diff --git a/CHANGELOG.md b/CHANGELOG.md index 54b849d..e6f5802 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v1.1.0 - [date] ### `Fixed` +- nf-core module updates to remove Anaconda references ### `Added` diff --git a/README.md b/README.md index fadddc5..3711b94 100644 --- a/README.md +++ b/README.md @@ -55,6 +55,7 @@ sanger-tol/sequencecomposition was originally written by [Matthieu Muffato](http We thank the following people for their assistance in the development of this pipeline: - [Priyanka Surana](https://github.com/priyanka-surana) for providing reviews. +- [Tyler Chafin](https://github.com/tkchafin) for updates. ## Contributions and Support diff --git a/modules.json b/modules.json index 411a3a0..17b2131 100644 --- a/modules.json +++ b/modules.json @@ -7,32 +7,32 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "custom/getchromsizes": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["modules"] }, "fastawindows": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "gunzip": { "branch": "master", - "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "tabix/bgzip": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "tabix/tabix": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] } } diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml new file mode 100644 index 0000000..9d79af9 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::multiqc=1.20 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index ebc8727..105f926 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.14" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_0' : + 'biocontainers/multiqc:1.20--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index c32657d..dc1e412 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,36 +1,43 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: custom_dumpsoftwareversions -description: Custom module used to dump software versions within the nf-core pipeline template +description: Custom module used to dump software versions within the nf-core pipeline + template keywords: - custom - dump - version tools: - custom: - description: Custom module used to dump software versions within the nf-core pipeline template + description: Custom module used to dump software versions within the nf-core pipeline + template homepage: https://github.com/nf-core/tools documentation: https://github.com/nf-core/tools licence: ["MIT"] + identifier: "" input: - - versions: - type: file - description: YML file containing software versions - pattern: "*.yml" - + - - versions: + type: file + description: YML file containing software versions + pattern: "*.yml" output: - yml: - type: file - description: Standard YML file containing software versions - pattern: "software_versions.yml" + - software_versions.yml: + type: file + description: Standard YML file containing software versions + pattern: "software_versions.yml" - mqc_yml: - type: file - description: MultiQC custom content YML file containing software versions - pattern: "software_versions_mqc.yml" + - software_versions_mqc.yml: + type: file + description: MultiQC custom content YML file containing software versions + pattern: "software_versions_mqc.yml" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" +maintainers: + - "@drpatelh" + - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py index da03340..b83b32c 100755 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -3,11 +3,11 @@ """Provide functions to merge multiple versions.yml files.""" - -import yaml import platform from textwrap import dedent +import yaml + def _make_versions_html(versions): """Generate a tabular HTML output of all versions for MultiQC.""" diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test new file mode 100644 index 0000000..b1e1630 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -0,0 +1,43 @@ +nextflow_process { + + name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" + script "../main.nf" + process "CUSTOM_DUMPSOFTWAREVERSIONS" + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "dumpsoftwareversions" + tag "custom/dumpsoftwareversions" + + test("Should run without failures") { + when { + process { + """ + def tool1_version = ''' + TOOL1: + tool1: 0.11.9 + '''.stripIndent() + + def tool2_version = ''' + TOOL2: + tool2: 1.9 + '''.stripIndent() + + input[0] = Channel.of(tool1_version, tool2_version).collectFile() + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.mqc_yml[0]).readLines()[0..10], + file(process.out.yml[0]).readLines()[0..7] + ).match() + } + ) + } + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap new file mode 100644 index 0000000..5f59a93 