ "test_1.clumped.fastq.gz:md5,27e51643262c1ef3905c4be184c3814c",
+ "test_2.clumped.fastq.gz:md5,c70ab7bbd44d6b6fadd6a1a79ef1648f"
+ ]
+ ]
+ ],
+ "test.clumpify.log",
+ [
+ "versions.yml:md5,ec30171b7944e601f3fd733bb5408bf6"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T06:43:39.816170993"
+ },
+ "test-bbmap-clumpify-single-end": {
+ "content": [
+ [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.clumped.fastq.gz:md5,27e51643262c1ef3905c4be184c3814c"
+ ]
+ ],
+ "test.clumpify.log",
+ [
+ "versions.yml:md5,ec30171b7944e601f3fd733bb5408bf6"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T06:43:28.923674245"
+ }
+}
\ 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/bbmap/sendsketch/meta.yml b/modules/nf-core/bbmap/sendsketch/meta.yml
index 38a5fb3fe6a..76f3e9472ba 100644
--- a/modules/nf-core/bbmap/sendsketch/meta.yml
+++ b/modules/nf-core/bbmap/sendsketch/meta.yml
@@ -12,7 +12,7 @@ tools:
description: "BBMap is a short read aligner, as well as various other bioinformatic 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/"
- licence: "['UC-LBL license (see package)']"
+ licence: ["UC-LBL license (see package)"]
input:
- meta:
type: map
@@ -34,7 +34,7 @@ output:
description: File containing software versions
pattern: "versions.yml"
- hits:
- type: txt
+ type: file
description: .txt file containing hits from a query seuqnce to various reference sequences output
pattern: "*.{txt}"
authors:
diff --git a/modules/nf-core/bbmap/sendsketch/tests/main.nf.test b/modules/nf-core/bbmap/sendsketch/tests/main.nf.test
new file mode 100644
index 00000000000..744feadfcb1
--- /dev/null
+++ b/modules/nf-core/bbmap/sendsketch/tests/main.nf.test
@@ -0,0 +1,70 @@
+
+nextflow_process {
+
+ name "Test Process BBMAP_SENDSKETCH"
+ script "../main.nf"
+ process "BBMAP_SENDSKETCH"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "bbmap"
+ tag "bbmap/sendsketch"
+
+ test("test-bbmap-sendsketch-single") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:true], // meta map
+ [
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+ ]
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ file(process.out.hits[0][1]).readLines()[3..7],
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+ test("test-bbmap-sendsketch-paired") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false], // meta map
+ [
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)
+ ]
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(
+ file(process.out.hits[0][1]).readLines()[3..7],
+ process.out.versions
+ ).match()
+ }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/bbmap/sendsketch/tests/main.nf.test.snap b/modules/nf-core/bbmap/sendsketch/tests/main.nf.test.snap
new file mode 100644
index 00000000000..c516ae720ac
--- /dev/null
+++ b/modules/nf-core/bbmap/sendsketch/tests/main.nf.test.snap
@@ -0,0 +1,40 @@
+{
+ "test-bbmap-sendsketch-paired": {
+ "content": [
+ [
+ "0.52%\t0.14%\t82.66%\t.\t26.68%\t1.03%\t60\t10\t9534\t30656K\t46\tChlorocebus aethiops",
+ "0.46%\t0.12%\t82.30%\t.\t26.38%\t1.10%\t53\t7\t33548\t30986K\t46\tColobus guereza",
+ "9.02%\t0.03%\t91.56%\t.\t0.34%\t1.88%\t48\t8\t9606\t2387M\t26130\tHomo sapiens",
+ "0.30%\t0.08%\t80.90%\t.\t27.42%\t1.23%\t35\t8\t9523\t29749K\t44\tPlecturocebus moloch",
+ "6.70%\t0.02%\t90.53%\t.\t0.34%\t4.10%\t36\t0\t9595\t2355M\t5730\tGorilla gorilla gorilla"
+ ],
+ [
+ "versions.yml:md5,694697087b868316aa450d1bc3775373"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T14:29:22.985067"
+ },
+ "test-bbmap-sendsketch-single": {
+ "content": [
+ [
+ "0.66%\t0.53%\t83.30%\t.\t80.66%\t0.56%\t20\t17\t9593\t47555\t9\tGorilla gorilla",
+ "0.14%\t0.07%\t78.52%\t.\t48.11%\t1.09%\t4\t4\t27679\t78571\t4\tSaimiri boliviensis",
+ "7.69%\t0.01%\t90.45%\t.\t0.12%\t3.85%\t4\t1\t9534\t30656K\t46\tChlorocebus aethiops",
+ "0.17%\t0.04%\t79.27%\t.\t23.69%\t1.26%\t3\t1\t67082\t158942\t1\tBeAn 58058 virus",
+ "5.56%\t0.01%\t89.72%\t.\t0.12%\t5.56%\t3\t0\t9523\t29749K\t44\tPlecturocebus moloch"
+ ],
+ [
+ "versions.yml:md5,694697087b868316aa450d1bc3775373"
+ ]
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T14:29:03.529673"
+ }
+}
\ 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/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/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/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/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/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/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/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/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/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/shiftfasta/tests/main.nf.test b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test
new file mode 100644
index 00000000000..d11d144ea6e
--- /dev/null
+++ b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test
@@ -0,0 +1,44 @@
+
+nextflow_process {
+
+ name "Test Process GATK4_SHIFTFASTA"
+ script "../main.nf"
+ process "GATK4_SHIFTFASTA"
+ config "./nextflow.config"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gatk4"
+ tag "gatk4/shiftfasta"
+
+ test("test-gatk4-shiftfasta") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+ ]
+ input[1] = [
+ [ id:'genome' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', 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/shiftfasta/tests/main.nf.test.snap b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test.snap
new file mode 100644
index 00000000000..bb7e5aa0191
--- /dev/null
+++ b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test.snap
@@ -0,0 +1,133 @@
+{
+ "test-gatk4-shiftfasta": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test_shift.fasta:md5,d65f6e323b25f03a350651e040ad9823"
+ ]
+ ],
