diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index fcc074a4..38377c6c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -104,7 +104,7 @@ jobs: --shard ${{ matrix.shard }}/${{ strategy.job-total }} \ --changed-since HEAD^ \ --profile "+${{ matrix.profile }}" \ - --filter pipeline + --filter pipeline,workflow - name: Publish Test Report uses: mikepenz/action-junit-report@v3 diff --git a/modules.json b/modules.json index b34d3d6e..53e3c295 100644 --- a/modules.json +++ b/modules.json @@ -7,12 +7,12 @@ "nf-core": { "bismark/align": { "branch": "master", - "git_sha": "0755c617637d21b2c290b26d225debe3070aa109", + "git_sha": "9c4438173b1fcbf3f9004080e3af74af19d5f56e", "installed_by": ["modules"] }, "bismark/coverage2cytosine": { "branch": "master", - "git_sha": "0755c617637d21b2c290b26d225debe3070aa109", + "git_sha": "430bcb24e43dabcafb5174c955300730e5ad23f7", "installed_by": ["modules"] }, "bismark/deduplicate": { @@ -22,7 +22,7 @@ }, "bismark/genomepreparation": { "branch": "master", - "git_sha": "0755c617637d21b2c290b26d225debe3070aa109", + "git_sha": "3ab4739901f600a16ede0f491abfb6bf5d993cb2", "installed_by": ["modules"] }, "bismark/methylationextractor": { @@ -42,17 +42,17 @@ }, "bwameth/align": { "branch": "master", - "git_sha": "aa2f43221437b20cd204fb7ddbc7302fe859780f", + "git_sha": "9c4438173b1fcbf3f9004080e3af74af19d5f56e", "installed_by": ["modules"] }, "bwameth/index": { "branch": "master", - "git_sha": "aa2f43221437b20cd204fb7ddbc7302fe859780f", + "git_sha": "a716d10039f9728f2674f45c33a95b605851ea50", "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["modules"] }, "fastqc": { @@ -82,12 +82,12 @@ }, "picard/markduplicates": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["modules"] }, "preseq/lcextrap": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["modules"] }, "qualimap/bamqc": { @@ -127,7 +127,7 @@ }, "trimgalore": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["modules"] }, "untar": { diff --git a/modules/nf-core/bismark/align/main.nf b/modules/nf-core/bismark/align/main.nf index f6f04b93..d8ce3d01 100644 --- a/modules/nf-core/bismark/align/main.nf +++ b/modules/nf-core/bismark/align/main.nf @@ -56,7 +56,9 @@ process BISMARK_ALIGN { } } """ - mv $fasta $index/ + if [ ! -f $index/$fasta ]; then + ln -s \$(readlink $fasta) $index/$fasta; + fi bismark \\ $fastq \\ diff --git a/modules/nf-core/bismark/align/tests/main.nf.test b/modules/nf-core/bismark/align/tests/main.nf.test index 2ee01b84..fcd693c8 100644 --- a/modules/nf-core/bismark/align/tests/main.nf.test +++ b/modules/nf-core/bismark/align/tests/main.nf.test @@ -33,7 +33,7 @@ nextflow_process { input[0] = Channel.of([ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) - ]) + ]) input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) input[2] = BISMARK_GENOMEPREPARATION.out.index """ @@ -63,10 +63,10 @@ nextflow_process { input[0] = Channel.of([ [ id:'test', single_end:true ], [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) ] - ]) + ]) input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) input[2] = BISMARK_GENOMEPREPARATION.out.index """ @@ -96,7 +96,7 @@ nextflow_process { input[0] = Channel.of([ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) - ]) + ]) input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) input[2] = BISMARK_GENOMEPREPARATION.out.index """ @@ -126,10 +126,10 @@ nextflow_process { input[0] = Channel.of([ [ id:'test', single_end:true ], [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) ] - ]) + ]) input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) input[2] = BISMARK_GENOMEPREPARATION.out.index """ @@ -159,7 +159,7 @@ nextflow_process { input[0] = Channel.of([ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) - ]) + ]) input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) input[2] = BISMARK_GENOMEPREPARATION.out.index """ @@ -179,5 +179,4 @@ nextflow_process { ) } } - } diff --git a/modules/nf-core/bismark/coverage2cytosine/main.nf b/modules/nf-core/bismark/coverage2cytosine/main.nf index 37ce2e5c..fe65c658 100644 --- a/modules/nf-core/bismark/coverage2cytosine/main.nf +++ b/modules/nf-core/bismark/coverage2cytosine/main.nf @@ -25,7 +25,9 @@ process BISMARK_COVERAGE2CYTOSINE { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - mv $fasta $index/ + if [ ! -f $index/$fasta ]; then + ln -s \$(readlink $fasta) $index/$fasta; + fi coverage2cytosine \\ $coverage_file \\ diff --git a/modules/nf-core/bismark/genomepreparation/main.nf b/modules/nf-core/bismark/genomepreparation/main.nf index e8b9feda..c94e9fec 100644 --- a/modules/nf-core/bismark/genomepreparation/main.nf +++ b/modules/nf-core/bismark/genomepreparation/main.nf @@ -8,7 +8,7 @@ process BISMARK_GENOMEPREPARATION { 'biocontainers/bismark:0.24.2--hdfd78af_0' }" input: - tuple val(meta), path(fasta) + tuple val(meta), path(fasta, name:"BismarkIndex/") output: tuple val(meta), path("BismarkIndex"), emit: index @@ -20,14 +20,11 @@ process BISMARK_GENOMEPREPARATION { script: def args = task.ext.args ?: '' """ - mkdir BismarkIndex - mv $fasta BismarkIndex/ - bismark_genome_preparation \\ $args \\ BismarkIndex - rm BismarkIndex/$fasta + rm $fasta cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -38,8 +35,25 @@ process BISMARK_GENOMEPREPARATION { stub: def args = task.ext.args ?: '' """ - mkdir BismarkIndex - touch BismarkIndex/$fasta + rm $fasta + + mkdir -p BismarkIndex/Bisulfite_Genome/CT_conversion + touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.1.bt2 + touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.2.bt2 + touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.3.bt2 + touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.4.bt2 + touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.rev.1.bt2 + touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.rev.2.bt2 + touch BismarkIndex/Bisulfite_Genome/CT_conversion/genome_mfa.CT_conversion.fa + + mkdir -p BismarkIndex/Bisulfite_Genome/GA_conversion + touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.1.bt2 + touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.2.bt2 + touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.3.bt2 + touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.4.bt2 + touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.1.bt2 + touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.2.bt2 + touch BismarkIndex/Bisulfite_Genome/GA_conversion/genome_mfa.GA_conversion.fa cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap b/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap index caf8afc8..d56b414d 100644 --- a/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap +++ b/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap @@ -8,7 +8,26 @@ "id": "test" }, [ - "genome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + [ + "BS_CT.