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -0,0 +1,33 @@ +{ + "Should run without failures": { + "content": [ + [ + "versions.yml:md5,76d454d92244589d32455833f7c1ba6d" + ], + [ + "data: \"\\n\\n \\n \\n \\n \\n \\n \\n \\n\\", + " \\n\\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n \\n \\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n\\n\\n \\n\\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\" + ], + [ + "CUSTOM_DUMPSOFTWAREVERSIONS:", + " python: 3.11.7", + " yaml: 5.4.1", + "TOOL1:", + " tool1: 0.11.9", + "TOOL2:", + " tool2: '1.9'", + "Workflow:" + ] + ], + "timestamp": "2024-01-09T23:01:18.710682" + } +} \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml new file mode 100644 index 0000000..405aa24 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml @@ -0,0 +1,2 @@ +custom/dumpsoftwareversions: + - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml new file mode 100644 index 0000000..2bcd47e --- /dev/null +++ b/modules/nf-core/custom/getchromsizes/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + +dependencies: + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf index 060a2e8..d8c7405 100644 --- a/modules/nf-core/custom/getchromsizes/main.nf +++ b/modules/nf-core/custom/getchromsizes/main.nf @@ -2,10 +2,10 @@ process CUSTOM_GETCHROMSIZES { tag "$fasta" label 'process_single' - conda "bioconda::samtools=1.16.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'biocontainers/samtools:1.16.1--h6899075_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(fasta) @@ -35,6 +35,9 @@ process CUSTOM_GETCHROMSIZES { """ touch ${fasta}.fai touch ${fasta}.sizes + if [[ "${fasta.extension}" == "gz" ]]; then + touch ${fasta}.gzi + fi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/custom/getchromsizes/meta.yml b/modules/nf-core/custom/getchromsizes/meta.yml index 219ca1d..2a0e8da 100644 --- a/modules/nf-core/custom/getchromsizes/meta.yml +++ b/modules/nf-core/custom/getchromsizes/meta.yml @@ -12,42 +12,58 @@ tools: tool_dev_url: https://github.com/samtools/samtools doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] - + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta,fna,fas}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta,fna,fas}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sizes: - type: file - description: File containing chromosome lengths - pattern: "*.{sizes}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sizes": + type: file + description: File containing chromosome lengths + pattern: "*.{sizes}" - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fai": + type: file + description: FASTA index file + pattern: "*.{fai}" - gzi: - type: file - description: Optional gzip index file for compressed inputs - pattern: "*.gzi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gzi": + type: file + description: Optional gzip index file for compressed inputs + pattern: "*.gzi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tamara-hodgetts" - "@chris-cheshire" - "@muffato" +maintainers: + - "@tamara-hodgetts" + - "@chris-cheshire" + - "@muffato" diff --git a/modules/nf-core/custom/getchromsizes/tests/main.nf.test b/modules/nf-core/custom/getchromsizes/tests/main.nf.test new file mode 100644 index 0000000..2f741a4 --- /dev/null +++ b/modules/nf-core/custom/getchromsizes/tests/main.nf.test @@ -0,0 +1,99 @@ +nextflow_process { + + name "Test Process CUSTOM_GETCHROMSIZES" + script "../main.nf" + process "CUSTOM_GETCHROMSIZES" + + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "custom/getchromsizes" + + test("test_custom_getchromsizes") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_custom_getchromsizes_bgzip") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_custom_getchromsizes - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_custom_getchromsizes_bgzip - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap b/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap new file mode 100644 index 0000000..d2072e2 --- /dev/null +++ b/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap @@ -0,0 +1,242 @@ +{ + "test_custom_getchromsizes_bgzip - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.sizes:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.fai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" + ], + "fai": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.fai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gzi": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "sizes": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.sizes:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:11:37.459094476" + }, + "test_custom_getchromsizes": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "genome.fasta.