diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 4ecfbfe3..4a9bc5c7 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -18,11 +18,11 @@
"python.linting.flake8Path": "/opt/conda/bin/flake8",
"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
- "python.linting.pylintPath": "/opt/conda/bin/pylint"
+ "python.linting.pylintPath": "/opt/conda/bin/pylint",
},
// Add the IDs of extensions you want installed when the container is created.
- "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
- }
- }
+ "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"],
+ },
+ },
}
diff --git a/CHANGELOG.md b/CHANGELOG.md
index fd5261af..87e86cee 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,23 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## v1.1.4 - Augmented Akita Patch [2024-01-24]
+
+### `Added`
+
+### `Fixed`
+
+- [#431](https://github.com/nf-core/modules/pull/4781#event-11555493525) Updated kaiju2table module to report taxon names (fix by @Joon-Klaps)
+- [#430](https://github.com/nf-core/taxprofiler/pull/430) Fix the fastq output in the module LONGREAD_HOSTREMOVAL. (fix by @LilyAnderssonLee)
+
+### `Dependencies`
+
+| Tool | Previous version | New version |
+| ----- | ---------------- | ----------- |
+| kaiju | 1.8.2 | 1.10.0 |
+
+### `Deprecated`
+
## v1.1.3 - Augmented Akita Patch [2024-01-12]
### `Added`
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 58524b75..7a6b1290 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
report_comment: >
- This report has been generated by the nf-core/taxprofiler
+ This report has been generated by the nf-core/taxprofiler
analysis pipeline. For information about how to interpret these results, please see the
- documentation.
+ documentation.
report_section_order:
"nf-core-taxprofiler-methods-description":
diff --git a/conf/modules.config b/conf/modules.config
index b45267be..a6c0f82b 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -380,7 +380,7 @@ process {
[
path: { "${params.outdir}/samtools/fastq" },
mode: params.publish_dir_mode,
- pattern: '*.fastq.gz',
+ pattern: '*_other.fastq.gz',
enabled: params.save_hostremoval_unmapped
],
[
diff --git a/modules.json b/modules.json
index 9f195992..938aaf58 100644
--- a/modules.json
+++ b/modules.json
@@ -103,17 +103,17 @@
},
"kaiju/kaiju": {
"branch": "master",
- "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+ "git_sha": "3db50674956b1fb3741a44eb917458d788a50197",
"installed_by": ["modules"]
},
"kaiju/kaiju2krona": {
"branch": "master",
- "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+ "git_sha": "3db50674956b1fb3741a44eb917458d788a50197",
"installed_by": ["modules"]
},
"kaiju/kaiju2table": {
"branch": "master",
- "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+ "git_sha": "3db50674956b1fb3741a44eb917458d788a50197",
"installed_by": ["modules"]
},
"kmcp/profile": {
diff --git a/modules/nf-core/kaiju/kaiju/environment.yml b/modules/nf-core/kaiju/kaiju/environment.yml
new file mode 100644
index 00000000..baac450b
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju/environment.yml
@@ -0,0 +1,7 @@
+name: kaiju_kaiju
+channels:
+ - conda-forge
+ - bioconda
+ - defaults
+dependencies:
+ - bioconda::kaiju=1.10.0
diff --git a/modules/nf-core/kaiju/kaiju/main.nf b/modules/nf-core/kaiju/kaiju/main.nf
index 12f51f2c..2f5f6e7d 100644
--- a/modules/nf-core/kaiju/kaiju/main.nf
+++ b/modules/nf-core/kaiju/kaiju/main.nf
@@ -2,10 +2,10 @@ process KAIJU_KAIJU {
tag "$meta.id"
label 'process_high'
- conda "bioconda::kaiju=1.8.2"
+ conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
- 'biocontainers/kaiju:1.8.2--h5b5514e_1' }"
+ 'https://depot.galaxyproject.org/singularity/kaiju:1.10.0--h43eeafb_0':
+ 'biocontainers/kaiju:1.10.0--h43eeafb_0' }"
input:
tuple val(meta), path(reads)
@@ -38,4 +38,18 @@ process KAIJU_KAIJU {
kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
END_VERSIONS
"""
+
+ stub:
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ def input = meta.single_end ? "-i ${reads}" : "-i ${reads[0]} -j ${reads[1]}"
+ """
+ touch ${prefix}.tsv
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
+ END_VERSIONS
+ """
+
}
diff --git a/modules/nf-core/kaiju/kaiju/meta.yml b/modules/nf-core/kaiju/kaiju/meta.yml
index e24c8efc..33c85690 100644
--- a/modules/nf-core/kaiju/kaiju/meta.yml
+++ b/modules/nf-core/kaiju/kaiju/meta.yml
@@ -13,7 +13,6 @@ tools:
tool_dev_url: https://github.com/bioinformatics-centre/kaiju
doi: "10.1038/ncomms11257"
licence: ["GNU GPL v3"]
-
input:
- meta:
type: map
@@ -27,11 +26,10 @@ input:
respectively.