+ "1": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test_shift.fasta.fai:md5,5324f610259af3846db7216b42626519"
+ ]
+ ],
+ "2": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test_shift.back_chain:md5,513b4ccf3d1fe1578450795216a054ce"
+ ]
+ ],
+ "3": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test_shift.dict:md5,a46de767b35d329f438b682a3bc0d5a9"
+ ]
+ ],
+ "4": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ [
+ "test.intervals:md5,2cf9d6be2fd5d65364526f9a4ec8cef0",
+ "test.shifted.intervals:md5,6d8d74cd94813e56ec9f09933884f45d"
+ ]
+ ]
+ ],
+ "5": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.shifted.intervals:md5,6d8d74cd94813e56ec9f09933884f45d"
+ ]
+ ],
+ "6": [
+ "versions.yml:md5,afdffb5981aa10bdf40af3a50323fd54"
+ ],
+ "dict": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test_shift.dict:md5,a46de767b35d329f438b682a3bc0d5a9"
+ ]
+ ],
+ "intervals": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ [
+ "test.intervals:md5,2cf9d6be2fd5d65364526f9a4ec8cef0",
+ "test.shifted.intervals:md5,6d8d74cd94813e56ec9f09933884f45d"
+ ]
+ ]
+ ],
+ "shift_back_chain": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test_shift.back_chain:md5,513b4ccf3d1fe1578450795216a054ce"
+ ]
+ ],
+ "shift_fa": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test_shift.fasta:md5,d65f6e323b25f03a350651e040ad9823"
+ ]
+ ],
+ "shift_fai": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test_shift.fasta.fai:md5,5324f610259af3846db7216b42626519"
+ ]
+ ],
+ "shift_intervals": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ "test.shifted.intervals:md5,6d8d74cd94813e56ec9f09933884f45d"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,afdffb5981aa10bdf40af3a50323fd54"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-26T11:11:50.342225"
+ }
+}
\ No newline at end of file
diff --git a/tests/modules/nf-core/gatk4/shiftfasta/nextflow.config b/modules/nf-core/gatk4/shiftfasta/tests/nextflow.config
similarity index 59%
rename from tests/modules/nf-core/gatk4/shiftfasta/nextflow.config
rename to modules/nf-core/gatk4/shiftfasta/tests/nextflow.config
index bf109c3347b..de1be8e6b7d 100644
--- a/tests/modules/nf-core/gatk4/shiftfasta/nextflow.config
+++ b/modules/nf-core/gatk4/shiftfasta/tests/nextflow.config
@@ -1,7 +1,4 @@
process {
-
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
withName: 'GATK4_SHIFTFASTA' {
ext.args = "--intervals MT192765.1:576-16024 --shift-offset-list 8000 --interval-file-name test"
}
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/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/last/dotplot/environment.yml b/modules/nf-core/last/dotplot/environment.yml
index b013d4d8b0e..064a3a459da 100644
--- a/modules/nf-core/last/dotplot/environment.yml
+++ b/modules/nf-core/last/dotplot/environment.yml
@@ -6,4 +6,4 @@ channels:
- bioconda
- defaults
dependencies:
- - "bioconda::last=1542"
+ - "bioconda::last=1571"
diff --git a/modules/nf-core/last/dotplot/main.nf b/modules/nf-core/last/dotplot/main.nf
index 93f311d87cf..1ac3c9ff980 100644
--- a/modules/nf-core/last/dotplot/main.nf
+++ b/modules/nf-core/last/dotplot/main.nf
@@ -4,8 +4,8 @@ process LAST_DOTPLOT {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/last:1542--h43eeafb_1' :
- 'biocontainers/last:1542--h43eeafb_1' }"
+ 'https://depot.galaxyproject.org/singularity/last:1571--h43eeafb_0' :
+ 'biocontainers/last:1571--h43eeafb_0' }"
input:
tuple val(meta), path(maf), path(annot_b)
diff --git a/modules/nf-core/last/dotplot/tests/main.nf.test.snap b/modules/nf-core/last/dotplot/tests/main.nf.test.snap
index cff5b566404..41b3b7e92f7 100644
--- a/modules/nf-core/last/dotplot/tests/main.nf.test.snap
+++ b/modules/nf-core/last/dotplot/tests/main.nf.test.snap
@@ -2,37 +2,37 @@
"sarscov2 - contigs - genome - gif": {
"content": [
[
- "versions.yml:md5,8a86fe4a0227c77ecfcc0aa21a3ece07"
+ "versions.yml:md5,2b5085f9eec6d9623d34b918b66ffe58"
]
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-06-27T09:19:30.116358"
+ "timestamp": "2024-08-26T15:39:30.517622"
},
"sarscov2 - contigs - genome - png - stub": {
"content": [
[
- "versions.yml:md5,8a86fe4a0227c77ecfcc0aa21a3ece07"
+ "versions.yml:md5,2b5085f9eec6d9623d34b918b66ffe58"
]
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-06-27T09:19:46.588825"
+ "timestamp": "2024-08-26T15:39:46.73375"
},
"sarscov2 - contigs - genome - png": {
"content": [
[
- "versions.yml:md5,8a86fe4a0227c77ecfcc0aa21a3ece07"
+ "versions.yml:md5,2b5085f9eec6d9623d34b918b66ffe58"
]
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-06-27T09:19:08.959252"
+ "timestamp": "2024-08-26T15:39:14.058511"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/last/lastal/environment.yml b/modules/nf-core/last/lastal/environment.yml
index c3a87c68c1f..49f3e794c0c 100644
--- a/modules/nf-core/last/lastal/environment.yml
+++ b/modules/nf-core/last/lastal/environment.yml
@@ -6,4 +6,4 @@ channels:
- bioconda
- defaults
dependencies:
- - "bioconda::last=1542"
+ - "bioconda::last=1571"
diff --git a/modules/nf-core/last/lastal/main.nf b/modules/nf-core/last/lastal/main.nf
index 560ada11b32..470e87ccf1e 100644
--- a/modules/nf-core/last/lastal/main.nf
+++ b/modules/nf-core/last/lastal/main.nf
@@ -4,8 +4,8 @@ process LAST_LASTAL {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/last:1542--h43eeafb_1' :
- 'biocontainers/last:1542--h43eeafb_1' }"
+ 'https://depot.galaxyproject.org/singularity/last:1571--h43eeafb_0' :
+ 'biocontainers/last:1571--h43eeafb_0' }"
input:
tuple val(meta), path(fastx), path (param_file)
diff --git a/modules/nf-core/last/lastal/tests/main.nf.test.snap b/modules/nf-core/last/lastal/tests/main.nf.test.snap
index 9245a96252e..d9a09c9aef6 100644
--- a/modules/nf-core/last/lastal/tests/main.nf.test.snap
+++ b/modules/nf-core/last/lastal/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