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" + ], + "fai": [ + [ + { + "id": "test" + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + + ], + "sizes": [ + [ + { + "id": "test" + }, + "genome.fasta.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c" + ] + ], + "versions": [ + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:11:01.526301351" + }, + "test_custom_getchromsizes_bgzip": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" + ] + ], + "3": [ + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" + ], + "fai": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" + ] + ], + "sizes": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c" + ] + ], + "versions": [ + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:11:14.32456385" + }, + "test_custom_getchromsizes - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "genome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" + ], + "fai": [ + [ + { + "id": "test" + }, + "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gzi": [ + + ], + "sizes": [ + [ + { + "id": "test" + }, + "genome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:11:26.505487624" + } +} \ No newline at end of file diff --git a/modules/nf-core/custom/getchromsizes/tests/tags.yml b/modules/nf-core/custom/getchromsizes/tests/tags.yml new file mode 100644 index 0000000..d89a805 --- /dev/null +++ b/modules/nf-core/custom/getchromsizes/tests/tags.yml @@ -0,0 +1,2 @@ +custom/getchromsizes: + - modules/nf-core/custom/getchromsizes/** diff --git a/modules/nf-core/fastawindows/environment.yml b/modules/nf-core/fastawindows/environment.yml new file mode 100644 index 0000000..6775fb2 --- /dev/null +++ b/modules/nf-core/fastawindows/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::fasta_windows=0.2.4 diff --git a/modules/nf-core/fastawindows/main.nf b/modules/nf-core/fastawindows/main.nf index c65a051..bf5a3b7 100644 --- a/modules/nf-core/fastawindows/main.nf +++ b/modules/nf-core/fastawindows/main.nf @@ -2,7 +2,7 @@ process FASTAWINDOWS { tag "$meta.id" label 'process_low' - conda "bioconda::fasta_windows=0.2.4" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fasta_windows:0.2.4--hec16e2b_0': 'biocontainers/fasta_windows:0.2.4--hec16e2b_0' }" @@ -32,6 +32,25 @@ process FASTAWINDOWS { --fasta $fasta \\ --output ${prefix} + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fasta_windows: \$(fasta_windows --version | cut -d' ' -f3) + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mkdir -p fw_out + + touch fw_out/${prefix}_freq_windows.tsv + touch fw_out/${prefix}_mononuc_windows.tsv + touch fw_out/${prefix}_dinuc_windows.tsv + touch fw_out/${prefix}_trinuc_windows.tsv + touch fw_out/${prefix}_tetranuc_windows.tsv + + cat <<-END_VERSIONS > versions.yml "${task.process}": fasta_windows: \$(fasta_windows --version | cut -d' ' -f3) diff --git a/modules/nf-core/fastawindows/meta.yml b/modules/nf-core/fastawindows/meta.yml index 9342af9..f8ee004 100644 --- a/modules/nf-core/fastawindows/meta.yml +++ b/modules/nf-core/fastawindows/meta.yml @@ -7,51 +7,79 @@ keywords: - bed tools: - "fastawindows": - description: "fasta_windows is a tool written for Darwin Tree of Life chromosomal level genome assemblies. The executable takes a fasta formatted file and calculates some statistics of interest in windows" + description: "fasta_windows is a tool written for Darwin Tree of Life chromosomal + level genome assemblies. The executable takes a fasta formatted file and calculates + some statistics of interest in windows" homepage: "https://github.com/tolkit/fasta_windows" - - licence: "['MIT']" - + licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta,fna}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - freq: - type: file - description: TSV file with frequencies and statistics - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fw_out/*_freq_windows.tsv: + type: file + description: TSV file with frequencies and statistics + pattern: "*.{tsv}" - mononuc: - type: file - description: TSV file with mononucleotide counts - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fw_out/*_mononuc_windows.tsv: + type: file + description: TSV file with mononucleotide counts + pattern: "*.{tsv}" - dinuc: - type: file - description: TSV file with dinucleotide counts - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fw_out/*_dinuc_windows.tsv: + type: file + description: TSV file with dinucleotide counts + pattern: "*.{tsv}" - trinuc: - type: file - description: TSV file with trinucleotide counts - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fw_out/*_trinuc_windows.tsv: + type: file + description: TSV file with trinucleotide counts + pattern: "*.