pattern: "*.{fastq,fq,fasta,fa,fsa,fas,fna,fastq.gz,fq.gz,fasta.gz,fa.gz,fsa.gz,fas.gz,fna.gz}"
- db:
- type: files
+ type: directory
description: |
List containing the database and nodes files for Kaiju
e.g. [ 'database.fmi', 'nodes.dmp' ]
-
output:
- meta:
type: map
@@ -46,8 +44,11 @@ output:
type: file
description: Results with taxonomic classification of each read
pattern: "*.tsv"
-
authors:
- "@talnor"
- "@sofstam"
- "@jfy133"
+maintainers:
+ - "@talnor"
+ - "@sofstam"
+ - "@jfy133"
diff --git a/modules/nf-core/kaiju/kaiju/tests/main.nf.test b/modules/nf-core/kaiju/kaiju/tests/main.nf.test
new file mode 100644
index 00000000..ede2f952
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju/tests/main.nf.test
@@ -0,0 +1,117 @@
+nextflow_process {
+
+ name "Test Process KAIJU_KAIJU"
+ script "../main.nf"
+ process "KAIJU_KAIJU"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "kaiju"
+ tag "kaiju/kaiju"
+ tag "untar"
+
+ test("sarscov2 - fastq - single-end") {
+
+ setup {
+ run ("UNTAR"){
+ script "../../../untar/main.nf"
+ process {
+ """
+ input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kaiju.tar.gz', checkIfExists: true) ]
+ """
+ }
+ }
+ }
+
+ 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)
+ ]
+ input[1] = UNTAR.out.untar.map{ it[1] }
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert path(process.out.results[0][1]).getText().contains("C\tERR5069949.2257580\t2697049") }
+ )
+ }
+
+ }
+
+ test("sarscov2 - fastq - paired-end") {
+
+ setup {
+ run ("UNTAR"){
+ script "../../../untar/main.nf"
+ process {
+ """
+ input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kaiju.tar.gz', checkIfExists: true) ]
+ """
+ }
+ }
+ }
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ],
+ [ 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)]
+ ]
+ input[1] = UNTAR.out.untar.map{ it[1] }
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert path(process.out.results[0][1]).getText().contains("C\tERR5069949.2257580\t2697049") }
+ )
+ }
+ }
+
+ test("sarscov2 - fastq - stub") {
+
+ options '-stub'
+
+ setup {
+ run ("UNTAR"){
+ script "../../../untar/main.nf"
+ process {
+ """
+ input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kaiju.tar.gz', checkIfExists: true) ]
+ """
+ }
+ }
+ }
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test', single_end:false ],
+ [ 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)]
+ ]
+ input[1] = UNTAR.out.untar.map{ it[1] }
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(file(process.out.results[0][1]).name).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/kaiju/kaiju/tests/main.nf.test.snap b/modules/nf-core/kaiju/kaiju/tests/main.nf.test.snap
new file mode 100644
index 00000000..08735f47
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju/tests/main.nf.test.snap
@@ -0,0 +1,8 @@
+{
+ "sarscov2 - fastq - stub": {
+ "content": [
+ "test.tsv"
+ ],
+ "timestamp": "2024-01-20T14:44:57.116024519"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/kaiju/kaiju/tests/tags.yml b/modules/nf-core/kaiju/kaiju/tests/tags.yml
new file mode 100644
index 00000000..c73d4df5
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju/tests/tags.yml
@@ -0,0 +1,2 @@
+kaiju/kaiju:
+ - "modules/nf-core/kaiju/kaiju/**"
diff --git a/modules/nf-core/kaiju/kaiju2krona/environment.yml b/modules/nf-core/kaiju/kaiju2krona/environment.yml
new file mode 100644
index 00000000..2905be97
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju2krona/environment.yml
@@ -0,0 +1,7 @@
+name: kaiju_kaiju2krona
+channels:
+ - conda-forge
+ - bioconda
+ - defaults
+dependencies:
+ - bioconda::kaiju=1.10.0
diff --git a/modules/nf-core/kaiju/kaiju2krona/main.nf b/modules/nf-core/kaiju/kaiju2krona/main.nf
