$group
\n" - summary_section += "| Process Name | -Software | -Version | -
|---|---|---|
| {process if (i == 0) else ''} | -{tool} | -{version} | -
| Process Name | \\n\\", - " \\ Software | \\nVersion | \\n
|---|---|---|
| CUSTOM_DUMPSOFTWAREVERSIONS | \\npython | \\n\\", - " \\3.11.7 | \\n
| \\n \\", - " \\ | yaml | \\n5.4.1 | \\n
| TOOL1 | \\ntool1 | \\n\\", - " \\0.11.9 | \\n
| TOOL2 | \\n\\", - " \\tool2 | \\n1.9 | \\n
| Workflow | \\nNextflow | \\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 deleted file mode 100644 index 405aa24a..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -custom/dumpsoftwareversions: - - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/phantompeakqualtools/environment.yml b/modules/nf-core/phantompeakqualtools/environment.yml new file mode 100644 index 00000000..095b7b4b --- /dev/null +++ b/modules/nf-core/phantompeakqualtools/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +name: "phantompeakqualtools" +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - "bioconda::phantompeakqualtools=1.2.2" diff --git a/modules/nf-core/phantompeakqualtools/main.nf b/modules/nf-core/phantompeakqualtools/main.nf index edcdf2ce..f0f7dc63 100644 --- a/modules/nf-core/phantompeakqualtools/main.nf +++ b/modules/nf-core/phantompeakqualtools/main.nf @@ -3,10 +3,10 @@ process PHANTOMPEAKQUALTOOLS { label 'process_medium' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda "bioconda::phantompeakqualtools=1.2.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0' : - 'biocontainers/phantompeakqualtools:1.2.2--0' }" + 'oras://community.wave.seqera.io/library/phantompeakqualtools:1.2.2--50be7727b2a72700' : + 'community.wave.seqera.io/library/phantompeakqualtools:1.2.2--f8026fe2526a5e18' }" input: tuple val(meta), path(bam) @@ -34,4 +34,18 @@ process PHANTOMPEAKQUALTOOLS { phantompeakqualtools: $VERSION END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '1.2.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + """ + touch ${prefix}.spp.pdf + touch ${prefix}.spp.Rdata + touch ${prefix}.spp.out + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + phantompeakqualtools: $VERSION + END_VERSIONS + """ } diff --git a/modules/nf-core/phantompeakqualtools/meta.yml b/modules/nf-core/phantompeakqualtools/meta.yml index c8290fbd..276f6fdd 100644 --- a/modules/nf-core/phantompeakqualtools/meta.yml +++ b/modules/nf-core/phantompeakqualtools/meta.yml @@ -1,5 +1,4 @@ name: "phantompeakqualtools" - description: | "This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used @@ -16,12 +15,10 @@ tools: for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays." - documentation: "https://github.com/kundajelab/phantompeakqualtools" tool_dev_url: "https://github.com/kundajelab/phantompeakqualtools" doi: "10.1101/gr.136184.111" - licence: "['BSD-3-clause']" - + licence: ["BSD-3-clause"] input: - meta: type: map @@ -32,7 +29,6 @@ input: type: file description: BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" - output: - meta: type: map @@ -57,8 +53,11 @@ output: type: file description: Rdata file containing the R session pattern: "*.{Rdata}" - authors: - "@drpatelh" - - "@Emiller88" + - "@edmundmiller" + - "@JoseEspinosa" +maintainers: + - "@drpatelh" + - "@edmundmiller" - "@JoseEspinosa" diff --git a/modules/nf-core/phantompeakqualtools/tests/main.nf.test b/modules/nf-core/phantompeakqualtools/tests/main.nf.test new file mode 100644 index 00000000..ea096bcf --- /dev/null +++ b/modules/nf-core/phantompeakqualtools/tests/main.nf.test @@ -0,0 +1,90 @@ +// nf-core modules test phantompeakqualtools +nextflow_process { + + name "Test Process PHANTOMPEAKQUALTOOLS" + script "../main.nf" + process "PHANTOMPEAKQUALTOOLS" + + tag "modules" + tag "modules_nfcore" + tag "phantompeakqualtools" + + test("sarscov2 - bam - single_end") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.spp, + file(process.out.pdf.get(0).get(1)).name, + file(process.out.rdata.get(0).get(1)).name, + process.out.versions) + .match() + } + ) + } + + } + + test("sarscov2 - bam - paired_end") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // 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.spp, + file(process.out.pdf.get(0).get(1)).name, + file(process.out.rdata.get(0).get(1)).name, + process.out.versions) + .match() + } + ) + } + + } + + test("sarscov2 - bam - stub") { + + options "-stub" + + 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() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/phantompeakqualtools/tests/main.nf.test.snap b/modules/nf-core/phantompeakqualtools/tests/main.nf.test.snap new file mode 100644 index 00000000..1021aeb8 --- /dev/null +++ b/modules/nf-core/phantompeakqualtools/tests/main.nf.test.snap @@ -0,0 +1,119 @@ +{ + "sarscov2 - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.spp.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.spp.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.spp.Rdata:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,e0a48a40af2cf7d5de72c4c3cb47a4fc" + ], + "pdf": [ + [ + { + "id": "test", + "single_end": false + }, + "test.spp.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "rdata": [ + [ + { + "id": "test", + "single_end": false + }, + "test.spp.Rdata:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "spp": [ + [ + { + "id": "test", + "single_end": false + }, + "test.spp.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e0a48a40af2cf7d5de72c4c3cb47a4fc" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-27T10:46:22.786363" + }, + "sarscov2 - bam - single_end": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.spp.out:md5,b01d976506b6fe45b66c821b1e8a1d15" + ] + ], + "test.spp.pdf", + "test.spp.Rdata", + [ + "versions.yml:md5,e0a48a40af2cf7d5de72c4c3cb47a4fc" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-27T16:21:12.000709154" + }, + "sarscov2 - bam - paired_end": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.spp.out:md5,eed46e75eab119224f397a7a8b5924e6" + ] + ], + "test.spp.pdf", + "test.spp.Rdata", + [ + "versions.yml:md5,e0a48a40af2cf7d5de72c4c3cb47a4fc" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-27T16:21:22.432426907" + } +} \ No newline at end of file diff --git a/modules/nf-core/phantompeakqualtools/tests/tags.yml b/modules/nf-core/phantompeakqualtools/tests/tags.yml new file mode 100644 index 00000000..9031749e --- /dev/null +++ b/modules/nf-core/phantompeakqualtools/tests/tags.yml @@ -0,0 +1,2 @@ +phantompeakqualtools: + - "modules/nf-core/phantompeakqualtools/**" diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index bd7033cb..b7878aaf 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -27,7 +27,18 @@ include { STAR_GENOMEGENERATE } from '../../modules/local/star_genomegenera workflow PREPARE_GENOME { take: + genome // string: genome name + genomes // map: genome attributes prepare_tool_index // string : tool to prepare index for + fasta // path: path to genome fasta file + gtf // file: /path/to/genome.gtf + gff // file: /path/to/genome.gff + blacklist // file: /path/to/blacklist.bed + gene_bed // file: /path/to/gene.bed + bwa_index // file: /path/to/bwa/index/ + bowtie2_index // file: /path/to/bowtie2/index/ + chromap_index // file: /path/to/chromap/index/ + star_index // file: /path/to/star/index/ main: @@ -37,29 +48,29 @@ workflow PREPARE_GENOME { // Uncompress genome fasta file if required // ch_fasta = Channel.empty() - if (params.fasta.endsWith('.gz')) { - ch_fasta = GUNZIP_FASTA ( [ [:], params.fasta ] ).gunzip.map{ it[1] } + if (fasta.endsWith('.gz')) { + ch_fasta = GUNZIP_FASTA ( [ [:], fasta ] ).gunzip.map{ it[1] } ch_versions = ch_versions.mix(GUNZIP_FASTA.out.versions) } else { - ch_fasta = Channel.value(file(params.fasta)) + ch_fasta = Channel.value(file(fasta)) } // // Uncompress