{tsv}" - tetranuc: - type: file - description: TSV file with tetranucleotide counts - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fw_out/*_tetranuc_windows.tsv: + type: file + description: TSV file with tetranucleotide counts + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@muffato" +maintainers: + - "@muffato" diff --git a/modules/nf-core/fastawindows/tests/main.nf.test b/modules/nf-core/fastawindows/tests/main.nf.test new file mode 100644 index 0000000..f4bea49 --- /dev/null +++ b/modules/nf-core/fastawindows/tests/main.nf.test @@ -0,0 +1,57 @@ + +nextflow_process { + + name "Test Process FASTAWINDOWS" + script "../main.nf" + process "FASTAWINDOWS" + + tag "modules" + tag "modules_nfcore" + tag "fastawindows" + + test("test-fastawindows") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-fastawindows-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + 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/fastawindows/tests/main.nf.test.snap b/modules/nf-core/fastawindows/tests/main.nf.test.snap new file mode 100644 index 0000000..f3474d3 --- /dev/null +++ b/modules/nf-core/fastawindows/tests/main.nf.test.snap @@ -0,0 +1,196 @@ +{ + "test-fastawindows-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_freq_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test_mononuc_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test_dinuc_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "test_trinuc_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test" + }, + "test_tetranuc_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + "versions.yml:md5,4e46686969aa8883f8092693ebcf7dab" + ], + "dinuc": [ + [ + { + "id": "test" + }, + "test_dinuc_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "freq": [ + [ + { + "id": "test" + }, + "test_freq_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "mononuc": [ + [ + { + "id": "test" + }, + "test_mononuc_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tetranuc": [ + [ + { + "id": "test" + }, + "test_tetranuc_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "trinuc": [ + [ + { + "id": "test" + }, + "test_trinuc_windows.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,4e46686969aa8883f8092693ebcf7dab" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-30T09:58:57.148076" + }, + "test-fastawindows": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_freq_windows.tsv:md5,237d50ac5ec2bef3142020d569fa5765" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test_mononuc_windows.tsv:md5,a1b4437d0c71d9cfd676de6bda2633f0" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test_dinuc_windows.tsv:md5,696a9f2a4b2114dfbd6b414694f56a11" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "test_trinuc_windows.tsv:md5,dfb05b758f0474e937e2d6ba6fe46dae" + ] + ], + "4": [ + [ + { + "id": "test" + }, + "test_tetranuc_windows.tsv:md5,e621537175ee8019360f8b6e8f4330b7" + ] + ], + "5": [ + "versions.yml:md5,4e46686969aa8883f8092693ebcf7dab" + ], + "dinuc": [ + [ + { + "id": "test" + }, + "test_dinuc_windows.tsv:md5,696a9f2a4b2114dfbd6b414694f56a11" + ] + ], + "freq": [ + [ + { + "id": "test" + }, + "test_freq_windows.tsv:md5,237d50ac5ec2bef3142020d569fa5765" + ] + ], + "mononuc": [ + [ + { + "id": "test" + }, + "test_mononuc_windows.tsv:md5,a1b4437d0c71d9cfd676de6bda2633f0" + ] + ], + "tetranuc": [ + [ + { + "id": "test" + }, + "test_tetranuc_windows.tsv:md5,e621537175ee8019360f8b6e8f4330b7" + ] + ], + "trinuc": [ + [ + { + "id": "test" + }, + "test_trinuc_windows.tsv:md5,dfb05b758f0474e937e2d6ba6fe46dae" + ] + ], + "versions": [ + "versions.yml:md5,4e46686969aa8883f8092693ebcf7dab" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-29T21:22:58.322943" + } +} \ No newline at end of file diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml new file mode 100644 index 0000000..c779485 --- /dev/null +++ b/modules/nf-core/gunzip/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda +dependencies: + - conda-forge::grep=3.11 + - conda-forge::sed=4.8 + - conda-forge::tar=1.34 diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index 73bf08c..5e67e3b 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -2,10 +2,10 @@ process GUNZIP { tag "$archive" label 'process_single' - conda "conda-forge::sed=4.7" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' : + 'nf-core/ubuntu:22.04' }" input: tuple val(meta), path(archive) @@ -18,8 +18,11 @@ process GUNZIP { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - gunzip = archive.toString() - '.gz' + def args = task.ext.args ?: '' + def extension = ( archive.toString() - '.gz' ).tokenize('.')