"id": "contigs",
"single_end": false
},
- "contigs.maf.gz:md5,902274b72657f62d270d284dc211aa7f"
+ "contigs.maf.gz:md5,dd02b4855c49bb3d46106177f5a08955"
]
],
"1": [
@@ -21,7 +21,7 @@
]
],
"2": [
- "versions.yml:md5,e0a425d7cbca674252a1e4328b247ca2"
+ "versions.yml:md5,12f5da2547baed9f5b15b31b1cd22951"
],
"maf": [
[
@@ -29,7 +29,7 @@
"id": "contigs",
"single_end": false
},
- "contigs.maf.gz:md5,902274b72657f62d270d284dc211aa7f"
+ "contigs.maf.gz:md5,dd02b4855c49bb3d46106177f5a08955"
]
],
"multiqc": [
@@ -42,15 +42,15 @@
]
],
"versions": [
- "versions.yml:md5,e0a425d7cbca674252a1e4328b247ca2"
+ "versions.yml:md5,12f5da2547baed9f5b15b31b1cd22951"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-07-02T17:57:48.589408"
+ "timestamp": "2024-08-26T15:23:20.411461"
},
"sarscov2 - contigs - genome - stub": {
"content": [
@@ -74,7 +74,7 @@
]
],
"2": [
- "versions.yml:md5,e0a425d7cbca674252a1e4328b247ca2"
+ "versions.yml:md5,12f5da2547baed9f5b15b31b1cd22951"
],
"maf": [
[
@@ -95,15 +95,15 @@
]
],
"versions": [
- "versions.yml:md5,e0a425d7cbca674252a1e4328b247ca2"
+ "versions.yml:md5,12f5da2547baed9f5b15b31b1cd22951"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-07-02T17:58:30.521811"
+ "timestamp": "2024-08-26T15:24:03.533878"
},
"sarscov2 - contigs - genome - withparams": {
"content": [
@@ -114,7 +114,7 @@
"id": "contigs",
"single_end": false
},
- "contigs.maf.gz:md5,8cb97b6daa34dbf9c723a2c4a984992d"
+ "contigs.maf.gz:md5,8e4058c39c8ea92da0fa063398b6346d"
]
],
"1": [
@@ -127,7 +127,7 @@
]
],
"2": [
- "versions.yml:md5,e0a425d7cbca674252a1e4328b247ca2"
+ "versions.yml:md5,12f5da2547baed9f5b15b31b1cd22951"
],
"maf": [
[
@@ -135,7 +135,7 @@
"id": "contigs",
"single_end": false
},
- "contigs.maf.gz:md5,8cb97b6daa34dbf9c723a2c4a984992d"
+ "contigs.maf.gz:md5,8e4058c39c8ea92da0fa063398b6346d"
]
],
"multiqc": [
@@ -148,14 +148,14 @@
]
],
"versions": [
- "versions.yml:md5,e0a425d7cbca674252a1e4328b247ca2"
+ "versions.yml:md5,12f5da2547baed9f5b15b31b1cd22951"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-07-02T17:58:09.677672"
+ "timestamp": "2024-08-26T15:23:42.107503"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/last/lastdb/environment.yml b/modules/nf-core/last/lastdb/environment.yml
index 9e98a10ae20..e8249083e74 100644
--- a/modules/nf-core/last/lastdb/environment.yml
+++ b/modules/nf-core/last/lastdb/environment.yml
@@ -6,4 +6,4 @@ channels:
- bioconda
- defaults
dependencies:
- - "bioconda::last=1542"
+ - "bioconda::last=1571"
diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf
index 856b3643c77..916838450ae 100644
--- a/modules/nf-core/last/lastdb/main.nf
+++ b/modules/nf-core/last/lastdb/main.nf
@@ -4,8 +4,8 @@ process LAST_LASTDB {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/last:1542--h43eeafb_1' :
- 'biocontainers/last:1542--h43eeafb_1' }"
+ 'https://depot.galaxyproject.org/singularity/last:1571--h43eeafb_0' :
+ 'biocontainers/last:1571--h43eeafb_0' }"
input:
tuple val(meta), path(fastx)
diff --git a/modules/nf-core/last/lastdb/tests/main.nf.test.snap b/modules/nf-core/last/lastdb/tests/main.nf.test.snap
index ee2a1130338..3ff3212f6f8 100644
--- a/modules/nf-core/last/lastdb/tests/main.nf.test.snap
+++ b/modules/nf-core/last/lastdb/tests/main.nf.test.snap
@@ -19,7 +19,7 @@
]
],
"1": [
- "versions.yml:md5,c7fa6cfa252a61c600a73d6341d47557"
+ "versions.yml:md5,00a5bd5d4a9df81b83a6279cecb34701"
],
"index": [
[
@@ -38,15 +38,15 @@
]
],
"versions": [
- "versions.yml:md5,c7fa6cfa252a61c600a73d6341d47557"
+ "versions.yml:md5,00a5bd5d4a9df81b83a6279cecb34701"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-06-06T16:42:08.735561"
+ "timestamp": "2024-08-26T15:34:34.647102"
},
"sarscov2 - fastq gzipped": {
"content": [
@@ -59,7 +59,7 @@
[
"test.bck:md5,05b14d8ac418b3193d9cc921086cea05",
"test.des:md5,26ab49015cc572172b9efa50fc5190bc",
- "test.prj:md5,b50003077b7c7357fb8bacdf6f87653d",
+ "test.prj:md5,e668d4ee5fb0c2e9c82bd4a2fc3e7998",
"test.sds:md5,d3deb4c985081c9f5ad6684d405bd20b",
"test.ssp:md5,5c17139a9022b0cb97f007146fa1c6da",
"test.suf:md5,9ac359afa86a8964d81a87a1d4f05ef0",
@@ -68,7 +68,7 @@
]
],
"1": [
- "versions.yml:md5,c7fa6cfa252a61c600a73d6341d47557"
+ "versions.yml:md5,00a5bd5d4a9df81b83a6279cecb34701"
],
"index": [
[
@@ -78,7 +78,7 @@
[
"test.bck:md5,05b14d8ac418b3193d9cc921086cea05",
"test.des:md5,26ab49015cc572172b9efa50fc5190bc",
- "test.prj:md5,b50003077b7c7357fb8bacdf6f87653d",
+ "test.prj:md5,e668d4ee5fb0c2e9c82bd4a2fc3e7998",
"test.sds:md5,d3deb4c985081c9f5ad6684d405bd20b",
"test.ssp:md5,5c17139a9022b0cb97f007146fa1c6da",
"test.suf:md5,9ac359afa86a8964d81a87a1d4f05ef0",
@@ -87,15 +87,15 @@
]
],
"versions": [
- "versions.yml:md5,c7fa6cfa252a61c600a73d6341d47557"
+ "versions.yml:md5,00a5bd5d4a9df81b83a6279cecb34701"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-06-06T16:41:07.4512"
+ "timestamp": "2024-08-26T15:34:18.336299"
},
"sarscov2 - fasta": {
"content": [
@@ -108,7 +108,7 @@
[
"test.bck:md5,157526d333b88523cb15ac4efe00738f",
"test.des:md5,3a9ea6d336e113a74d7fdca5e7b623fc",
- "test.prj:md5,b937b1565cb4c983c8fcd3780d3e151e",
+ "test.prj:md5,f7e7445a3ff008efe127ca841f59fe9c",
"test.sds:md5,e7729db27ac7a5a109c9d48cfcdc9015",
"test.ssp:md5,53524efdea3d8989201419a29e81ec1f",
"test.suf:md5,ef7482260705bb8146acbbbdce6c0068",
@@ -117,7 +117,7 @@
]
],
"1": [
- "versions.yml:md5,c7fa6cfa252a61c600a73d6341d47557"
+ "versions.yml:md5,00a5bd5d4a9df81b83a6279cecb34701"
],
"index": [
[
@@ -127,7 +127,7 @@
[
"test.bck:md5,157526d333b88523cb15ac4efe00738f",
"test.des:md5,3a9ea6d336e113a74d7fdca5e7b623fc",
- "test.prj:md5,b937b1565cb4c983c8fcd3780d3e151e",
+ "test.prj:md5,f7e7445a3ff008efe127ca841f59fe9c",
"test.sds:md5,e7729db27ac7a5a109c9d48cfcdc9015",
"test.ssp:md5,53524efdea3d8989201419a29e81ec1f",