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_mfa.CT_conversion.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "BS_GA.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_mfa.GA_conversion.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ] ] ], @@ -21,7 +40,26 @@ "id": "test" }, [ - "genome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + [ + "BS_CT.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_mfa.CT_conversion.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "BS_GA.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_mfa.GA_conversion.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ] ] ], @@ -34,7 +72,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-13T08:26:30.051110425" + "timestamp": "2024-10-18T15:50:44.009733" }, "sarscov2 genome [fasta]": { "content": [ diff --git a/modules/nf-core/bwameth/align/main.nf b/modules/nf-core/bwameth/align/main.nf index 8ce2ee32..2e6ff2d0 100644 --- a/modules/nf-core/bwameth/align/main.nf +++ b/modules/nf-core/bwameth/align/main.nf @@ -28,7 +28,10 @@ process BWAMETH_ALIGN { # Modify the timestamps so that bwameth doesn't complain about building the index # See https://github.com/nf-core/methylseq/pull/217 touch -c $index/* - mv $fasta $index/ + + if [ ! -f $index/$fasta ]; then + ln -s \$(readlink $fasta) $index/$fasta; + fi bwameth.py \\ $args \\ diff --git a/modules/nf-core/bwameth/align/tests/main.nf.test b/modules/nf-core/bwameth/align/tests/main.nf.test index 211e0956..37dd4ad2 100644 --- a/modules/nf-core/bwameth/align/tests/main.nf.test +++ b/modules/nf-core/bwameth/align/tests/main.nf.test @@ -88,7 +88,7 @@ nextflow_process { } } - test("test-bwameth-align-paired-end-stub") { + test("sarscov2 methylated paired_end [fastq] - stub") { options '-stub' when { diff --git a/modules/nf-core/bwameth/align/tests/main.nf.test.snap b/modules/nf-core/bwameth/align/tests/main.nf.test.snap index a9010810..8f44bb78 100644 --- a/modules/nf-core/bwameth/align/tests/main.nf.test.snap +++ b/modules/nf-core/bwameth/align/tests/main.nf.test.snap @@ -12,7 +12,20 @@ }, "timestamp": "2024-10-16T07:50:08.241201566" }, - "test-bwameth-align-paired-end-stub": { + "sarscov2 methylated paired_end [fastq]": { + "content": [ + "cbd5cfa8b446e26987898a45a94770ba", + [ + "versions.yml:md5,c00660f78aeab4fabe00092c70656098" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-16T07:50:20.75109829" + }, + "sarscov2 methylated paired_end [fastq] - stub": { "content": [ { "0": [ @@ -45,19 +58,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-16T08:00:51.770330645" - }, - "sarscov2 methylated paired_end [fastq]": { - "content": [ - "cbd5cfa8b446e26987898a45a94770ba", - [ - "versions.yml:md5,c00660f78aeab4fabe00092c70656098" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-16T07:50:20.75109829" + "timestamp": "2024-10-21T12:43:43.563953696" } } \ No newline at end of file diff --git a/modules/nf-core/bwameth/index/main.nf b/modules/nf-core/bwameth/index/main.nf index 5059f134..b4327a7b 100644 --- a/modules/nf-core/bwameth/index/main.nf +++ b/modules/nf-core/bwameth/index/main.nf @@ -8,7 +8,7 @@ process BWAMETH_INDEX { 'biocontainers/bwameth:0.2.7--pyh7cba7a3_0' }" input: - tuple val(meta), path(fasta) + tuple val(meta), path(fasta, name:"BwamethIndex/") output: tuple val(meta), path("BwamethIndex"), emit: index @@ -20,12 +20,10 @@ process BWAMETH_INDEX { script: def args = task.ext.args ?: '' """ - mkdir BwamethIndex - mv $fasta BwamethIndex/ - bwameth.py index BwamethIndex/$fasta + bwameth.py index $fasta - rm BwamethIndex/$fasta + rm $fasta cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -36,8 +34,16 @@ process BWAMETH_INDEX { stub: def args = task.ext.args ?: '' """ - mkdir BwamethIndex - touch BwamethIndex/$fasta + rm $fasta + + mkdir -p BwamethIndex/ + touch BwamethIndex/genome.fasta.bwameth.c2t + touch BwamethIndex/genome.fasta.bwameth.c2t.amb + touch BwamethIndex/genome.fasta.bwameth.c2t.ann + touch BwamethIndex/genome.fasta.bwameth.c2t.bwt + touch BwamethIndex/genome.fasta.bwameth.c2t.pac + touch BwamethIndex/genome.fasta.bwameth.c2t.sa + cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index c7eb9bd1..71e04c3d 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::coreutils=8.30 + - conda-forge::coreutils=9.5 diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index b68e5f91..4364a389 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -4,8 +4,8 @@ process CAT_FASTQ { 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://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' : + 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' }" input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap index aec119a9..f8689a1c 100644 --- a/modules/nf-core/cat/fastq/tests/main.nf.test.snap +++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:30:39.816981" + "timestamp": "2024-10-19T20:02:07.519211144" }, "test_cat_fastq_single_end_same_name": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -59,15 +59,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:32:35.229332" + "timestamp": "2024-10-19T20:02:31.618628921" }, "test_cat_fastq_single_end_single_file": { "content": [ @@ -82,7 +82,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -94,15 +94,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:34:00.058829" + "timestamp": "2024-10-19T20:02:57.904149581" }, "test_cat_fastq_paired_end_same_name": { "content": [ @@ -120,7 +120,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -135,15 +135,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:33:33.031555" + "timestamp": "2024-10-19T20:02:44.577183829" }, "test_cat_fastq_single_end - stub": { "content": [ @@ -158,7 +158,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -170,15 +170,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:07:28.244999" + "timestamp": "2024-10-19T20:03:10.603734777" }, "test_cat_fastq_paired_end_same_name - stub": { "content": [ @@ -196,7 +196,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -211,15 +211,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:07:57.070911" + "timestamp": "2024-10-19T20:03:46.041808828" }, "test_cat_fastq_single_end_same_name - stub": { "content": [ @@ -234,7 +234,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -246,15 +246,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:07:46.796254" + "timestamp": "2024-10-19T20:03:34.13865402" }, "test_cat_fastq_paired_end": { "content": [ @@ -272,7 +272,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -287,15 +287,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:32:02.270935" + "timestamp": "2024-10-19T20:02:19.64383573" }, "test_cat_fastq_paired_end - stub": { "content": [ @@ -313,7 +313,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -328,15 +328,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:07:37.807553" + "timestamp": "2024-10-19T20:03:22.597246066" }, "test_cat_fastq_single_end_single_file - stub": { "content": [ @@ -351,7 +351,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -363,14 +363,14 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:14:51.861264" + "timestamp": "2024-10-19T20:03:58.44849001" } } \ No newline at end of file diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml index ff4a85ed..1d715d56 100644 --- a/modules/nf-core/picard/markduplicates/environment.yml +++ b/modules/nf-core/picard/markduplicates/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index cf18ac35..8a2ed64e 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -4,8 +4,8 @@ process PICARD_MARKDUPLICATES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap index 8b37e65b..13770a8e 100644 --- a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap @@ -27,7 +27,7 @@ ] ], "4": [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ], "bai": [ @@ -54,15 +54,15 @@ ] ], "versions": [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T11:56:32.025869" + "timestamp": "2024-10-18T10:58:50.046420643" }, "sarscov2 [unsorted bam] - stub": { "content": [ @@ -92,7 +92,7 @@ ] ], "4": [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ], "bai": [ @@ -119,69 +119,69 @@ ] ], "versions": [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T11:56:20.497105" + "timestamp": "2024-10-18T10:58:36.738907079" }, "sarscov2 [unsorted bam]": { "content": [ "test.marked.bam", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T11:50:14.881666" + "timestamp": "2024-10-18T10:57:16.683233382" }, "sarscov2 [sorted bam]": { "content": [ "test.marked.bam", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T11:52:03.11428" + "timestamp": "2024-10-18T10:57:47.416956759" }, "homo_sapiens [cram]": { "content": [ "test.marked.cram", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T11:53:05.403139" + "timestamp": "2024-10-18T10:58:15.143314223" }, "homo_sapiens [cram] - stub": { "content": [ @@ -211,7 +211,7 @@ ] ], "4": [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ], "bai": [ @@ -238,14 +238,14 @@ ] ], "versions": [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T11:56:43.438188" + "timestamp": "2024-10-18T10:59:03.402916523" } } \ No newline at end of file diff --git a/modules/nf-core/preseq/lcextrap/environment.yml b/modules/nf-core/preseq/lcextrap/environment.yml index 926d7aec..6300d3f3 100644 --- a/modules/nf-core/preseq/lcextrap/environment.yml +++ b/modules/nf-core/preseq/lcextrap/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::preseq=3.1.2 + - bioconda::preseq=3.2.0 diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf index 3fec468e..540a5fb2 100644 --- a/modules/nf-core/preseq/lcextrap/main.nf +++ b/modules/nf-core/preseq/lcextrap/main.nf @@ -5,8 +5,8 @@ process PRESEQ_LCEXTRAP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2': - 'biocontainers/preseq:3.1.2--h445547b_2' }" + 'https://depot.galaxyproject.org/singularity/preseq:3.2.0--hdcf5f25_6': + 'biocontainers/preseq:3.2.0--hdcf5f25_6' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap b/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap index 3f95cd49..c725d8e8 100644 --- a/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap +++ b/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap @@ -30,14 +30,14 @@ "single_end - versions": { "content": [ [ - "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922" + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T17:20:40.74601" + "timestamp": "2024-10-19T16:55:55.821665692" }, "sarscov2 - single_end - stub": { "content": [ @@ -61,7 +61,7 @@ ] ], "2": [ - "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922" + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" ], "lc_extrap": [ [ @@ -82,27 +82,27 @@ ] ], "versions": [ - "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922" + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-20T18:43:12.689062" + "timestamp": "2024-10-19T16:56:11.779385911" }, "paired_end - versions": { "content": [ [ - "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922" + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T17:20:52.02843" + "timestamp": "2024-10-19T16:56:31.353046182" }, "single_end - log": { "content": [ @@ -154,7 +154,7 @@ ] ], "2": [ - "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922" + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" ], "lc_extrap": [ [ @@ -175,14 +175,14 @@ ] ], "versions": [ - "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922" + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-20T18:43:32.569811" + "timestamp": "2024-10-19T16:56:45.034808313" } } \ No newline at end of file diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index c3315ab5..910ffa88 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::cutadapt=3.4 - - bioconda::trim-galore=0.6.7 + - bioconda::cutadapt=4.2 + - bioconda::trim-galore=0.6.10 diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 0e2f3290..30d17edc 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -4,8 +4,8 @@ process TRIMGALORE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0' : - 'biocontainers/trim-galore:0.6.7--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.10--hdfd78af_0' : + 'biocontainers/trim-galore:0.6.10--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index 6cb31c9f..61b3504a 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "test_trimgalore_single_end": { "content": [ [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T16:33:20.401347" + "timestamp": "2024-10-18T12:50:36.440264431" }, "test_trimgalore_single_end - stub": { "content": [ @@ -42,7 +42,7 @@ ], "5": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ], "html": [ @@ -69,7 +69,7 @@ ], "versions": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ], "zip": [ @@ -77,10 +77,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:27:44.964166" + "timestamp": "2024-10-18T12:50:51.25902234" }, "test_trimgalore_paired_end - stub": { "content": [ @@ -119,7 +119,7 @@ ], "5": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ], "html": [ @@ -152,7 +152,7 @@ ], "versions": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ], "zip": [ @@ -160,21 +160,21 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:28:07.611496" + "timestamp": "2024-10-18T12:51:19.024228479" }, "test_trimgalore_paired_end": { "content": [ [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T16:33:28.960497" + "timestamp": "2024-10-18T12:51:02.471703095" } } \ No newline at end of file diff --git a/subworkflows/local/bismark/tests/bismark_hisat.nf.test b/subworkflows/local/bismark/tests/bismark_hisat.nf.test index 1dee3d98..1f1070b3 100644 --- a/subworkflows/local/bismark/tests/bismark_hisat.nf.test +++ b/subworkflows/local/bismark/tests/bismark_hisat.nf.test @@ -1,6 +1,6 @@ nextflow_workflow { - name "Test Workflow BISMARK_Hisat" + name "Test Workflow BISMARK_HISAT" script "../main.nf" workflow "BISMARK" config "../nextflow.config" @@ -19,7 +19,7 @@ nextflow_workflow { } } - test("Bismark_Hisat: save_reference") { + test("Bismark_Hisat | save_reference") { when { params { @@ -28,6 +28,7 @@ nextflow_workflow { unmapped = false save_align_intermeds = false skip_deduplication = false + cytosine_report = false rrbs = false nomeseq = false slamseq = false @@ -36,16 +37,18 @@ nextflow_workflow { } workflow { """ - skip_deduplication = false - cytosine_report = false input[0] = Channel.of([ [ id:'test', single_end:true ], file(params.pipelines_testdata_base_path + 'testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) ]) - input[1] = UNTAR.out.untar.map { it[1] } - input[2] = skip_deduplication - input[3] = cytosine_report + input[1] = Channel.of([ + [:], + file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) + ]) + input[2] = UNTAR.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report """ } } diff --git a/subworkflows/local/bismark/tests/bismark_hisat.nf.test.snap b/subworkflows/local/bismark/tests/bismark_hisat.nf.test.snap index 1c1bc6db..a531a2e7 100644 --- a/subworkflows/local/bismark/tests/bismark_hisat.nf.test.snap +++ b/subworkflows/local/bismark/tests/bismark_hisat.nf.test.snap @@ -1,5 +1,5 @@ { - "Bismark_Hisat: save_reference": { + "Bismark_Hisat | save_reference": { "content": [ [ "3a6485d719fcaf868c7f95c8f10a3f3c" @@ -8,20 +8,20 @@ "dae445da532c973dc9149f3ceba2d2c5" ], [ - "versions.yml:md5,37c90312d5685ae87bcb080e0cab48de", - "versions.yml:md5,66f7b51aeee12e293634cb74fea2f091", - "versions.yml:md5,701e44c4be43ad049c16c7fc8686a21d", - "versions.yml:md5,75082556508926250285e70e1932fa74", - "versions.yml:md5,bff10f08bf0238c3303ef33749b7a93c", + "versions.yml:md5,2273d537ccb64f2260adeb6844523d73", + "versions.yml:md5,6a04613f312dd68246d992a7f6fa03a5", "versions.yml:md5,c06f3e25000330e948f7a35708270f3f", "versions.yml:md5,c2ad6c469b4d15c963f03b2228376a80", - "versions.yml:md5,cb4a7015750ef1e0e504c56acb72a799" + "versions.yml:md5,cb4a7015750ef1e0e504c56acb72a799", + "versions.yml:md5,cb8dda62996be2045f2ad33831c6b74c", + "versions.yml:md5,cd3f634936e8c40265e766e5f5d07f15", + "versions.yml:md5,cfb4c81c53e84715cbf50b702a84e457" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-29T14:19:18.719515297" + "timestamp": "2024-10-20T11:17:46.351442694" } -} \ No newline at end of file +} diff --git a/subworkflows/local/bismark/tests/main.nf.test b/subworkflows/local/bismark/tests/main.nf.test index e8ae5a77..b38cbdbc 100644 --- a/subworkflows/local/bismark/tests/main.nf.test +++ b/subworkflows/local/bismark/tests/main.nf.test @@ -19,7 +19,7 @@ nextflow_workflow { } } - test("Bismark: save_reference") { + test("Bismark | save_reference") { when { params { @@ -28,6 +28,7 @@ nextflow_workflow { unmapped = false save_align_intermeds = false skip_deduplication = false + cytosine_report = false rrbs = false nomeseq = false slamseq = false @@ -36,16 +37,18 @@ nextflow_workflow { } workflow { """ - skip_deduplication = false - cytosine_report = false input[0] = Channel.of([ [ id:'test', single_end:true ], file(params.pipelines_testdata_base_path + 'testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) ]) - input[1] = UNTAR.out.untar.map { it[1] } - input[2] = skip_deduplication - input[3] = cytosine_report + input[1] = Channel.of([ + [:], + file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) + ]) + input[2] = UNTAR.