[-1] + def name = archive.toString() - '.gz' - ".$extension" + def prefix = task.ext.prefix ?: name + gunzip = prefix + ".$extension" """ # Not calling gunzip itself because it creates files # with the original group ownership rather than the @@ -37,7 +40,11 @@ process GUNZIP { """ stub: - gunzip = archive.toString() - '.gz' + def args = task.ext.args ?: '' + def extension = ( archive.toString() - '.gz' ).tokenize('.')[-1] + def name = archive.toString() - '.gz' - ".$extension" + def prefix = task.ext.prefix ?: name + gunzip = prefix + ".$extension" """ touch $gunzip cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml index 4cdcdf4..9066c03 100644 --- a/modules/nf-core/gunzip/meta.yml +++ b/modules/nf-core/gunzip/meta.yml @@ -10,26 +10,38 @@ tools: gzip is a file format and a software application used for file compression and decompression. documentation: https://www.gnu.org/software/gzip/manual/gzip.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Optional groovy Map containing meta information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be compressed/uncompressed - pattern: "*.*" + - - meta: + type: map + description: | + Optional groovy Map containing meta information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be compressed/uncompressed + pattern: "*.*" output: - gunzip: - type: file - description: Compressed/uncompressed file - pattern: "*.*" + - meta: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - $gunzip: + type: file + description: Compressed/uncompressed file + pattern: "*.*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" - "@jfy133" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" + - "@gallvp" diff --git a/modules/nf-core/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test new file mode 100644 index 0000000..776211a --- /dev/null +++ b/modules/nf-core/gunzip/tests/main.nf.test @@ -0,0 +1,121 @@ +nextflow_process { + + name "Test Process GUNZIP" + script "../main.nf" + process "GUNZIP" + tag "gunzip" + tag "modules_nfcore" + tag "modules" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [], + 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).match() } + ) + } + + } + + test("Should run without failures - prefix") { + + config './nextflow.config' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - stub") { + + options '-stub' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [], + 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).match() } + ) + } + + } + + test("Should run without failures - prefix - stub") { + + options '-stub' + config './nextflow.config' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id: 'test' ], + 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).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gunzip/tests/main.nf.test.snap b/modules/nf-core/gunzip/tests/main.nf.test.snap new file mode 100644 index 0000000..069967e --- /dev/null +++ b/modules/nf-core/gunzip/tests/main.nf.test.snap @@ -0,0 +1,134 @@ +{ + "Should run without failures - prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:35:10.861293" + }, + "Should run without failures - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + [ + + ], + "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:35:05.857145" + }, + "Should run without failures": { + "content": [ + { + "0": [ + [ + [ + + ], + "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + [ + + ], + "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2023-10-17T15:35:37.690477896" + }, + "Should run without failures - prefix": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:33:32.921739" + } +} \ No newline at end of file diff --git a/modules/nf-core/gunzip/tests/nextflow.config b/modules/nf-core/gunzip/tests/nextflow.config new file mode 100644 index 0000000..dec7764 --- /dev/null +++ b/modules/nf-core/gunzip/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GUNZIP { + ext.prefix = { "${meta.id}.xyz" } + } +} diff --git a/modules/nf-core/gunzip/tests/tags.yml b/modules/nf-core/gunzip/tests/tags.yml new file mode 100644 index 0000000..fd3f691 --- /dev/null +++ b/modules/nf-core/gunzip/tests/tags.yml @@ -0,0 +1,2 @@ +gunzip: + - modules/nf-core/gunzip/** diff --git a/modules/nf-core/tabix/bgzip/environment.yml b/modules/nf-core/tabix/bgzip/environment.yml new file mode 100644 index 0000000..017c259 --- /dev/null +++ b/modules/nf-core/tabix/bgzip/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + +dependencies: + - bioconda::htslib=1.20 + - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/bgzip/main.nf b/modules/nf-core/tabix/bgzip/main.nf index 8c47d9e..67991c7 100644 --- a/modules/nf-core/tabix/bgzip/main.nf +++ b/modules/nf-core/tabix/bgzip/main.nf @@ -2,10 +2,10 @@ process TABIX_BGZIP { tag "$meta.id" label 'process_single' - conda "bioconda::tabix=1.11" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'biocontainers/tabix:1.11--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' : + 'biocontainers/htslib:1.20--h5efdd21_2' }" input: tuple val(meta), path(input) @@ -44,7 +44,8 @@ process TABIX_BGZIP { output = in_bgzip ? input.getBaseName() : "${prefix}.