"test.suf:md5,ef7482260705bb8146acbbbdce6c0068",
@@ -136,14 +136,14 @@
]
],
"versions": [
- "versions.yml:md5,c7fa6cfa252a61c600a73d6341d47557"
+ "versions.yml:md5,00a5bd5d4a9df81b83a6279cecb34701"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-06-06T16:40:05.874954"
+ "timestamp": "2024-08-26T15:34:01.800286"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/last/mafconvert/environment.yml b/modules/nf-core/last/mafconvert/environment.yml
index 009cb82f4ac..9aea0cbe6ee 100644
--- a/modules/nf-core/last/mafconvert/environment.yml
+++ b/modules/nf-core/last/mafconvert/environment.yml
@@ -6,4 +6,4 @@ channels:
- bioconda
- defaults
dependencies:
- - "bioconda::last=1542"
+ - "bioconda::last=1571"
diff --git a/modules/nf-core/last/mafconvert/main.nf b/modules/nf-core/last/mafconvert/main.nf
index 3bed0600bf8..bbe6c75d9a6 100644
--- a/modules/nf-core/last/mafconvert/main.nf
+++ b/modules/nf-core/last/mafconvert/main.nf
@@ -4,8 +4,8 @@ process LAST_MAFCONVERT {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/last:1542--h43eeafb_1' :
- 'biocontainers/last:1542--h43eeafb_1' }"
+ 'https://depot.galaxyproject.org/singularity/last:1571--h43eeafb_0' :
+ 'biocontainers/last:1571--h43eeafb_0' }"
input:
tuple val(meta), path(maf)
diff --git a/modules/nf-core/last/mafconvert/tests/main.nf.test.snap b/modules/nf-core/last/mafconvert/tests/main.nf.test.snap
index 3693b980836..f1c41c08189 100644
--- a/modules/nf-core/last/mafconvert/tests/main.nf.test.snap
+++ b/modules/nf-core/last/mafconvert/tests/main.nf.test.snap
@@ -35,7 +35,7 @@
],
"9": [
- "versions.yml:md5,d759c732b33af95ef94f98c01fcc041b"
+ "versions.yml:md5,4e515249c766dcf398f517bb837adce5"
],
"axt_gz": [
@@ -70,15 +70,15 @@
],
"versions": [
- "versions.yml:md5,d759c732b33af95ef94f98c01fcc041b"
+ "versions.yml:md5,4e515249c766dcf398f517bb837adce5"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-06-06T18:12:33.604233"
+ "timestamp": "2024-08-26T15:26:55.89707"
},
"sarscov2 - bam": {
"content": [
@@ -116,7 +116,7 @@
],
"9": [
- "versions.yml:md5,d759c732b33af95ef94f98c01fcc041b"
+ "versions.yml:md5,4e515249c766dcf398f517bb837adce5"
],
"axt_gz": [
@@ -151,14 +151,14 @@
],
"versions": [
- "versions.yml:md5,d759c732b33af95ef94f98c01fcc041b"
+ "versions.yml:md5,4e515249c766dcf398f517bb837adce5"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-06-06T18:11:32.396233"
+ "timestamp": "2024-08-26T15:26:39.429173"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/last/mafswap/environment.yml b/modules/nf-core/last/mafswap/environment.yml
index cc112af83d4..15e3c6b8ba5 100644
--- a/modules/nf-core/last/mafswap/environment.yml
+++ b/modules/nf-core/last/mafswap/environment.yml
@@ -6,4 +6,4 @@ channels:
- bioconda
- defaults
dependencies:
- - "bioconda::last=1542"
+ - "bioconda::last=1571"
diff --git a/modules/nf-core/last/mafswap/main.nf b/modules/nf-core/last/mafswap/main.nf
index 875a6af3498..4dadf391ff4 100644
--- a/modules/nf-core/last/mafswap/main.nf
+++ b/modules/nf-core/last/mafswap/main.nf
@@ -4,8 +4,8 @@ process LAST_MAFSWAP {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/last:1542--h43eeafb_1' :
- 'biocontainers/last:1542--h43eeafb_1' }"
+ 'https://depot.galaxyproject.org/singularity/last:1571--h43eeafb_0' :
+ 'biocontainers/last:1571--h43eeafb_0' }"
input:
tuple val(meta), path(maf)
diff --git a/modules/nf-core/last/mafswap/tests/main.nf.test.snap b/modules/nf-core/last/mafswap/tests/main.nf.test.snap
index cc085dffe1b..5c41a422a0b 100644
--- a/modules/nf-core/last/mafswap/tests/main.nf.test.snap
+++ b/modules/nf-core/last/mafswap/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
]
],
"1": [
- "versions.yml:md5,9819f8873c15cc665cbee998cefb72dd"
+ "versions.yml:md5,1a6fc970e6952d90c3b560162af8fb1f"
],
"maf": [
[
@@ -22,15 +22,15 @@
]
],
"versions": [
- "versions.yml:md5,9819f8873c15cc665cbee998cefb72dd"
+ "versions.yml:md5,1a6fc970e6952d90c3b560162af8fb1f"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-06-04T17:59:43.47396"
+ "timestamp": "2024-08-26T15:31:41.694631"
},
"sarscov2 - contigs - genome - stub": {
"content": [
@@ -44,7 +44,7 @@
]
],
"1": [
- "versions.yml:md5,9819f8873c15cc665cbee998cefb72dd"
+ "versions.yml:md5,1a6fc970e6952d90c3b560162af8fb1f"
],
"maf": [
[
@@ -55,14 +55,14 @@
]
],
"versions": [
- "versions.yml:md5,9819f8873c15cc665cbee998cefb72dd"
+ "versions.yml:md5,1a6fc970e6952d90c3b560162af8fb1f"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-06-06T19:41:29.891962"
+ "timestamp": "2024-08-26T15:31:58.257208"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/last/postmask/environment.yml b/modules/nf-core/last/postmask/environment.yml
index 75ee281150d..899e8fee491 100644
--- a/modules/nf-core/last/postmask/environment.yml
+++ b/modules/nf-core/last/postmask/environment.yml
@@ -6,4 +6,4 @@ channels:
- bioconda
- defaults
dependencies:
- - "bioconda::last=1542"
+ - "bioconda::last=1571"
diff --git a/modules/nf-core/last/postmask/main.nf b/modules/nf-core/last/postmask/main.nf
index ed2b5f0c060..e9ff4878fde 100644
--- a/modules/nf-core/last/postmask/main.nf
+++ b/modules/nf-core/last/postmask/main.nf
@@ -4,8 +4,8 @@ process LAST_POSTMASK {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/last:1542--h43eeafb_1' :
- 'biocontainers/last:1542--h43eeafb_1' }"
+ 'https://depot.galaxyproject.org/singularity/last:1571--h43eeafb_0' :
+ 'biocontainers/last:1571--h43eeafb_0' }"
input:
tuple val(meta), path(maf)
diff --git a/modules/nf-core/last/postmask/tests/main.nf.test.snap b/modules/nf-core/last/postmask/tests/main.nf.test.snap
index 3d924744615..3af5efbc4b8 100644
--- a/modules/nf-core/last/postmask/tests/main.nf.test.snap
+++ b/modules/nf-core/last/postmask/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
]
],
"1": [