index efa05d4d..85d2dfd2 100644
--- a/modules/nf-core/kaiju/kaiju2krona/main.nf
+++ b/modules/nf-core/kaiju/kaiju2krona/main.nf
@@ -2,10 +2,10 @@ process KAIJU_KAIJU2KRONA {
tag "$meta.id"
label 'process_single'
- conda "bioconda::kaiju=1.8.2"
+ conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
- 'biocontainers/kaiju:1.8.2--h5b5514e_1' }"
+ 'https://depot.galaxyproject.org/singularity/kaiju:1.10.0--h43eeafb_0':
+ 'biocontainers/kaiju:1.10.0--h43eeafb_0' }"
input:
tuple val(meta), path(tsv)
@@ -36,4 +36,17 @@ process KAIJU_KAIJU2KRONA {
kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
END_VERSIONS
"""
+
+ stub:
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ """
+ touch ${prefix}.txt
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
+ END_VERSIONS
+ """
}
+
diff --git a/modules/nf-core/kaiju/kaiju2krona/meta.yml b/modules/nf-core/kaiju/kaiju2krona/meta.yml
index a0dc2fdb..355416f8 100644
--- a/modules/nf-core/kaiju/kaiju2krona/meta.yml
+++ b/modules/nf-core/kaiju/kaiju2krona/meta.yml
@@ -13,7 +13,6 @@ tools:
tool_dev_url: https://github.com/bioinformatics-centre/kaiju
doi: "10.1038/ncomms11257"
licence: ["GNU GPL v3"]
-
input:
- meta:
type: map
@@ -24,7 +23,6 @@ input:
type: file
description: Kaiju tab-separated output file
pattern: "*.{tsv,txt}"
-
output:
- meta:
type: map
@@ -39,6 +37,7 @@ output:
type: file
description: Krona text-based input file converted from Kaiju report
pattern: "*.{txt,krona}"
-
authors:
- "@MillironX"
+maintainers:
+ - "@MillironX"
diff --git a/modules/nf-core/kaiju/kaiju2krona/tests/main.nf.test b/modules/nf-core/kaiju/kaiju2krona/tests/main.nf.test
new file mode 100644
index 00000000..cf522cd0
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju2krona/tests/main.nf.test
@@ -0,0 +1,105 @@
+nextflow_process {
+
+ name "Test Process KAIJU_KAIJU2KRONA"
+ script "../main.nf"
+ process "KAIJU_KAIJU2KRONA"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "kaiju"
+ tag "kaiju/kaiju2krona"
+ tag "kaiju/kaiju"
+ tag "untar"
+
+ test("sarscov2 - fastq - single-end") {
+
+
+ setup {
+ run ("UNTAR"){
+ script "../../../untar/main.nf"
+ process {
+ """
+ input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kaiju.tar.gz', checkIfExists: true) ]
+ """
+ }
+ }
+
+ run("KAIJU_KAIJU") {
+ script "../../kaiju/main.nf"
+ 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)
+ ]
+ input[1] = UNTAR.out.untar.map{ it[1] }
+ """
+ }
+ }
+ }
+
+ when {
+ process {
+ """
+ input[0] = KAIJU_KAIJU.out.results
+ input[1] = UNTAR.out.untar.map{ it[1] }
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+
+ }
+
+ test("sarscov2 - fastq - stub") {
+
+ options "-stub"
+
+ setup {
+ run ("UNTAR"){
+ script "../../../untar/main.nf"
+ process {
+ """
+ input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kaiju.tar.gz', checkIfExists: true) ]
+ """
+ }
+ }
+
+ run("KAIJU_KAIJU") {
+ script "../../kaiju/main.nf"
+ 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)
+ ]
+ input[1] = UNTAR.out.untar.map{ it[1] }
+ """
+ }
+ }
+ }
+
+ when {
+ process {
+ """
+ input[0] = KAIJU_KAIJU.out.results
+ input[1] = UNTAR.out.untar.map{ it[1] }
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(file(process.out.txt[0][1]).name).match() }
+ )
+ }
+
+ }
+
+}
diff --git a/modules/nf-core/kaiju/kaiju2krona/tests/main.nf.test.snap b/modules/nf-core/kaiju/kaiju2krona/tests/main.nf.test.snap
new file mode 100644
index 00000000..5532a694
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju2krona/tests/main.nf.test.snap
@@ -0,0 +1,39 @@
+{
+ "sarscov2 - fastq - stub": {
+ "content": [
+ "test.txt"
+ ],
+ "timestamp": "2024-01-20T15:06:32.789121011"
+ },
