diff --git a/CHANGELOG.md b/CHANGELOG.md index 8776e166..0be11a30 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -31,6 +31,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 4.0.2](https://github.com/nf-core/tools/releases/tag/4.0.2). - [[#519] (https://github.com/nf-core/chipseq/issues/519)] - Changed merged libraries suffix to `.mLb.`. - [[#456] (https://github.com/nf-core/chipseq/issues/456)] - Use `--skip_preseq` by default. +- [[#531] (https://github.com/nf-core/chipseq/issues/531)] - Changed chromap decompression - untarfiles (depreciated) to untar modules ### Parameters diff --git a/modules.json b/modules.json index 3693b49d..d99831a9 100644 --- a/modules.json +++ b/modules.json @@ -198,11 +198,6 @@ "branch": "master", "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf", "installed_by": ["modules"] - }, - "untarfiles": { - "branch": "master", - "git_sha": "bc71bfe17a9c2057f1781b5b16987dcc14d1063f", - "installed_by": ["modules"] } } }, diff --git a/modules/nf-core/untarfiles/environment.yml b/modules/nf-core/untarfiles/environment.yml deleted file mode 100644 index cdd3d462..00000000 --- a/modules/nf-core/untarfiles/environment.yml +++ /dev/null @@ -1,10 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -channels: - - conda-forge - - bioconda - -dependencies: - - bioconda::grep=3.4 - - conda-forge::sed=4.8 - - conda-forge::tar=1.34 diff --git a/modules/nf-core/untarfiles/main.nf b/modules/nf-core/untarfiles/main.nf deleted file mode 100644 index 8abf8825..00000000 --- a/modules/nf-core/untarfiles/main.nf +++ /dev/null @@ -1,66 +0,0 @@ -process UNTARFILES { - tag "$archive" - label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/88/88e03525287eaeb8bb74114aaee2c67118c1cdcfb99ee52e3ddc71a1acce35d4/data' : - 'community.wave.seqera.io/library/grep_sed_tar:db2951cd23a1ffde' }" - - input: - tuple val(meta), path(archive) - - output: - tuple val(meta), path("${prefix}/**") , emit: files - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def deprecation_message = """ -WARNING: This module has been deprecated. - -Reason: -This module is no longer recommended for use. It is recommended to use nf-core/modules/untar -""" - assert false: deprecation_message - def args = task.ext.args ?: '' - def args2 = task.ext.args2 ?: '' - prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, "")) - - """ - mkdir $prefix - - tar \\ - -C $prefix \\ - -xavf \\ - $args \\ - $archive \\ - $args2 - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//') - END_VERSIONS - """ - - stub: - def deprecation_message = """ -WARNING: This module has been deprecated. - -Reason: -This module is no longer recommended for use. It is recommended to use nf-core/modules/untar -""" - assert false: deprecation_message - prefix = task.ext.prefix ?: "${meta.id}" - """ - mkdir $prefix - touch ${prefix}/file.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//') - END_VERSIONS - """ -} diff --git a/modules/nf-core/untarfiles/meta.yml b/modules/nf-core/untarfiles/meta.yml deleted file mode 100644 index fadf6744..00000000 --- a/modules/nf-core/untarfiles/meta.yml +++ /dev/null @@ -1,56 +0,0 @@ -name: untarfiles -description: Extract files. -keywords: - - untar - - uncompress - - files -tools: - - untar: - description: | - Extract tar.gz files. - documentation: https://www.gnu.org/software/tar/manual/ - licence: ["GPL-3.0-or-later"] - identifier: "" -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be untar - pattern: "*.{tar}.{gz}" - ontologies: - - edam: http://edamontology.org/format_3981 # TAR format - - edam: http://edamontology.org/format_3989 # GZIP format -output: - files: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ${prefix}/**: - type: string - description: A list containing references to individual archive files - pattern: "*/**" - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML -authors: - - "@joseespinosa" - - "@drpatelh" - - "@matthdsm" - - "@jfy133" - - "@pinin4fjords" -maintainers: - - "@joseespinosa" - - "@drpatelh" - - "@matthdsm" - - "@jfy133" - - "@pinin4fjords" diff --git a/modules/nf-core/untarfiles/tests/main.nf.test b/modules/nf-core/untarfiles/tests/main.nf.test deleted file mode 100644 index 52a92a82..00000000 --- a/modules/nf-core/untarfiles/tests/main.nf.test +++ /dev/null @@ -1,96 +0,0 @@ - -nextflow_process { - - name "Test Process UNTARFILES" - script "../main.nf" - process "UNTARFILES" - - tag "modules" - tag "modules_nfcore" - tag "untarfiles" - - test("test-untarfiles") { - - when { - process { - """ - input[0] = [ - [id: 'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) - ] - - """ - } - } - - then { - assertAll( - { assert process.failed } - ) - } - } - - test("test-untarfiles-subdirectories") { - - when { - process { - """ - input[0] = [ - [id: 'test'], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz', checkIfExists: true) - ] - - """ - } - } - - then { - assertAll( - { assert process.failed } - ) - } - } - - test("test-untarfiles-onlyfiles") { - - when { - process { - """ - input[0] = [ - [id: 'test'], - file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) - ] - - """ - } - } - - then { - assertAll( - { assert process.failed } - ) - } - } - - test("test-untarfiles-onlyfiles-stub") { - options '-stub' - when { - process { - """ - input[0] = [ - [id: 'test'], - file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) - ] - - """ - } - } - - then { - assertAll( - { assert process.failed } - ) - } - } - -} diff --git a/modules/nf-core/untarfiles/tests/main.nf.test.snap b/modules/nf-core/untarfiles/tests/main.nf.test.snap deleted file mode 100644 index 33452a08..00000000 --- a/modules/nf-core/untarfiles/tests/main.nf.test.snap +++ /dev/null @@ -1,356 +0,0 @@ -{ - "test-untarfiles-onlyfiles-stub": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "file.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - "versions.yml:md5,4414b00143ed6076881ba7c68ed8b6cf" - ], - "files": [ - [ - { - "id": "test" - }, - "file.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,4414b00143ed6076881ba7c68ed8b6cf" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-29T12:22:11.239416" - }, - "test-untarfiles-subdirectories": { - "content": [ - [ - "ControlMetricsOut.bin", - "CorrectedIntMetricsOut.bin", - "ErrorMetricsOut.bin", - "ExtractionMetricsOut.bin", - "IndexMetricsOut.bin", - "QMetricsOut.bin", - "RTAConfiguration.xml", - "RunInfo.xml", - "TileMetricsOut.bin", - "config.xml", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - "s_1_1101.bcl", - 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] - ] - ], - "1": [ - "versions.yml:md5,4414b00143ed6076881ba7c68ed8b6cf" - ], - "files": [ - [ - { - "id": "test" - }, - [ - "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", - "opts.k2d:md5,a033d00cf6759407010b21700938f543", - "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" - ] - ] - ], - "versions": [ - "versions.yml:md5,4414b00143ed6076881ba7c68ed8b6cf" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-29T12:21:44.153411" - }, - "test-untarfiles-onlyfiles": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "hello.txt:md5,e59ff97941044f85df5297e1c302d260" - ] - ], - "1": [ - "versions.yml:md5,4414b00143ed6076881ba7c68ed8b6cf" - ], - "files": [ - [ - { - "id": "test" - }, - "hello.txt:md5,e59ff97941044f85df5297e1c302d260" - ] - ], - "versions": [ - "versions.yml:md5,4414b00143ed6076881ba7c68ed8b6cf" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-29T12:22:06.329486" - } -} diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index 9768301f..f8ea8d07 100644 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -10,9 +10,9 @@ include { GUNZIP as GUNZIP_BLACKLIST } from '../../../modules/nf-core/gunzip' include { UNTAR as UNTAR_BWA_INDEX } from '../../../modules/nf-core/untar' include { UNTAR as UNTAR_BOWTIE2_INDEX } from '../../../modules/nf-core/untar' +include { UNTAR as UNTAR_CHROMAP_INDEX } from '../../../modules/nf-core/untar' include { UNTAR as UNTAR_STAR_INDEX } from '../../../modules/nf-core/untar' -include { UNTARFILES } from '../../../modules/nf-core/untarfiles' include { GFFREAD } from '../../../modules/nf-core/gffread' include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx' include { BWA_INDEX } from '../../../modules/nf-core/bwa/index' @@ -146,7 +146,7 @@ workflow PREPARE_GENOME { ch_bwa_index = [[:], file(bwa_index)] } } else { - ch_bwa_index = BWA_INDEX(ch_fasta.map { [[:], it] }).index + ch_bwa_index = BWA_INDEX(ch_fasta.map { it -> [[:], it] }).index } } @@ -162,7 +162,7 @@ workflow PREPARE_GENOME { ch_bowtie2_index = [[:], file(bowtie2_index)] } } else { - ch_bowtie2_index = BOWTIE2_BUILD(ch_fasta.map { [[:], it] }).index + ch_bowtie2_index = BOWTIE2_BUILD(ch_fasta.map { it -> [[:], it] }).index } } @@ -173,12 +173,12 @@ workflow PREPARE_GENOME { if (prepare_tool_index == 'chromap') { if (chromap_index) { if (chromap_index.endsWith('.tar.gz')) { - ch_chromap_index = UNTARFILES([[:], chromap_index]).files + ch_chromap_index = UNTAR_CHROMAP_INDEX([[:], chromap_index]).untar } else { ch_chromap_index = [[:], file(chromap_index)] } } else { - ch_chromap_index = CHROMAP_INDEX(ch_fasta.map { [[:], it] }).index + ch_chromap_index = CHROMAP_INDEX(ch_fasta.map { it -> [[:], it] }).index } } @@ -189,7 +189,7 @@ workflow PREPARE_GENOME { if (prepare_tool_index == 'star') { if (star_index) { if (star_index.endsWith('.tar.gz')) { - ch_star_index = UNTAR_STAR_INDEX([[:], star_index]).untar.map { it[1] } + ch_star_index = UNTAR_STAR_INDEX([[:], star_index]).untar.map { it -> it[1] } } else { ch_star_index = channel.value(file(star_index)) } diff --git a/tests/bowtie2.nf.test.snap b/tests/bowtie2.nf.test.snap index d1852a1f..a84ebb28 100644 --- a/tests/bowtie2.nf.test.snap +++ b/tests/bowtie2.nf.test.snap @@ -946,7 +946,7 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], - "timestamp": "2026-07-15T11:34:27.414025", + "timestamp": "2026-07-21T12:38:39.799024", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -956,7 +956,7 @@ "content": [ 20 ], - "timestamp": "2026-07-15T11:35:01.664286", + "timestamp": "2026-07-21T12:39:15.303231", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/tests/chromap.nf.test.snap b/tests/chromap.nf.test.snap index 996dac69..7e85ec16 100644 --- a/tests/chromap.nf.test.snap +++ b/tests/chromap.nf.test.snap @@ -951,7 +951,7 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], - "timestamp": "2026-07-15T11:45:39.473638", + "timestamp": "2026-07-21T12:49:50.568622", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -961,7 +961,7 @@ "content": [ 20 ], - "timestamp": "2026-07-15T11:46:07.963583", + "timestamp": "2026-07-21T12:50:29.057511", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index dcb933ee..ab8d3b70 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -945,7 +945,7 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], - "timestamp": "2026-07-15T11:55:46.742037", + "timestamp": "2026-07-21T13:00:00.044632", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/tests/skip_consensus_peaks.nf.test.snap b/tests/skip_consensus_peaks.nf.test.snap index 368c77b1..fca42d7c 100644 --- a/tests/skip_consensus_peaks.nf.test.snap +++ b/tests/skip_consensus_peaks.nf.test.snap @@ -3,7 +3,7 @@ "content": [ 20 ], - "timestamp": "2026-07-15T12:05:47.280876", + "timestamp": "2026-07-21T13:10:05.459362", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -886,7 +886,7 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], - "timestamp": "2026-07-15T12:05:20.927401", + "timestamp": "2026-07-21T13:09:28.447257", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index af3f6bce..b8dd4697 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -823,7 +823,7 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], - "timestamp": "2026-07-15T12:14:38.105873", + "timestamp": "2026-07-21T13:19:06.842802", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -833,7 +833,7 @@ "content": [ 190 ], - "timestamp": "2026-07-15T12:18:14.397449", + "timestamp": "2026-07-21T13:23:05.44245", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/tests/star.nf.test.snap b/tests/star.nf.test.snap index 4ccb35ff..2fc7272b 100644 --- a/tests/star.nf.test.snap +++ b/tests/star.nf.test.snap @@ -977,7 +977,7 @@ "SPT5_T15_REP2.mLb.clN.sorted.bam.idxstats:md5,aa2db2bcb3aa876cfbfe24b49d98aabd" ] ], - "timestamp": "2026-07-15T12:28:14.404035", + "timestamp": "2026-07-21T13:32:52.982946", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -987,7 +987,7 @@ "content": [ 20 ], - "timestamp": "2026-07-15T12:28:44.226288", + "timestamp": "2026-07-21T13:33:34.284729", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0"