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report """ } } diff --git a/subworkflows/local/bismark/tests/main.nf.test.snap b/subworkflows/local/bismark/tests/main.nf.test.snap index b2fea83b..6757ea79 100644 --- a/subworkflows/local/bismark/tests/main.nf.test.snap +++ b/subworkflows/local/bismark/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "Bismark: save_reference": { + "Bismark | save_reference": { "content": [ [ "d6951f6d3381e22becf62553a37c0f3f" @@ -8,20 +8,20 @@ "35d55bee1ca653931716e40dac4aba30" ], [ - "versions.yml:md5,37c90312d5685ae87bcb080e0cab48de", - "versions.yml:md5,66f7b51aeee12e293634cb74fea2f091", - "versions.yml:md5,701e44c4be43ad049c16c7fc8686a21d", - "versions.yml:md5,75082556508926250285e70e1932fa74", - "versions.yml:md5,bff10f08bf0238c3303ef33749b7a93c", + "versions.yml:md5,2273d537ccb64f2260adeb6844523d73", + "versions.yml:md5,6a04613f312dd68246d992a7f6fa03a5", "versions.yml:md5,c06f3e25000330e948f7a35708270f3f", "versions.yml:md5,c2ad6c469b4d15c963f03b2228376a80", - "versions.yml:md5,cb4a7015750ef1e0e504c56acb72a799" + "versions.yml:md5,cb4a7015750ef1e0e504c56acb72a799", + "versions.yml:md5,cb8dda62996be2045f2ad33831c6b74c", + "versions.yml:md5,cd3f634936e8c40265e766e5f5d07f15", + "versions.yml:md5,cfb4c81c53e84715cbf50b702a84e457" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-29T13:55:29.087420554" + "timestamp": "2024-10-20T11:14:29.732866935" } -} \ No newline at end of file +} diff --git a/subworkflows/local/bwameth/tests/main.nf.test b/subworkflows/local/bwameth/tests/main.nf.test index 799bda84..21aadf8a 100644 --- a/subworkflows/local/bwameth/tests/main.nf.test +++ b/subworkflows/local/bwameth/tests/main.nf.test @@ -19,7 +19,7 @@ nextflow_workflow { } } - test("Bwameth: save_reference") { + test("Bwameth | save_reference") { when { params { @@ -36,14 +36,16 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.of([ [ id:'test', single_end:true ], file(params.pipelines_testdata_base_path + 'testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) ]) - input[1] = UNTAR.out.untar.map { it[1] } // bwameth_index - input[2] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true)) // fasta - input[3] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/genome.fa.fai', checkIfExists: true)) //fasta_index + input[1] = UNTAR.out.untar + input[2] = Channel.of([ + [:], + file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) + ]) + input[3] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/genome.fa.fai', checkIfExists: true)) input[4] = params.skip_deduplication """ } diff --git a/subworkflows/local/bwameth/tests/main.nf.test.snap b/subworkflows/local/bwameth/tests/main.nf.test.snap index 3f95d4a0..3834e919 100644 --- a/subworkflows/local/bwameth/tests/main.nf.test.snap +++ b/subworkflows/local/bwameth/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "Bwameth: save_reference": { + "Bwameth | save_reference": { "content": [ [ "37ec1c6338cc3fee7ab1cb2d48dba38" @@ -13,15 +13,15 @@ "versions.yml:md5,2b54b53cdedbbd547bc6bc3623dcc622", "versions.yml:md5,38a8061118fdcb6215a31e60419df107", "versions.yml:md5,5e8c932b160898dbcf29469f4ea6c978", - "versions.yml:md5,68051491abbd025bd108d86911c5bf00", "versions.yml:md5,88592f164662fc6e5389899dbf472f53", - "versions.yml:md5,b935a799534fa7094fe81a723df04ecf" + "versions.yml:md5,b935a799534fa7094fe81a723df04ecf", + "versions.yml:md5,c3658cdda0f57c6d7f0c57e820921eb4" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-29T13:56:40.754742484" + "timestamp": "2024-10-21T18:23:18.006459111" } } \ No newline at end of file diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test index 483c302b..c7f20b6a 100644 --- a/subworkflows/local/prepare_genome/tests/main.nf.test +++ b/subworkflows/local/prepare_genome/tests/main.nf.test @@ -5,7 +5,7 @@ nextflow_workflow { workflow "PREPARE_GENOME" config "../nextflow.config" - test("BISMARK - Generate Index") { + test("Generate Bismark Index (bowtie2)") { when { params { @@ -37,7 +37,39 @@ nextflow_workflow { } - test("BWAMETH - Generate Index") { + test("Generate Bismark Index (hisat2)") { + + when { + params { + aligner = "bismark_hisat" + publish_dir_mode = copy + save_reference = false + slamseq = false + } + workflow { + """ + input[0] = file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) // fasta + input[1] = [] // fasta_index + input[2] = [] // bismark_index + input[3] = [] // bwameth_index + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.fasta, + workflow.out.bismark_index, + workflow.out.versions + ).match() } + ) + } + + } + + test("Generate Bwameth Index") { when { params { diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap index d8d2f218..73d4db88 100644 --- a/subworkflows/local/prepare_genome/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_genome/tests/main.nf.test.snap @@ -1,61 +1,83 @@ { - "BISMARK - Generate Index": { + "Generate Bismark Index (hisat2)": { "content": [ [ - "/nf-core/test-datasets/raw/methylseq/reference/genome.fa" + [ + { + + }, + "/nf-core/test-datasets/raw/methylseq/reference/genome.fa" + ] ], [ [ + { + + }, [ [ - "BS_CT.1.bt2:md5,d53bef7d951c7d08e327944581c911eb", - "BS_CT.2.bt2:md5,752a03fc364115fc910e5a28ae154382", - "BS_CT.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee", - "BS_CT.4.bt2:md5,02b3d1855a67fd9cbb4c411406a22fde", - "BS_CT.rev.1.bt2:md5,52ae603fff473b3b25eecd36c533edb9", - "BS_CT.rev.2.bt2:md5,0e290e05f7dae065cae54e29ed97afe5", - "genome_mfa.CT_conversion.fa:md5,4dd181b65f1f3549f4132c9a3759eee8" - ], - [ - "BS_GA.1.bt2:md5,9aff51b1712758b891b0c427a988977f", - "BS_GA.2.bt2:md5,579241d95941538b2e75bbdb6cfaa73d", - "BS_GA.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee", - "BS_GA.4.bt2:md5,6b64fa496ffa2af2af235e1c87f06a25", - "BS_GA.rev.1.bt2:md5,dabf2d6f80ba7e8fc96dfdc203f6bbfd", - "BS_GA.rev.2.bt2:md5,fac2f8b39b0e15dec7aa79a0ecf12b49", - "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f" + [ + "BS_CT.1.ht2:md5,273c7686fc1dc7d93e36433592367f81", + "BS_CT.2.ht2:md5,752a03fc364115fc910e5a28ae154382", + "BS_CT.3.ht2:md5,b41e72eefad74e8ede411c78a5bd5dee", + "BS_CT.4.ht2:md5,02b3d1855a67fd9cbb4c411406a22fde", + "BS_CT.5.ht2:md5,d117de4c2c910a1ae7f0459c11ba6018", + "BS_CT.6.ht2:md5,4097a785a8d1ca92489d83b4c613a50b", + "BS_CT.7.ht2:md5,9013eccd91ad614d7893c739275a394f", + "BS_CT.