+ "sarscov2 - fastq - single-end": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.txt:md5,68b2309d37767e444193fa6cea7c0494"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,f75aa349971d581981d3a0399450b395"
+ ],
+ "txt": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.txt:md5,68b2309d37767e444193fa6cea7c0494"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,f75aa349971d581981d3a0399450b395"
+ ]
+ }
+ ],
+ "timestamp": "2024-01-20T15:06:08.840865115"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/kaiju/kaiju2krona/tests/tags.yml b/modules/nf-core/kaiju/kaiju2krona/tests/tags.yml
new file mode 100644
index 00000000..661fe924
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju2krona/tests/tags.yml
@@ -0,0 +1,2 @@
+kaiju/kaiju2krona:
+ - "modules/nf-core/kaiju/kaiju2krona/**"
diff --git a/modules/nf-core/kaiju/kaiju2table/environment.yml b/modules/nf-core/kaiju/kaiju2table/environment.yml
new file mode 100644
index 00000000..18685f41
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju2table/environment.yml
@@ -0,0 +1,7 @@
+name: kaiju_kaiju2table
+channels:
+ - conda-forge
+ - bioconda
+ - defaults
+dependencies:
+ - bioconda::kaiju=1.10.0
diff --git a/modules/nf-core/kaiju/kaiju2table/main.nf b/modules/nf-core/kaiju/kaiju2table/main.nf
index e426a062..44049744 100644
--- a/modules/nf-core/kaiju/kaiju2table/main.nf
+++ b/modules/nf-core/kaiju/kaiju2table/main.nf
@@ -2,13 +2,13 @@ process KAIJU_KAIJU2TABLE {
tag "$meta.id"
label 'process_single'
- conda "bioconda::kaiju=1.8.2"
+ conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
- 'biocontainers/kaiju:1.8.2--h2e03b76_0' }"
+ 'https://depot.galaxyproject.org/singularity/kaiju:1.10.0--h43eeafb_0':
+ 'biocontainers/kaiju:1.10.0--h43eeafb_0' }"
input:
- tuple val(meta), path(results)
+ tuple val(meta), path(input)
path db
val taxon_rank
@@ -24,13 +24,25 @@ process KAIJU_KAIJU2TABLE {
def prefix = task.ext.prefix ?: "${meta.id}"
"""
dbnodes=`find -L ${db} -name "*nodes.dmp"`
- dbname=`find -L ${db} -name "*.fmi" -not -name "._*"`
+ dbnames=`find -L ${db} -name "*names.dmp"`
kaiju2table $args \\
-t \$dbnodes \\
- -n \$dbname \\
+ -n \$dbnames \\
-r ${taxon_rank} \\
-o ${prefix}.txt \\
- ${results}
+ ${input}
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
+ END_VERSIONS
+ """
+
+ stub:
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.prefix ?: "${meta.id}"
+ """
+ touch ${prefix}.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
diff --git a/modules/nf-core/kaiju/kaiju2table/meta.yml b/modules/nf-core/kaiju/kaiju2table/meta.yml
index bc3e85d7..0f62374e 100644
--- a/modules/nf-core/kaiju/kaiju2table/meta.yml
+++ b/modules/nf-core/kaiju/kaiju2table/meta.yml
@@ -3,6 +3,7 @@ description: write your description here
keywords:
- classify
- metagenomics
+ - taxonomic profiling
tools:
- kaiju:
description: Fast and sensitive taxonomic classification for metagenomics
@@ -11,7 +12,6 @@ tools:
tool_dev_url: https://github.com/bioinformatics-centre/kaiju
doi: "10.1038/ncomms11257"
licence: ["GNU GPL v3"]
-
input:
- meta:
type: map
@@ -27,7 +27,6 @@ input:
description: |
Taxonomic rank to display in report
pattern: "phylum|class|order|family|genus|species"
-
output:
- meta:
type: map
@@ -43,8 +42,11 @@ output:
description: |
Summary table for a given taxonomic rank
pattern: "*.{tsv}"
-
authors:
- "@sofstam"
- "@talnor"
- "@jfy133"
+maintainers:
+ - "@sofstam"
+ - "@talnor"
+ - "@jfy133"
diff --git a/modules/nf-core/kaiju/kaiju2table/tests/main.nf.test b/modules/nf-core/kaiju/kaiju2table/tests/main.nf.test
new file mode 100644
index 00000000..d93fb31a
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju2table/tests/main.nf.test
@@ -0,0 +1,106 @@