GTF annotation file or create from GFF3 if required // - if (params.gtf) { - if (params.gtf.endsWith('.gz')) { - ch_gtf = GUNZIP_GTF ( [ [:], params.gtf ] ).gunzip.map{ it[1] } + if (gtf) { + if (gtf.endsWith('.gz')) { + ch_gtf = GUNZIP_GTF ( [ [:], gtf ] ).gunzip.map{ it[1] } ch_versions = ch_versions.mix(GUNZIP_GTF.out.versions) } else { - ch_gtf = file(params.gtf) + ch_gtf = Channel.value(file(gtf)) } - } else if (params.gff) { - if (params.gff.endsWith('.gz')) { - ch_gff = GUNZIP_GFF ( [ [:], params.gff ] ).gunzip.map{ it[1] } + } else if (gff) { + if (gff.endsWith('.gz')) { + ch_gff = GUNZIP_GFF ( [ [:], gff ] ).gunzip.map{ it[1] } ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions) } else { - ch_gff = file(params.gff) + ch_gff = Channel.value(file(gff)) } ch_gtf = GFFREAD ( ch_gff ).gtf ch_versions = ch_versions.mix(GFFREAD.out.versions) @@ -69,12 +80,12 @@ workflow PREPARE_GENOME { // Uncompress blacklist file if required // ch_blacklist = Channel.empty() - if (params.blacklist) { - if (params.blacklist.endsWith('.gz')) { - ch_blacklist = GUNZIP_BLACKLIST ( [ [:], params.blacklist ] ).gunzip.map{ it[1] } + if (blacklist) { + if (blacklist.endsWith('.gz')) { + ch_blacklist = GUNZIP_BLACKLIST ( [ [:], blacklist ] ).gunzip.map{ it[1] } ch_versions = ch_versions.mix(GUNZIP_BLACKLIST.out.versions) } else { - ch_blacklist = Channel.fromPath(file(params.blacklist)) + ch_blacklist = Channel.value(file(blacklist)) } } @@ -85,10 +96,10 @@ workflow PREPARE_GENOME { // If --gtf is supplied along with --genome // Make gene bed from supplied --gtf instead of using iGenomes one automatically def make_bed = false - if (!params.gene_bed) { + if (!gene_bed) { make_bed = true - } else if (params.genome && params.gtf) { - if (params.genomes[ params.genome ].gtf != params.gtf) { + } else if (genome && gtf) { + if (genomes[ genome ].gtf != gtf) { make_bed = true } } @@ -97,11 +108,11 @@ workflow PREPARE_GENOME { ch_gene_bed = GTF2BED ( ch_gtf ).bed ch_versions = ch_versions.mix(GTF2BED.out.versions) } else { - if (params.gene_bed.endsWith('.gz')) { - ch_gene_bed = GUNZIP_GENE_BED ( [ [:], params.gene_bed ] ).gunzip.map{ it[1] } + if (gene_bed.endsWith('.gz')) { + ch_gene_bed = GUNZIP_GENE_BED ( [ [:], gene_bed ] ).gunzip.map{ it[1] } ch_versions = ch_versions.mix(GUNZIP_GENE_BED.out.versions) } else { - ch_gene_bed = Channel.value(file(params.gene_bed)) + ch_gene_bed = Channel.value(file(gene_bed)) } } @@ -119,24 +130,23 @@ workflow PREPARE_GENOME { ch_genome_filtered_bed = Channel.empty() GENOME_BLACKLIST_REGIONS ( - CUSTOM_GETCHROMSIZES.out.sizes.map{ it[1] }, + ch_chrom_sizes, ch_blacklist.ifEmpty([]) ) ch_genome_filtered_bed = GENOME_BLACKLIST_REGIONS.out.bed ch_versions = ch_versions.mix(GENOME_BLACKLIST_REGIONS.out.versions) - // // Uncompress BWA index or generate from scratch if required // ch_bwa_index = Channel.empty() if (prepare_tool_index == 'bwa') { - if (params.bwa_index) { - if (params.bwa_index.endsWith('.tar.gz')) { - ch_bwa_index = UNTAR_BWA_INDEX ( [ [:], params.bwa_index ] ).untar + if (bwa_index) { + if (bwa_index.endsWith('.tar.gz')) { + ch_bwa_index = UNTAR_BWA_INDEX ( [ [:], bwa_index ] ).untar ch_versions = ch_versions.mix(UNTAR_BWA_INDEX.out.versions) } else { - ch_bwa_index = file(params.bwa_index) + ch_bwa_index = file(bwa_index) } } else { ch_bwa_index = BWA_INDEX ( ch_fasta.map { [ [:], it ] } ).index @@ -149,12 +159,12 @@ workflow PREPARE_GENOME { // ch_bowtie2_index = Channel.empty() if (prepare_tool_index == 'bowtie2') { - if (params.bowtie2_index) { - if (params.bowtie2_index.endsWith('.tar.gz')) { - ch_bowtie2_index = UNTAR_BOWTIE2_INDEX ( [ [:], params.bowtie2_index ] ).untar + if (bowtie2_index) { + if (bowtie2_index.endsWith('.tar.gz')) { + ch_bowtie2_index = UNTAR_BOWTIE2_INDEX ( [ [:], bowtie2_index ] ).untar ch_versions = ch_versions.mix(UNTAR_BOWTIE2_INDEX.out.versions) } else { - ch_bowtie2_index = [ [:], file(params.bowtie2_index) ] + ch_bowtie2_index = [ [:], file(bowtie2_index) ] } } else { ch_bowtie2_index = BOWTIE2_BUILD ( ch_fasta.map { [ [:], it ] } ).index @@ -167,12 +177,12 @@ workflow PREPARE_GENOME { // ch_chromap_index = Channel.empty() if (prepare_tool_index == 'chromap') { - if (params.chromap_index) { - if (params.chromap_index.endsWith('.tar.gz')) { - ch_chromap_index = UNTARFILES ( [ [:], params.chromap_index ] ).files + if (chromap_index) { + if (chromap_index.endsWith('.tar.gz')) { + ch_chromap_index = UNTARFILES ( [ [:], chromap_index ] ).files ch_versions = ch_versions.mix(UNTARFILES.out.versions) } else { - ch_chromap_index = [ [:], file(params.chromap_index) ] + ch_chromap_index = [ [:], file(chromap_index) ] } } else { ch_chromap_index = CHROMAP_INDEX ( ch_fasta.map { [ [:], it ] } ).index @@ -185,12 +195,12 @@ workflow PREPARE_GENOME { // ch_star_index = Channel.empty() if (prepare_tool_index == 'star') { - if (params.star_index) { - if (params.star_index.endsWith('.tar.gz')) { - ch_star_index = UNTAR_STAR_INDEX ( [ [:], params.star_index ] ).untar.map{ it[1] } + if (star_index) { + if (star_index.endsWith('.tar.gz')) { + ch_star_index = UNTAR_STAR_INDEX ( [ [:], star_index ] ).untar.map{ it[1] } ch_versions = ch_versions.mix(UNTAR_STAR_INDEX.out.versions) } else { - ch_star_index = Channel.value(file(params.star_index)) + ch_star_index = Channel.value(file(star_index)) } } else { ch_star_index = STAR_GENOMEGENERATE ( ch_fasta, ch_gtf ).index @@ -209,6 +219,5 @@ workflow PREPARE_GENOME { bowtie2_index = ch_bowtie2_index // path: bowtie2/index/ chromap_index = ch_chromap_index // path: genome.index star_index = ch_star_index // path: star/index/ - - versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ] + versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ] } diff --git a/subworkflows/local/utils_nfcore_chipseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_chipseq_pipeline/main.nf new file mode 100644 index 00000000..a1433174 --- /dev/null +++ b/subworkflows/local/utils_nfcore_chipseq_pipeline/main.nf @@ -0,0 +1,268 @@ +// +// Subworkflow with functionality specific to the nf-core/chipseq pipeline +// + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' +include { paramsSummaryMap } from 'plugin/nf-validation' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' +include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' +include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' +include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' +include { imNotification } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' +include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' + +/* +======================================================================================== + SUBWORKFLOW TO INITIALISE PIPELINE +======================================================================================== +*/ + +workflow PIPELINE_INITIALISATION { + + take: + version // boolean: Display version and exit + help // boolean: Display help text + validate_params // boolean: Boolean whether to validate parameters against the schema at runtime + monochrome_logs // boolean: Do not use coloured log outputs + nextflow_cli_args // array: List of positional nextflow CLI args + outdir // string: The output directory where the results will be saved + + main: + + // + // Print version and exit if required and dump pipeline parameters to JSON file + // + UTILS_NEXTFLOW_PIPELINE ( + version, + true, + outdir, + workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 + ) + + // + // Validate parameters and generate parameter summary to stdout + // + pre_help_text = nfCoreLogo(monochrome_logs) + post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) + def String workflow_command = "nextflow run ${workflow.manifest.name} -profile