- "versions.yml:md5,5bfe6a9059961e1533daf7a021899249"
+ "versions.yml:md5,d1f6eee514bd694a0aeead8ee815a19e"
],
"maf": [
[
@@ -22,15 +22,15 @@
]
],
"versions": [
- "versions.yml:md5,5bfe6a9059961e1533daf7a021899249"
+ "versions.yml:md5,d1f6eee514bd694a0aeead8ee815a19e"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-06-03T15:21:37.870786"
+ "timestamp": "2024-08-26T15:36:54.898194"
},
"sarscov2 - contigs - genome - stub": {
"content": [
@@ -44,7 +44,7 @@
]
],
"1": [
- "versions.yml:md5,5bfe6a9059961e1533daf7a021899249"
+ "versions.yml:md5,d1f6eee514bd694a0aeead8ee815a19e"
],
"maf": [
[
@@ -55,14 +55,14 @@
]
],
"versions": [
- "versions.yml:md5,5bfe6a9059961e1533daf7a021899249"
+ "versions.yml:md5,d1f6eee514bd694a0aeead8ee815a19e"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-06-06T19:55:47.691726"
+ "timestamp": "2024-08-26T15:37:11.363434"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/last/split/environment.yml b/modules/nf-core/last/split/environment.yml
index 7d76b55fca1..c4608dd218c 100644
--- a/modules/nf-core/last/split/environment.yml
+++ b/modules/nf-core/last/split/environment.yml
@@ -6,4 +6,4 @@ channels:
- bioconda
- defaults
dependencies:
- - "bioconda::last=1542"
+ - "bioconda::last=1571"
diff --git a/modules/nf-core/last/split/main.nf b/modules/nf-core/last/split/main.nf
index 410d16f1d27..9fcf3588d57 100644
--- a/modules/nf-core/last/split/main.nf
+++ b/modules/nf-core/last/split/main.nf
@@ -4,8 +4,8 @@ process LAST_SPLIT {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/last:1542--h43eeafb_1' :
- 'biocontainers/last:1542--h43eeafb_1' }"
+ 'https://depot.galaxyproject.org/singularity/last:1571--h43eeafb_0' :
+ 'biocontainers/last:1571--h43eeafb_0' }"
input:
tuple val(meta), path(maf)
diff --git a/modules/nf-core/last/split/tests/main.nf.test.snap b/modules/nf-core/last/split/tests/main.nf.test.snap
index 953a6542a80..603f9263f5a 100644
--- a/modules/nf-core/last/split/tests/main.nf.test.snap
+++ b/modules/nf-core/last/split/tests/main.nf.test.snap
@@ -19,7 +19,7 @@
]
],
"2": [
- "versions.yml:md5,9e429d0800988ae0bbe5000827d34ad1"
+ "versions.yml:md5,8b705a62c76f7753a51d3d387cf458f1"
],
"maf": [
[
@@ -38,15 +38,15 @@
]
],
"versions": [
- "versions.yml:md5,9e429d0800988ae0bbe5000827d34ad1"
+ "versions.yml:md5,8b705a62c76f7753a51d3d387cf458f1"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-07-02T11:45:00.535348"
+ "timestamp": "2024-08-26T15:20:43.307807"
},
"sarscov2 - contigs_genome - stub": {
"content": [
@@ -68,7 +68,7 @@
]
],
"2": [
- "versions.yml:md5,9e429d0800988ae0bbe5000827d34ad1"
+ "versions.yml:md5,8b705a62c76f7753a51d3d387cf458f1"
],
"maf": [
[
@@ -87,14 +87,14 @@
]
],
"versions": [
- "versions.yml:md5,9e429d0800988ae0bbe5000827d34ad1"
+ "versions.yml:md5,8b705a62c76f7753a51d3d387cf458f1"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-07-02T11:45:21.243325"
+ "timestamp": "2024-08-26T15:20:59.963034"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/last/train/environment.yml b/modules/nf-core/last/train/environment.yml
index 5edaf64fdfc..1a59871b7a5 100644
--- a/modules/nf-core/last/train/environment.yml
+++ b/modules/nf-core/last/train/environment.yml
@@ -6,4 +6,4 @@ channels:
- bioconda
- defaults
dependencies:
- - "bioconda::last=1542"
+ - "bioconda::last=1571"
diff --git a/modules/nf-core/last/train/main.nf b/modules/nf-core/last/train/main.nf
index 9f592b56e38..0829060f4ba 100644
--- a/modules/nf-core/last/train/main.nf
+++ b/modules/nf-core/last/train/main.nf
@@ -4,8 +4,8 @@ process LAST_TRAIN {
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/last:1542--h43eeafb_1' :
- 'biocontainers/last:1542--h43eeafb_1' }"
+ 'https://depot.galaxyproject.org/singularity/last:1571--h43eeafb_0' :
+ 'biocontainers/last:1571--h43eeafb_0' }"
input:
tuple val(meta), path(fastx)
diff --git a/modules/nf-core/last/train/tests/main.nf.test.snap b/modules/nf-core/last/train/tests/main.nf.test.snap
index a3a0cc8f000..0c9185d5216 100644
--- a/modules/nf-core/last/train/tests/main.nf.test.snap
+++ b/modules/nf-core/last/train/tests/main.nf.test.snap
@@ -21,7 +21,7 @@
]
],
"2": [
- "versions.yml:md5,c5578547acf9e77e1e8f6bf796e32ac2"
+ "versions.yml:md5,0a9cfea9e8b841939e040ff6d45de96f"
],
"multiqc": [
[
@@ -42,15 +42,15 @@
]
],
"versions": [
- "versions.yml:md5,c5578547acf9e77e1e8f6bf796e32ac2"
+ "versions.yml:md5,0a9cfea9e8b841939e040ff6d45de96f"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.04.3"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-07-10T14:50:11.528587"
+ "timestamp": "2024-08-26T15:29:24.633162"
},
"sarscov2 - genome - contigs": {
"content": [
@@ -61,7 +61,7 @@
"id": "contigs",
"single_end": false
},
- "contigs.genome.train:md5,3d7e1c630705d83c6a11b6f28d5aefcb"
+ "contigs.genome.train:md5,c269b6fee0f0b3011c4cb2764645955c"
]
],
"1": [
@@ -74,7 +74,7 @@
]
],
"2": [
- "versions.yml:md5,38234cf053c708e57cc080990f777411"
+ "versions.yml:md5,1d8eb88ebe5170b8a0e561f5a3491f0e"
],
"multiqc": [
[
@@ -91,18 +91,18 @@
"id": "contigs",
"single_end": false
},
- "contigs.genome.train:md5,3d7e1c630705d83c6a11b6f28d5aefcb"
+ "contigs.genome.train:md5,c269b6fee0f0b3011c4cb2764645955c"
]
],
"versions": [
- "versions.yml:md5,38234cf053c708e57cc080990f777411"
+ "versions.yml:md5,1d8eb88ebe5170b8a0e561f5a3491f0e"
]
}
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-07-03T18:04:34.914789"
+ "timestamp": "2024-08-26T15:29:03.278235"
}
}
\ No newline at end of file
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/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 f4ce031ef77..11dd9514e35 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -25,39 +25,15 @@ ataqv/ataqv:
ataqv/mkarv:
- modules/nf-core/ataqv/mkarv/**
- tests/modules/nf-core/ataqv/mkarv/**
-atlas/call:
- - modules/nf-core/atlas/call/**
- - tests/modules/nf-core/atlas/call/**