+nextflow_process {
+
+ name "Test Process KAIJU_KAIJU2TABLE"
+ script "../main.nf"
+ process "KAIJU_KAIJU2TABLE"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "kaiju"
+ tag "kaiju/kaiju2table"
+ tag "kaiju/kaiju"
+ tag "untar"
+
+ test("sarscov2 - fastq - single-end") {
+
+
+ setup {
+ run ("UNTAR"){
+ script "../../../untar/main.nf"
+ process {
+ """
+ input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kaiju.tar.gz', checkIfExists: true) ]
+ """
+ }
+ }
+
+ run("KAIJU_KAIJU") {
+ script "../../kaiju/main.nf"
+ 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)
+ ]
+ input[1] = UNTAR.out.untar.map{ it[1] }
+ """
+ }
+ }
+ }
+
+ when {
+ process {
+ """
+ input[0] = KAIJU_KAIJU.out.results
+ input[1] = UNTAR.out.untar.map{ it[1] }
+ input[2] = 'species'
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+
+ }
+
+ test("sarscov2 - fastq - stub") {
+
+ options "-stub"
+
+ setup {
+ run ("UNTAR"){
+ script "../../../untar/main.nf"
+ process {
+ """
+ input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kaiju.tar.gz', checkIfExists: true) ]
+ """
+ }
+ }
+
+ run("KAIJU_KAIJU") {
+ script "../../kaiju/main.nf"
+ 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)
+ ]
+ input[1] = UNTAR.out.untar.map{ it[1] }
+ """
+ }
+ }
+ }
+
+ when {
+ process {
+ """
+ input[0] = KAIJU_KAIJU.out.results
+ input[1] = UNTAR.out.untar.map{ it[1] }
+ input[2] = 'species'
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(file(process.out.summary[0][1]).name).match() }
+ )
+ }
+
+ }
+}
diff --git a/modules/nf-core/kaiju/kaiju2table/tests/main.nf.test.snap b/modules/nf-core/kaiju/kaiju2table/tests/main.nf.test.snap
new file mode 100644
index 00000000..e97eb8b8
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju2table/tests/main.nf.test.snap
@@ -0,0 +1,39 @@
+{
+ "sarscov2 - fastq - stub": {
+ "content": [
+ "test.txt"
+ ],
+ "timestamp": "2024-01-20T16:10:49.521322767"
+ },
+ "sarscov2 - fastq - single-end": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.txt:md5,0d9f8fd36fcf2888296ae12632c5f0a8"
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,2b2b98cb635a611e5eb964e5a77f6248"
+ ],
+ "summary": [
+ [
+ {
+ "id": "test",
+ "single_end": true
+ },
+ "test.txt:md5,0d9f8fd36fcf2888296ae12632c5f0a8"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,2b2b98cb635a611e5eb964e5a77f6248"
+ ]
+ }
+ ],
+ "timestamp": "2024-01-20T16:08:47.644443775"
+ }
+}
diff --git a/modules/nf-core/kaiju/kaiju2table/tests/tags.yml b/modules/nf-core/kaiju/kaiju2table/tests/tags.yml
new file mode 100644
index 00000000..0fa6b81e
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju2table/tests/tags.yml
@@ -0,0 +1,2 @@
+kaiju/kaiju2table:
+ - "modules/nf-core/kaiju/kaiju2table/**"
diff --git a/nextflow.config b/nextflow.config
index 518a4e92..5a955074 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -372,7 +372,7 @@ manifest {
description = """Taxonomic classification and profiling of shotgun short- and long-read metagenomic data"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
- version = '1.1.3'
+ version = '1.1.4'
doi = '10.1101/2023.10.20.563221'
}
diff --git a/subworkflows/local/longread_hostremoval.nf b/subworkflows/local/longread_hostremoval.nf
index c5a10436..bc146d6f 100644
--- a/subworkflows/local/longread_hostremoval.nf
+++ b/subworkflows/local/longread_hostremoval.nf
@@ -54,7 +54,7 @@ workflow LONGREAD_HOSTREMOVAL {
emit:
stats = SAMTOOLS_STATS.out.stats //channel: [val(meta), [reads ] ]
- reads = SAMTOOLS_FASTQ.out.fastq.mix( SAMTOOLS_FASTQ.out.other) // channel: [ val(meta), [ reads ] ]
+ reads = SAMTOOLS_FASTQ.out.other // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ]
mqc = ch_multiqc_files
}