${input.getExtension()}.gz" """ - touch ${output} + echo "" | gzip > ${output} + touch ${output}.gzi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/tabix/bgzip/meta.yml b/modules/nf-core/tabix/bgzip/meta.yml index c3ea210..131e92c 100644 --- a/modules/nf-core/tabix/bgzip/meta.yml +++ b/modules/nf-core/tabix/bgzip/meta.yml @@ -13,35 +13,49 @@ tools: documentation: http://www.htslib.org/doc/bgzip.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:tabix input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: file to compress or to decompress + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: file to compress or to decompress output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - output: - type: file - description: Output compressed/decompressed file - pattern: "*." + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output}: + type: file + description: Output compressed/decompressed file + pattern: "*." - gzi: - type: file - description: Optional gzip index file for compressed inputs - pattern: "*.gzi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output}.gzi: + type: file + description: Optional gzip index file for compressed inputs + pattern: "*.gzi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" - "@maxulysse" - "@nvnieuwk" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@maxulysse" + - "@nvnieuwk" diff --git a/modules/nf-core/tabix/bgzip/tests/bgzip_compress.config b/modules/nf-core/tabix/bgzip/tests/bgzip_compress.config new file mode 100644 index 0000000..6b6ff55 --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/bgzip_compress.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_BGZIP { + ext.args = ' -i' + } +} diff --git a/modules/nf-core/tabix/bgzip/tests/main.nf.test b/modules/nf-core/tabix/bgzip/tests/main.nf.test new file mode 100644 index 0000000..d784aa0 --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/main.nf.test @@ -0,0 +1,111 @@ +nextflow_process { + + name "Test Process TABIX_BGZIP" + script "modules/nf-core/tabix/bgzip/main.nf" + process "TABIX_BGZIP" + + tag "modules" + tag "modules_nfcore" + tag "tabix" + tag "tabix/bgzip" + + test("sarscov2_vcf_bgzip_compress") { + when { + process { + """ + input[0] = [ + [ id:'bgzip_test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.output[0][1]).name + ).match("bgzip_test") + } + ) + } + } + + test("homo_genome_bedgz_compress") { + when { + process { + """ + input[0] = [ + [ id:'bedgz_test' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.output[0][1]).name + ).match("bedgz_test") + } + ) + } + } + + test("sarscov2_vcf_bgzip_compress_stub") { + options '-stub' + config "./bgzip_compress.config" + + when { + process { + """ + input[0] = [ + [ id:"test_stub" ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.output[0][1]).name + ).match("test_stub") + } + ) + } + } + + test("sarscov2_vcf_bgzip_compress_gzi") { + config "./bgzip_compress.config" + when { + process { + """ + input[0] = [ + [ id:"gzi_compress_test" ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gzi[0][1]).name + ).match("gzi_compress_test") + } + ) + } + } +} diff --git a/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap b/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap new file mode 100644 index 0000000..0748143 --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap @@ -0,0 +1,218 @@ +{ + "gzi_compress_test": { + "content": [ + "gzi_compress_test.vcf.gz.gzi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:52:29.328146" + }, + "homo_genome_bedgz_compress": { + "content": [ + { + "0": [ + [ + { + "id": "bedgz_test" + }, + "bedgz_test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ], + "gzi": [ + + ], + "output": [ + [ + { + "id": "bedgz_test" + }, + "bedgz_test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "versions": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:28:34.159992362" + }, + "test_stub": { + "content": [ + "test_stub.vcf.gz" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:52:20.811489" + }, + "sarscov2_vcf_bgzip_compress": { + "content": [ + { + "0": [ + [ + { + "id": "bgzip_test" + }, + "bgzip_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ], + "gzi": [ + + ], + "output": [ + [ + { + "id": "bgzip_test" + }, + "bgzip_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "versions": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:28:22.087769106" + }, + "sarscov2_vcf_bgzip_compress_gzi": { + "content": [ + { + "0": [ + [ + { + "id": "gzi_compress_test" + }, + "gzi_compress_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "1": [ + [ + { + "id": "gzi_compress_test" + }, + "gzi_compress_test.vcf.gz.gzi:md5,26fd00d4e26141cd11561f6e7d4a2ad0" + ] + ], + "2": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ], + "gzi": [ + [ + { + "id": "gzi_compress_test" + }, + "gzi_compress_test.vcf.gz.gzi:md5,26fd00d4e26141cd11561f6e7d4a2ad0" + ] + ], + "output": [ + [ + { + "id": "gzi_compress_test" + }, + "gzi_compress_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "versions": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:28:57.15091665" + }, + "bgzip_test": { + "content": [ + "bgzip_test.vcf.gz" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:52:03.768295" + }, + "bedgz_test": { + "content": [ + "bedgz_test.bed" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:52:12.453855" + }, + "sarscov2_vcf_bgzip_compress_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test_stub" + }, + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test_stub" + }, + "test_stub.vcf.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ], + "gzi": [ + [ + { + "id": "test_stub" + }, + "test_stub.vcf.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "output": [ + [ + { + "id": "test_stub" + }, + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:28:45.219404786" + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/bgzip/tests/tags.yml b/modules/nf-core/tabix/bgzip/tests/tags.yml new file mode 100644 index 0000000..de0eec8 --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/tags.yml @@ -0,0 +1,2 @@ +tabix/bgzip: + - "modules/nf-core/tabix/bgzip/**" diff --git a/modules/nf-core/tabix/bgzip/tests/vcf_none.config b/modules/nf-core/tabix/bgzip/tests/vcf_none.config new file mode 100644 index 0000000..f3a3c46 --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/vcf_none.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_BGZIP { + ext.args = '' + } +} diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml new file mode 100644 index 0000000..017c259 --- /dev/null +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + +dependencies: + - bioconda::htslib=1.20 + - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index 5bf332e..13acd67 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -2,10 +2,10 @@ process TABIX_TABIX { tag "$meta.id" label 'process_single' - conda "bioconda::tabix=1.11" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'biocontainers/tabix:1.11--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' : + 'biocontainers/htslib:1.20--h5efdd21_2' }" input: tuple val(meta), path(tab) @@ -21,7 +21,10 @@ process TABIX_TABIX { script: def args = task.ext.args ?: '' """ - tabix $args $tab + tabix \\ + --threads $task.cpus \\ + $args \\ + $tab cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -30,11 +33,11 @@ process TABIX_TABIX { """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${tab}.tbi - cat <<-END_VERSIONS > versions.yml + touch ${tab}.csi + cat <<-END_VERSIONS > versions.yml "${task.process}": tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml index fcc6e52..7864832 100644 --- a/modules/nf-core/tabix/tabix/meta.yml +++ b/modules/nf-core/tabix/tabix/meta.yml @@ -11,35 +11,48 @@ tools: documentation: https://www.htslib.org/doc/tabix.1.html doi: 10.1093/bioinformatics/btq671 licence: ["MIT"] + identifier: biotools:tabix input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tab: - type: file - description: TAB-delimited genome position file compressed with bgzip - pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tab: + type: file + description: TAB-delimited genome position file compressed with bgzip + pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - tbi: - type: file - description: tabix index file - pattern: "*.{tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: tabix index file + pattern: "*.{tbi}" - csi: - type: file - description: coordinate sorted index file - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: coordinate sorted index file + pattern: "*.