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb", + "genome_mfa.CT_conversion.fa:md5,4dd181b65f1f3549f4132c9a3759eee8" + ], + [ + "BS_GA.1.ht2:md5,c2b02b7987f4ac0578332204678674cd", + "BS_GA.2.ht2:md5,579241d95941538b2e75bbdb6cfaa73d", + "BS_GA.3.ht2:md5,b41e72eefad74e8ede411c78a5bd5dee", + "BS_GA.4.ht2:md5,6b64fa496ffa2af2af235e1c87f06a25", + "BS_GA.5.ht2:md5,43aa1c78c6ec18c4165cf25159578fee", + "BS_GA.6.ht2:md5,2dc0f049d7d0f2a51822df8b195dce41", + "BS_GA.7.ht2:md5,9013eccd91ad614d7893c739275a394f", + "BS_GA.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb", + "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f" + ] ] - ], - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de" + ] ] ], [ - "versions.yml:md5,48a4baa99421c3dd839946dd1af8d7aa" + "versions.yml:md5,8e4e91d03b368e548eeafee8dd263e70" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-08T12:38:22.021170374" + "timestamp": "2024-10-20T15:44:14.403574883" }, - "BWAMETH - Generate Index": { + "Generate Bwameth Index": { "content": [ [ - "/nf-core/test-datasets/raw/methylseq/reference/genome.fa" + [ + { + + }, + "/nf-core/test-datasets/raw/methylseq/reference/genome.fa" + ] ], [ "genome.fa.fai:md5,84f5b44c25877ac58b154706cc8bc451" ], [ [ - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", - "genome.fa.bwameth.c2t:md5,e51d48ed28fa0c26e2f9c9f13d09403b", - "genome.fa.bwameth.c2t.amb:md5,010a242c6764efb30141868a45d698b3", - "genome.fa.bwameth.c2t.ann:md5,09b4db3d87a2d4dac9e10e807f377110", - "genome.fa.bwameth.c2t.bwt:md5,4646f8ae6bd523b7f4106bbd32eff95e", - "genome.fa.bwameth.c2t.pac:md5,a662d7add09698e25c8152fd2306ec66", - "genome.fa.bwameth.c2t.sa:md5,4a1e905b828396a1909669bc9c573d8d" + { + + }, + [ + "genome.fa.bwameth.c2t:md5,e51d48ed28fa0c26e2f9c9f13d09403b", + "genome.fa.bwameth.c2t.amb:md5,010a242c6764efb30141868a45d698b3", + "genome.fa.bwameth.c2t.ann:md5,09b4db3d87a2d4dac9e10e807f377110", + "genome.fa.bwameth.c2t.bwt:md5,4646f8ae6bd523b7f4106bbd32eff95e", + "genome.fa.bwameth.c2t.pac:md5,a662d7add09698e25c8152fd2306ec66", + "genome.fa.bwameth.c2t.sa:md5,4a1e905b828396a1909669bc9c573d8d" + ] ] ], [ @@ -67,6 +89,55 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-29T13:57:16.093473618" + "timestamp": "2024-10-20T11:27:38.06274051" + }, + "Generate Bismark Index (bowtie2)": { + "content": [ + [ + [ + { + + }, + "/nf-core/test-datasets/raw/methylseq/reference/genome.fa" + ] + ], + [ + [ + { + + }, + [ + [ + [ + "BS_CT.1.bt2:md5,d53bef7d951c7d08e327944581c911eb", + "BS_CT.2.bt2:md5,752a03fc364115fc910e5a28ae154382", + "BS_CT.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee", + "BS_CT.4.bt2:md5,02b3d1855a67fd9cbb4c411406a22fde", + "BS_CT.rev.1.bt2:md5,52ae603fff473b3b25eecd36c533edb9", + "BS_CT.rev.2.bt2:md5,0e290e05f7dae065cae54e29ed97afe5", + "genome_mfa.CT_conversion.fa:md5,4dd181b65f1f3549f4132c9a3759eee8" + ], + [ + "BS_GA.1.bt2:md5,9aff51b1712758b891b0c427a988977f", + "BS_GA.2.bt2:md5,579241d95941538b2e75bbdb6cfaa73d", + "BS_GA.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee", + "BS_GA.4.bt2:md5,6b64fa496ffa2af2af235e1c87f06a25", + "BS_GA.rev.1.bt2:md5,dabf2d6f80ba7e8fc96dfdc203f6bbfd", + "BS_GA.rev.2.bt2:md5,fac2f8b39b0e15dec7aa79a0ecf12b49", + "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f" + ] + ] + ] + ] + ], + [ + "versions.yml:md5,8e4e91d03b368e548eeafee8dd263e70" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-20T11:27:14.196959225" } } \ No newline at end of file diff --git a/tests/bismark_emseq_clip_r1.nf.test.snap b/tests/bismark_emseq_clip_r1.nf.test.snap index 7e505005..0f82b86b 100644 --- a/tests/bismark_emseq_clip_r1.nf.test.snap +++ b/tests/bismark_emseq_clip_r1.nf.test.snap @@ -16,8 +16,8 @@ "qualimap": 2.3 }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "Workflow": { "nf-core/methylseq": "v2.7.0" @@ -541,7 +541,7 @@ "multiqc_bismark_dedup.txt:md5,16e464f5bf2f1851a571ec87cbc1a0d9", "multiqc_bismark_methextract.txt:md5,ef3c68247a6254ae5e11e26052e3229e", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,9423377cea77c773f2ef2be03e5d1e04", + "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", "qualimap_coverage_histogram.txt:md5,7d321d1eb204be4c3661364cf928c3e3", "qualimap_gc_content.txt:md5,d914dc3ae413deb1db307910d9907ea9", "qualimap_genome_fraction.txt:md5,2f6d7ae8cfdafc69358ce6a6800bef54", @@ -574,6 +574,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T10:51:29.795278841" + "timestamp": "2024-10-21T17:43:14.505236122" } } \ No newline at end of file diff --git a/tests/bismark_hisat.nf.test.snap b/tests/bismark_hisat.nf.test.snap index a99eba8d..0e92c1eb 100644 --- a/tests/bismark_hisat.nf.test.snap +++ b/tests/bismark_hisat.nf.test.snap @@ -26,8 +26,8 @@ "qualimap": 2.3 }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "Workflow": { "nf-core/methylseq": "v2.7.0" @@ -553,7 +553,7 @@ "multiqc_bismark_dedup.txt:md5,5e58032548eda3c39384495cf0cfaa3d", "multiqc_bismark_methextract.txt:md5,5ce6739f6daa34276200f303c240e4b1", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,9423377cea77c773f2ef2be03e5d1e04", + "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", "qualimap_coverage_histogram.txt:md5,b78964924f4985d97f6dff7ced688d29", "qualimap_gc_content.txt:md5,ad345dd40fe367f2138776c8ea2b257f", "qualimap_genome_fraction.txt:md5,9a1c3d3f7349cf1c2af1c5878dac4185", @@ -586,6 +586,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T10:53:17.891178066" + "timestamp": "2024-10-21T17:44:48.196812536" } } \ No newline at end of file diff --git a/tests/bismark_hisat_rrbs.nf.test.snap b/tests/bismark_hisat_rrbs.nf.test.snap index 74c454a7..0eb368cc 100644 --- a/tests/bismark_hisat_rrbs.nf.test.snap +++ b/tests/bismark_hisat_rrbs.nf.test.snap @@ -16,8 +16,8 @@ "qualimap": 2.3 }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "Workflow": { "nf-core/methylseq": "v2.7.0" @@ -530,7 +530,7 @@ "multiqc_bismark_alignment.txt:md5,75a6ccfb5b5bff3a5b3d3e2174929fc3", "multiqc_bismark_methextract.txt:md5,d1312f03f47d7cc07ac18254cda720bd", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,c2575e27f3839e30ceeff079ada3386b", + "multiqc_cutadapt.txt:md5,b376b3816764859cfc345bf13cda536f", "qualimap_coverage_histogram.txt:md5,938111519a9ad1b2580f8f944fb659aa", "qualimap_gc_content.txt:md5,3263a2edb88dcbddf5654df1b233f66d", "qualimap_genome_fraction.txt:md5,5490f57857141d3e31a1f978bf1f7ead", @@ -579,6 +579,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T10:57:14.940936284" + "timestamp": "2024-10-21T17:48:05.852952347" } } \ No newline at end of file diff --git a/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap b/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap index e4f652be..c70f3bb4 100644 --- a/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap @@ -16,8 +16,8 @@ "qualimap": 2.3 }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "Workflow": { "nf-core/methylseq": "v2.7.0" @@ -592,7 +592,7 @@ "multiqc_bismark_dedup.txt:md5,5e58032548eda3c39384495cf0cfaa3d", "multiqc_bismark_methextract.txt:md5,5ce6739f6daa34276200f303c240e4b1", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,9423377cea77c773f2ef2be03e5d1e04", + "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", "qualimap_coverage_histogram.txt:md5,b78964924f4985d97f6dff7ced688d29", "qualimap_gc_content.txt:md5,ad345dd40fe367f2138776c8ea2b257f", "qualimap_genome_fraction.txt:md5,9a1c3d3f7349cf1c2af1c5878dac4185", @@ -657,6 +657,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T10:58:57.866094491" + "timestamp": "2024-10-21T17:49:33.437253199" } } \ No newline at end of file diff --git a/tests/bismark_nomeseq.nf.test.snap b/tests/bismark_nomeseq.nf.test.snap index 6b9830fe..d23aa5fe 100644 --- a/tests/bismark_nomeseq.nf.test.snap +++ b/tests/bismark_nomeseq.nf.test.snap @@ -16,8 +16,8 @@ "qualimap": 2.3 }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "Workflow": { "nf-core/methylseq": "v2.7.0" @@ -587,7 +587,7 @@ "multiqc_bismark_dedup.txt:md5,d09a5de4d81a3207efb6a8937d060e46", "multiqc_bismark_methextract.txt:md5,825f57cdf45203406e583beb495afccc", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,9423377cea77c773f2ef2be03e5d1e04", + "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", "qualimap_coverage_histogram.txt:md5,7cd194077fe839edf034b44cc73dd024", "qualimap_gc_content.txt:md5,4f6ec70d9fb71ffe5f2f99f44fe5ef0c", "qualimap_genome_fraction.txt:md5,3e528946a376ae752b57adaaa73f5cdf", @@ -620,6 +620,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T11:00:41.867543271" + "timestamp": "2024-10-21T17:50:56.499718354" } } \ No newline at end of file diff --git a/tests/bismark_rrbs.nf.test.snap b/tests/bismark_rrbs.nf.test.snap index 930f2618..fb7cc545 100644 --- a/tests/bismark_rrbs.nf.test.snap +++ b/tests/bismark_rrbs.nf.test.snap @@ -16,8 +16,8 @@ "qualimap": 2.3 }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "Workflow": { "nf-core/methylseq": "v2.7.0" @@ -530,7 +530,7 @@ "multiqc_bismark_alignment.txt:md5,f9f3e888d5176131440f6a8a6d1abccc", "multiqc_bismark_methextract.txt:md5,1a2967a22fa1522f9e8d672fc43ca78d", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,c2575e27f3839e30ceeff079ada3386b", + "multiqc_cutadapt.txt:md5,b376b3816764859cfc345bf13cda536f", "qualimap_coverage_histogram.txt:md5,22c70e761489597e34a3d71d036ff190", "qualimap_gc_content.txt:md5,c872803a08b92b36c136e2ba3bee96d4", "qualimap_genome_fraction.txt:md5,393f86423cc89983ab66fa29f93dd710", @@ -579,6 +579,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T11:02:40.067338396" + "timestamp": "2024-10-21T17:52:32.475797707" } } \ No newline at end of file diff --git a/tests/bismark_save_reference_save_align_intermeds.nf.test.snap b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap index 256ffab0..8ec9d79e 100644 --- a/tests/bismark_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap @@ -16,8 +16,8 @@ "qualimap": 2.3 }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "Workflow": { "nf-core/methylseq": "v2.7.0" @@ -584,7 +584,7 @@ "multiqc_bismark_dedup.txt:md5,d09a5de4d81a3207efb6a8937d060e46", "multiqc_bismark_methextract.txt:md5,825f57cdf45203406e583beb495afccc", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,9423377cea77c773f2ef2be03e5d1e04", + "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", "qualimap_coverage_histogram.txt:md5,7cd194077fe839edf034b44cc73dd024", "qualimap_gc_content.txt:md5,4f6ec70d9fb71ffe5f2f99f44fe5ef0c", "qualimap_genome_fraction.txt:md5,3e528946a376ae752b57adaaa73f5cdf", @@ -649,6 +649,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T11:04:20.592196335" + "timestamp": "2024-10-21T18:10:42.065837136" } } \ No newline at end of file diff --git a/tests/bismark_skip_deduplication.nf.test.snap b/tests/bismark_skip_deduplication.nf.test.snap index bc705db6..13bf50eb 100644 --- a/tests/bismark_skip_deduplication.nf.test.snap +++ b/tests/bismark_skip_deduplication.nf.test.snap @@ -16,8 +16,8 @@ "qualimap": 2.3 }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "Workflow": { "nf-core/methylseq": "v2.7.0" @@ -532,7 +532,7 @@ "multiqc_bismark_alignment.txt:md5,40ab86041f508d3f1a63bde20cab5440", "multiqc_bismark_methextract.txt:md5,374ad746b0cfa5143fc3606f77f53283", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,9423377cea77c773f2ef2be03e5d1e04", + "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", "qualimap_coverage_histogram.txt:md5,dfd099755c43854826eb71acca153a33", "qualimap_gc_content.txt:md5,55baed387d09b5a0583ce2b5abfc0d12", "qualimap_genome_fraction.txt:md5,bde4b1a12ad8ad0420b44fa3f1ed0512", @@ -581,6 +581,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T11:06:25.019219406" + "timestamp": "2024-10-21T17:54:28.816433456" } } \ No newline at end of file diff --git a/tests/bismark_skip_multiqc.nf.test.snap b/tests/bismark_skip_multiqc.nf.test.snap index de3ab473..84d72c00 100644 --- a/tests/bismark_skip_multiqc.nf.test.snap +++ b/tests/bismark_skip_multiqc.nf.test.snap @@ -16,8 +16,8 @@ "qualimap": 2.3 }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "Workflow": { "nf-core/methylseq": "v2.7.0" @@ -543,7 +543,7 @@ "multiqc_bismark_dedup.txt:md5,d09a5de4d81a3207efb6a8937d060e46", "multiqc_bismark_methextract.txt:md5,825f57cdf45203406e583beb495afccc", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,9423377cea77c773f2ef2be03e5d1e04", + "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", "qualimap_coverage_histogram.txt:md5,7cd194077fe839edf034b44cc73dd024", "qualimap_gc_content.txt:md5,4f6ec70d9fb71ffe5f2f99f44fe5ef0c", "qualimap_genome_fraction.txt:md5,3e528946a376ae752b57adaaa73f5cdf", @@ -576,6 +576,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T11:08:10.360287416" + "timestamp": "2024-10-21T17:55:48.550138313" } } \ No newline at end of file diff --git a/tests/bwameth.nf.test.snap b/tests/bwameth.nf.test.snap index 8c700268..6ce8c6d3 100644 --- a/tests/bwameth.nf.test.snap +++ b/tests/bwameth.nf.test.snap @@ -16,8 +16,8 @@ "qualimap": 2.3 }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "Workflow": { "nf-core/methylseq": "v2.7.0" @@ -394,7 +394,7 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,9e5712db9aa39b5754ea1e0c49cfff15", "fastqc_top_overrepresented_sequences_table.txt:md5,6dfc5334a09c05392ea17369aa742d01", "multiqc_citations.txt:md5,581df5b266851d0244e7cfb213351ffb", - "multiqc_cutadapt.txt:md5,9423377cea77c773f2ef2be03e5d1e04", + "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", "multiqc_picard_dups.txt:md5,82eaab96189f22fd93db38bb516ba6a5", "multiqc_samtools_flagstat.txt:md5,a8f5b45b8b3412a9adc3dd0d35208c73", "multiqc_samtools_stats.txt:md5,e24271a8111b06c1f545b6b1a077a4a7", @@ -438,7 +438,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T11:11:30.194587369" + "timestamp": "2024-10-21T17:58:28.435328799" }, "Params: bwameth with bwameth-index": { "content": [ diff --git a/tests/bwameth_rrbs.nf.test.snap b/tests/bwameth_rrbs.nf.test.snap index f0543205..59f497d9 100644 --- a/tests/bwameth_rrbs.nf.test.snap +++ b/tests/bwameth_rrbs.nf.test.snap @@ -16,8 +16,8 @@ "qualimap": 2.3 }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "Workflow": { "nf-core/methylseq": "v2.7.0" @@ -369,7 +369,7 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,9e5712db9aa39b5754ea1e0c49cfff15", "fastqc_top_overrepresented_sequences_table.txt:md5,6dfc5334a09c05392ea17369aa742d01", "multiqc_citations.txt:md5,581df5b266851d0244e7cfb213351ffb", - "multiqc_cutadapt.txt:md5,c2575e27f3839e30ceeff079ada3386b", + "multiqc_cutadapt.txt:md5,b376b3816764859cfc345bf13cda536f", "multiqc_samtools_flagstat.txt:md5,4389e377eb1db8dde26b0e8db6589c2d", "multiqc_samtools_stats.txt:md5,3843eed6fb6ec8d27729a8b901ada0cf", "qualimap_coverage_histogram.txt:md5,c5354816b9ce0a18d633506e2dd4e4ac", @@ -393,6 +393,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T11:15:01.789604127" + "timestamp": "2024-10-21T18:00:44.344954074" } } \ No newline at end of file diff --git a/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap b/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap index 06393b8a..546c1371 100644 --- a/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap @@ -16,8 +16,8 @@ "qualimap": 2.3 }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "Workflow": { "nf-core/methylseq": "v2.7.0" @@ -420,7 +420,7 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,9e5712db9aa39b5754ea1e0c49cfff15", "fastqc_top_overrepresented_sequences_table.txt:md5,6dfc5334a09c05392ea17369aa742d01", "multiqc_citations.txt:md5,581df5b266851d0244e7cfb213351ffb", - "multiqc_cutadapt.txt:md5,9423377cea77c773f2ef2be03e5d1e04", + "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", "multiqc_picard_dups.txt:md5,82eaab96189f22fd93db38bb516ba6a5", "multiqc_samtools_flagstat.txt:md5,a8f5b45b8b3412a9adc3dd0d35208c73", "multiqc_samtools_stats.txt:md5,e24271a8111b06c1f545b6b1a077a4a7", @@ -496,6 +496,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T11:16:48.40025727" + "timestamp": "2024-10-21T18:01:53.259560408" } } \ No newline at end of file diff --git a/tests/bwameth_skip_deduplication.nf.test.snap b/tests/bwameth_skip_deduplication.nf.test.snap index f4ad6f40..f73c18ae 100644 --- a/tests/bwameth_skip_deduplication.nf.test.snap +++ b/tests/bwameth_skip_deduplication.nf.test.snap @@ -16,8 +16,8 @@ "qualimap": 2.3 }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "Workflow": { "nf-core/methylseq": "v2.7.0" @@ -369,7 +369,7 @@ "fastqc_sequence_duplication_levels_plot.txt:md5,9e5712db9aa39b5754ea1e0c49cfff15", "fastqc_top_overrepresented_sequences_table.txt:md5,6dfc5334a09c05392ea17369aa742d01", "multiqc_citations.txt:md5,581df5b266851d0244e7cfb213351ffb", - "multiqc_cutadapt.txt:md5,9423377cea77c773f2ef2be03e5d1e04", + "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", "multiqc_samtools_flagstat.txt:md5,a8f5b45b8b3412a9adc3dd0d35208c73", "multiqc_samtools_stats.txt:md5,e24271a8111b06c1f545b6b1a077a4a7", "qualimap_coverage_histogram.txt:md5,c7c932e4d84b735bd434c1aaa713b6e6", @@ -393,6 +393,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T11:18:18.444989125" + "timestamp": "2024-10-21T18:02:51.160774031" } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 8aa7a734..675f4e67 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -26,8 +26,8 @@ "qualimap": 2.3 }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "Workflow": { "nf-core/methylseq": "v2.7.0" @@ -553,7 +553,7 @@ "multiqc_bismark_dedup.txt:md5,d09a5de4d81a3207efb6a8937d060e46", "multiqc_bismark_methextract.txt:md5,825f57cdf45203406e583beb495afccc", "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,9423377cea77c773f2ef2be03e5d1e04", + "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", "qualimap_coverage_histogram.txt:md5,7cd194077fe839edf034b44cc73dd024", "qualimap_gc_content.txt:md5,4f6ec70d9fb71ffe5f2f99f44fe5ef0c", "qualimap_genome_fraction.txt:md5,3e528946a376ae752b57adaaa73f5cdf", @@ -586,6 +586,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-17T11:21:37.75676038" + "timestamp": "2024-10-21T18:05:06.16706255" } } \ No newline at end of file