-atlas/pmd:
- - modules/nf-core/atlas/pmd/**
- - tests/modules/nf-core/atlas/pmd/**
-atlas/recal:
- - modules/nf-core/atlas/recal/**
- - tests/modules/nf-core/atlas/recal/**
-atlas/splitmerge:
- - modules/nf-core/atlas/splitmerge/**
- - tests/modules/nf-core/atlas/splitmerge/**
authentict/deam2cont:
- modules/nf-core/authentict/deam2cont/**
- tests/modules/nf-core/authentict/deam2cont/**
-bam2fastx/bam2fastq:
- - modules/nf-core/bam2fastx/bam2fastq/**
- - tests/modules/nf-core/bam2fastx/bam2fastq/**
bamtools/convert:
- modules/nf-core/bamtools/convert/**
- tests/modules/nf-core/bamtools/convert/**
bamtools/split:
- modules/nf-core/bamtools/split/**
- tests/modules/nf-core/bamtools/split/**
-bamtools/stats:
- - modules/nf-core/bamtools/stats/**
- - tests/modules/nf-core/bamtools/stats/**
-bamutil/trimbam:
- - modules/nf-core/bamutil/trimbam/**
- - tests/modules/nf-core/bamutil/trimbam/**
-bandage/image:
- - modules/nf-core/bandage/image/**
- - tests/modules/nf-core/bandage/image/**
basicpy:
- modules/nf-core/basicpy/**
- tests/modules/nf-core/basicpy/**
@@ -67,63 +43,30 @@ bbmap/align:
bbmap/bbnorm:
- modules/nf-core/bbmap/bbnorm/**
- tests/modules/nf-core/bbmap/bbnorm/**
-bbmap/clumpify:
- - modules/nf-core/bbmap/clumpify/**
- - tests/modules/nf-core/bbmap/clumpify/**
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/**
-bbmap/sendsketch:
- - modules/nf-core/bbmap/sendsketch/**
- - tests/modules/nf-core/bbmap/sendsketch/**
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/**
@@ -434,27 +377,15 @@ 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/**
@@ -467,18 +398,12 @@ 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/**
@@ -488,39 +413,21 @@ 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/**
@@ -620,9 +527,6 @@ 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/**
@@ -650,9 +554,6 @@ 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/**
@@ -1064,9 +965,6 @@ picard/filtersamreads:
picard/fixmateinformation:
- modules/nf-core/picard/fixmateinformation/**
- tests/modules/nf-core/picard/fixmateinformation/**
-picard/renamesampleinvcf:
- - modules/nf-core/picard/renamesampleinvcf/**
- - tests/modules/nf-core/picard/renamesampleinvcf/**
picard/scatterintervalsbyns:
- modules/nf-core/picard/scatterintervalsbyns/**
- tests/modules/nf-core/picard/scatterintervalsbyns/**
diff --git a/tests/modules/nf-core/atlas/call/main.nf b/tests/modules/nf-core/atlas/call/main.nf
deleted file mode 100644
index 5e2320b2c11..00000000000
--- a/tests/modules/nf-core/atlas/call/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ATLAS_CALL } from '../../../../../modules/nf-core/atlas/call/main.nf'
-
-workflow test_atlas_call {
-
- 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 = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
- fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
- known_alleles = []
- method = 'randomBase'
-
- ATLAS_CALL ( input, fasta, fai, known_alleles, method )
-}
diff --git a/tests/modules/nf-core/atlas/call/nextflow.config b/tests/modules/nf-core/atlas/call/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/atlas/call/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/atlas/call/test.yml b/tests/modules/nf-core/atlas/call/test.yml
deleted file mode 100644
index 78549fa3feb..00000000000
--- a/tests/modules/nf-core/atlas/call/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: atlas call test_atlas_call
- command: nextflow run ./tests/modules/nf-core/atlas/call -entry test_atlas_call -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/atlas/call/nextflow.config
- tags:
- - atlas
- - atlas/call
- files:
- - path: output/atlas/test.paired_end.sorted_randomBase.vcf.gz
- contains:
- - "##source=atlas"
diff --git a/tests/modules/nf-core/atlas/pmd/main.nf b/tests/modules/nf-core/atlas/pmd/main.nf
deleted file mode 100644
index bcba7dc3f4f..00000000000
--- a/tests/modules/nf-core/atlas/pmd/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ATLAS_PMD } from '../../../../../modules/nf-core/atlas/pmd/main.nf'
-
-workflow test_atlas_pmd {
-
- 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)
- fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-
- ATLAS_PMD ( input, fasta, fai )
-}
diff --git a/tests/modules/nf-core/atlas/pmd/nextflow.config b/tests/modules/nf-core/atlas/pmd/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/atlas/pmd/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/atlas/pmd/test.yml b/tests/modules/nf-core/atlas/pmd/test.yml
deleted file mode 100644
index bb2c3f973ac..00000000000
--- a/tests/modules/nf-core/atlas/pmd/test.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-- name: atlas pmd test_atlas_pmd
- command: nextflow run ./tests/modules/nf-core/atlas/pmd -entry test_atlas_pmd -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/atlas/pmd/nextflow.config
- tags:
- - atlas/pmd
- - atlas
- files:
- - path: output/atlas/test.paired_end.sorted_PMD_Table.txt
- md5sum: b28a9f4784f30a711046708eb7d94642
- - path: output/atlas/test.paired_end.sorted_PMD_Table_counts.txt
- md5sum: 1aabfb83cfff6e0413f52d016c943e3e
- - path: output/atlas/test.paired_end.sorted_PMD_input_Empiric.txt
- md5sum: 8ff876f50ce05dc9aac0646a31682df0
- - path: output/atlas/test.paired_end.sorted_PMD_input_Exponential.txt
- md5sum: 2421450ef643316f4eacf5cb811e4df7
diff --git a/tests/modules/nf-core/atlas/recal/main.nf b/tests/modules/nf-core/atlas/recal/main.nf
deleted file mode 100644
index fadda2019e6..00000000000
--- a/tests/modules/nf-core/atlas/recal/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ATLAS_RECAL } from '../../../../../modules/nf-core/atlas/recal/main.nf'
-
-workflow test_atlas_recal {
-
- 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),
- [],
- []
- ]
- alleles = []