{csi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" - "@maxulysse" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@maxulysse" diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test new file mode 100644 index 0000000..102b0d7 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test @@ -0,0 +1,136 @@ +nextflow_process { + + name "Test Process TABIX_TABIX" + script "modules/nf-core/tabix/tabix/main.nf" + process "TABIX_TABIX" + + tag "modules" + tag "modules_nfcore" + tag "tabix" + tag "tabix/tabix" + + test("sarscov2_bedgz_tbi") { + config "./tabix_bed.config" + when { + process { + """ + input[0] = [ + [ id:'tbi_bed' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.tbi[0][1]).name + ).match() } + ) + } + } + + test("sarscov2_gff_tbi") { + config "./tabix_gff.config" + when { + process { + """ + input[0] = [ + [ id:'tbi_gff' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.tbi[0][1]).name).match() } + ) + } + + } + + test("sarscov2_vcf_tbi") { + config "./tabix_vcf_tbi.config" + when { + process { + """ + input[0] = [ + [ id:'tbi_vcf' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.tbi[0][1]).name + ).match() } + ) + } + + } + + test("sarscov2_vcf_csi") { + config "./tabix_vcf_csi.config" + when { + process { + """ + input[0] = [ + [ id:'vcf_csi' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.csi[0][1]).name + ).match() } + ) + } + + } + + test("sarscov2_vcf_csi_stub") { + config "./tabix_vcf_csi.config" + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'vcf_csi_stub' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.csi[0][1]).name + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap new file mode 100644 index 0000000..c2b9ed0 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap @@ -0,0 +1,212 @@ +{ + "sarscov2_gff_tbi": { + "content": [ + { + "0": [ + [ + { + "id": "tbi_gff" + }, + "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "tbi_gff" + }, + "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926" + ] + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "genome.gff3.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:25.653807564" + }, + "sarscov2_bedgz_tbi": { + "content": [ + { + "0": [ + [ + { + "id": "tbi_bed" + }, + "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "tbi_bed" + }, + "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d" + ] + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "test.bed.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:09.754082161" + }, + "sarscov2_vcf_tbi": { + "content": [ + { + "0": [ + [ + { + "id": "tbi_vcf" + }, + "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "tbi_vcf" + }, + "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e" + ] + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "test.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:40.042648294" + }, + "sarscov2_vcf_csi_stub": { + "content": [ + { + "0": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "test.vcf.gz.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:07:08.700367261" + }, + "sarscov2_vcf_csi": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "vcf_csi" + }, + "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b" + ] + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + [ + { + "id": "vcf_csi" + }, + "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b" + ] + ], + "tbi": [ + + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "test.vcf.gz.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:55.362067748" + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tabix_bed.config b/modules/nf-core/tabix/tabix/tests/tabix_bed.config new file mode 100644 index 0000000..7ff0590 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_bed.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p bed' + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tabix_gff.config b/modules/nf-core/tabix/tabix/tests/tabix_gff.config new file mode 100644 index 0000000..20c0a1e --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_gff.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p gff' + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config b/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config new file mode 100644 index 0000000..eb4f2d7 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p vcf --csi' + } +} diff --git a/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config b/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config new file mode 100644 index 0000000..2774c8a --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p vcf' + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tags.yml b/modules/nf-core/tabix/tabix/tests/tags.yml new file mode 100644 index 0000000..6eda065 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tags.yml @@ -0,0 +1,2 @@ +tabix/tabix: + - "modules/nf-core/tabix/tabix/**"
Process Name \\", + " \\ Software Version
CUSTOM_DUMPSOFTWAREVERSIONSpython3.11.7
yaml5.4.1
TOOL1tool10.11.9
TOOL2tool21.9
WorkflowNextflow