- invariant_sites = []
-
- ATLAS_RECAL ( input, alleles, invariant_sites )
-}
-
-
diff --git a/tests/modules/nf-core/atlas/recal/nextflow.config b/tests/modules/nf-core/atlas/recal/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/atlas/recal/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/atlas/recal/test.yml b/tests/modules/nf-core/atlas/recal/test.yml
deleted file mode 100644
index a18b22c01dc..00000000000
--- a/tests/modules/nf-core/atlas/recal/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: atlas recal test_atlas_recal
- command: nextflow run ./tests/modules/nf-core/atlas/recal -entry test_atlas_recal -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/atlas/recal/nextflow.config
- tags:
- - atlas/recal
- - atlas
- files:
- - path: output/atlas/test_recalibrationEM.txt
- contains: ["readGroup"]
diff --git a/tests/modules/nf-core/atlas/splitmerge/main.nf b/tests/modules/nf-core/atlas/splitmerge/main.nf
deleted file mode 100644
index bde3c197329..00000000000
--- a/tests/modules/nf-core/atlas/splitmerge/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ATLAS_SPLITMERGE } from '../../../../../modules/nf-core/atlas/splitmerge/main.nf'
-
-//MAIN
-workflow test_atlas_splitmerge {
- meta = [ id:'test', single_end:false ]
- bam = file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
- bai = file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
- settings = file(params.test_data['homo_sapiens']['illumina']['read_group_settings_txt'], checkIfExists: true)
-
- ATLAS_SPLITMERGE ( [meta, bam, bai, settings, []] )
-}
diff --git a/tests/modules/nf-core/atlas/splitmerge/nextflow.config b/tests/modules/nf-core/atlas/splitmerge/nextflow.config
deleted file mode 100644
index ff5bc70147a..00000000000
--- a/tests/modules/nf-core/atlas/splitmerge/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
- withName: ATLAS_SPLITMERGE {
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
- }
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/atlas/splitmerge/test.yml b/tests/modules/nf-core/atlas/splitmerge/test.yml
deleted file mode 100644
index c41c8e06a69..00000000000
--- a/tests/modules/nf-core/atlas/splitmerge/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: atlas splitmerge test_atlas_splitmerge
- command: nextflow run ./tests/modules/nf-core/atlas/splitmerge -entry test_atlas_splitmerge -c ./tests/config/nextflow.config
- tags:
- - atlas
- - atlas/splitmerge
- files:
- - path: output/atlas/test.paired_end.sorted_ignoredReads.txt.gz
- md5sum: 9b64c47313d2de89c26790f713707ee6
- - path: output/atlas/test.paired_end.sorted_mergedReads.bam
- - path: output/atlas/versions.yml
- md5sum: 11735bec9c2f4b395b987fd00d4e4294
diff --git a/tests/modules/nf-core/bam2fastx/bam2fastq/main.nf b/tests/modules/nf-core/bam2fastx/bam2fastq/main.nf
deleted file mode 100644
index d8073765b6d..00000000000
--- a/tests/modules/nf-core/bam2fastx/bam2fastq/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BAM2FASTX_BAM2FASTQ } from '../../../../../modules/nf-core/bam2fastx/bam2fastq/main.nf'
-
-workflow test_bam2fastx_bam2fastq {
-
- input = [
- [ id:'test' ], // meta map
- file(params.test_data['homo_sapiens']['pacbio']['alz'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['pacbio']['alzpbi'], checkIfExists: true)
- ]
-
- BAM2FASTX_BAM2FASTQ ( input )
-}
diff --git a/tests/modules/nf-core/bam2fastx/bam2fastq/nextflow.config b/tests/modules/nf-core/bam2fastx/bam2fastq/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/bam2fastx/bam2fastq/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/bam2fastx/bam2fastq/test.yml b/tests/modules/nf-core/bam2fastx/bam2fastq/test.yml
deleted file mode 100644
index 18b9f144a72..00000000000
--- a/tests/modules/nf-core/bam2fastx/bam2fastq/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: bam2fastx bam2fastq test_bam2fastx_bam2fastq
- command: nextflow run ./tests/modules/nf-core/bam2fastx/bam2fastq -entry test_bam2fastx_bam2fastq -c ./tests/config/nextflow.config
- tags:
- - bam2fastx/bam2fastq
- - bam2fastx
- files:
- - path: output/bam2fastx/test.fastq.gz
- md5sum: f0329f9ea12324c6631ac9f3712f2ca5
- - path: output/bam2fastx/versions.yml
diff --git a/tests/modules/nf-core/bamtools/stats/main.nf b/tests/modules/nf-core/bamtools/stats/main.nf
deleted file mode 100644
index 6adbb060bea..00000000000
--- a/tests/modules/nf-core/bamtools/stats/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BAMTOOLS_STATS } from '../../../../../modules/nf-core/bamtools/stats/main.nf'
-
-workflow test_bamtools_stats {
-
- input = [
- [ id:'test', single_end:false ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
- ]
-
- BAMTOOLS_STATS ( input )
-}
diff --git a/tests/modules/nf-core/bamtools/stats/nextflow.config b/tests/modules/nf-core/bamtools/stats/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/bamtools/stats/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/bamtools/stats/test.yml b/tests/modules/nf-core/bamtools/stats/test.yml
deleted file mode 100644
index b8bd38e44bd..00000000000
--- a/tests/modules/nf-core/bamtools/stats/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: bamtools stats test_bamtools_stats
- command: nextflow run ./tests/modules/nf-core/bamtools/stats -entry test_bamtools_stats -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bamtools/stats/nextflow.config
- tags:
- - bamtools
- - bamtools/stats
- files:
- - path: output/bamtools/test.bam.stats
- md5sum: b7c3f01682673a652d664a2889b15b66
- - path: output/bamtools/versions.yml
diff --git a/tests/modules/nf-core/bamutil/trimbam/main.nf b/tests/modules/nf-core/bamutil/trimbam/main.nf
deleted file mode 100644
index b2359338d88..00000000000
--- a/tests/modules/nf-core/bamutil/trimbam/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BAMUTIL_TRIMBAM } from '../../../../../modules/nf-core/bamutil/trimbam/main.nf'
-
-workflow test_bamutil_trimbam {
-
- input = [ [ id:'test', single_end:false ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
- 2,
- 2 ]
-
- BAMUTIL_TRIMBAM ( input )
-}
diff --git a/tests/modules/nf-core/bamutil/trimbam/nextflow.config b/tests/modules/nf-core/bamutil/trimbam/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/bamutil/trimbam/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/bamutil/trimbam/test.yml b/tests/modules/nf-core/bamutil/trimbam/test.yml
deleted file mode 100644
index ec9371afd74..00000000000
--- a/tests/modules/nf-core/bamutil/trimbam/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bamutil trimbam test_bamutil_trimbam
- command: nextflow run ./tests/modules/nf-core/bamutil/trimbam -entry test_bamutil_trimbam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bamutil/trimbam/nextflow.config
- tags:
- - bamutil/trimbam
- - bamutil
- files:
- - path: output/bamutil/test.bam
- md5sum: 9ddd0ecca82f7f3433383f3d1308970e
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/clumpify/main.nf b/tests/modules/nf-core/bbmap/clumpify/main.nf
deleted file mode 100644
index 65b49acce8e..00000000000
--- a/tests/modules/nf-core/bbmap/clumpify/main.nf
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BBMAP_CLUMPIFY } from '../../../../../modules/nf-core/bbmap/clumpify/main.nf'
-
-workflow test_bbmap_clumpify_single_end {
-
- input = [ [ id:'test', single_end:true ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
- ]
-
- BBMAP_CLUMPIFY ( input )
-}
-
-workflow test_bbmap_clumpify_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) ]
- ]
-
- BBMAP_CLUMPIFY ( input )
-}
diff --git a/tests/modules/nf-core/bbmap/clumpify/nextflow.config b/tests/modules/nf-core/bbmap/clumpify/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/bbmap/clumpify/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/clumpify/test.yml b/tests/modules/nf-core/bbmap/clumpify/test.yml
deleted file mode 100644
index 65975b4f70d..00000000000
--- a/tests/modules/nf-core/bbmap/clumpify/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: bbmap clumpify test_bbmap_clumpify_single_end
- command: nextflow run ./tests/modules/nf-core/bbmap/clumpify -entry test_bbmap_clumpify_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/clumpify/nextflow.config
- tags:
- - bbmap/clumpify
- - bbmap
- files:
- - path: output/bbmap/test.clumped.fastq.gz
- - path: output/bbmap/test.clumpify.log
-
-- name: bbmap clumpify test_bbmap_clumpify_paired_end
- command: nextflow run ./tests/modules/nf-core/bbmap/clumpify -entry test_bbmap_clumpify_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/clumpify/nextflow.config
- tags:
- - bbmap/clumpify
- - bbmap
- files:
- - path: output/bbmap/test.clumpify.log
- - path: output/bbmap/test_1.clumped.fastq.gz
- - path: output/bbmap/test_2.clumped.fastq.gz
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/bbmap/sendsketch/main.nf b/tests/modules/nf-core/bbmap/sendsketch/main.nf
deleted file mode 100644
index dafc331573b..00000000000
--- a/tests/modules/nf-core/bbmap/sendsketch/main.nf
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BBMAP_SENDSKETCH } from '../../../../../modules/nf-core/bbmap/sendsketch/main.nf'
-
-workflow test_bbmap_sendsketch_single {
-
- input = [ [ id:'test', single_end:true], // meta map
- [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
- ]
- ]
-
- BBMAP_SENDSKETCH ( input )
-}
-
-workflow test_bbmap_sendsketch_paired {
-
- input = [ [ id:'test', single_end:false], // meta map
- [ file(params.test_data['homo_sapiens']['illumina']['test2_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test2_2_fastq_gz'], checkIfExists: true)
- ]
- ]
-
- BBMAP_SENDSKETCH ( input )
-}
-
diff --git a/tests/modules/nf-core/bbmap/sendsketch/nextflow.config b/tests/modules/nf-core/bbmap/sendsketch/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/bbmap/sendsketch/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/sendsketch/test.yml b/tests/modules/nf-core/bbmap/sendsketch/test.yml
deleted file mode 100644
index ffbb1d77327..00000000000
--- a/tests/modules/nf-core/bbmap/sendsketch/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: bbmap sendsketch test_bbmap_sendsketch_single
- command: nextflow run ./tests/modules/nf-core/bbmap/sendsketch -entry test_bbmap_sendsketch_single -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/sendsketch/nextflow.config
- tags:
- - bbmap/sendsketch
- - bbmap
- files:
- - path: output/bbmap/test.txt
- md5sum: ba6a78659eb15d0d130d5daee8c87ead
- - path: output/bbmap/versions.yml
-
-- name: bbmap sendsketch test_bbmap_sendsketch_paired
- command: nextflow run ./tests/modules/nf-core/bbmap/sendsketch -entry test_bbmap_sendsketch_paired -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bbmap/sendsketch/nextflow.config
- tags:
- - bbmap/sendsketch
- - bbmap
- files:
- - path: output/bbmap/test.txt
- md5sum: 651f7321cd0340844d23a1457a9651f9
- - path: output/bbmap/versions.yml
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/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/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/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/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/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/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/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/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/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/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/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/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/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