diff --git a/CHANGELOG.md b/CHANGELOG.md index 632d109f..fcf1a72b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,6 @@ # nf-core/methylseq -## [v2.7.2](https://github.com/nf-core/methylseq/releases/tag/2.7.2) - [] +## [v2.8.0](https://github.com/nf-core/methylseq/releases/tag/2.8.0) - [] ### Bug fixes & refactoring @@ -9,6 +9,8 @@ ### Pipeline Updates +- 🔧 Install `fastq_align_dedup_bismark` subworkflow from nf-core/subworkflows [#453](https://github.com/nf-core/methylseq/pull/457) + ## [v2.7.1](https://github.com/nf-core/methylseq/releases/tag/2.7.1) - [2024-10-27] ### Bug fixes & refactoring diff --git a/modules.json b/modules.json index f5aac912..403f0305 100644 --- a/modules.json +++ b/modules.json @@ -8,17 +8,17 @@ "bismark/align": { "branch": "master", "git_sha": "f5a291e827949778a3bb976479d6298b3abf99cd", - "installed_by": ["modules"] + "installed_by": ["fastq_align_dedup_bismark", "modules"] }, "bismark/coverage2cytosine": { "branch": "master", "git_sha": "79922141f1033bc3b56dabef0f0eff68b2b0fb03", - "installed_by": ["modules"] + "installed_by": ["fastq_align_dedup_bismark", "modules"] }, "bismark/deduplicate": { "branch": "master", "git_sha": "79922141f1033bc3b56dabef0f0eff68b2b0fb03", - "installed_by": ["modules"] + "installed_by": ["fastq_align_dedup_bismark", "modules"] }, "bismark/genomepreparation": { "branch": "master", @@ -28,17 +28,17 @@ "bismark/methylationextractor": { "branch": "master", "git_sha": "79922141f1033bc3b56dabef0f0eff68b2b0fb03", - "installed_by": ["modules"] + "installed_by": ["fastq_align_dedup_bismark", "modules"] }, "bismark/report": { "branch": "master", "git_sha": "79922141f1033bc3b56dabef0f0eff68b2b0fb03", - "installed_by": ["modules"] + "installed_by": ["fastq_align_dedup_bismark", "modules"] }, "bismark/summary": { "branch": "master", "git_sha": "dfd89399e3c6e2422c4cdcf0aaa8cf2393dc51c9", - "installed_by": ["modules"] + "installed_by": ["fastq_align_dedup_bismark", "modules"] }, "bwameth/align": { "branch": "master", @@ -113,12 +113,12 @@ "samtools/index": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": ["fastq_align_dedup_bismark", "modules"] }, "samtools/sort": { "branch": "master", "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b", - "installed_by": ["modules"] + "installed_by": ["fastq_align_dedup_bismark", "modules"] }, "samtools/stats": { "branch": "master", @@ -139,19 +139,24 @@ }, "subworkflows": { "nf-core": { + "fastq_align_dedup_bismark": { + "branch": "master", + "git_sha": "af84433c2e619cf28e026d4140b1b8763ae3690b", + "installed_by": ["subworkflows"] + }, "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", + "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", + "git_sha": "1b89f75f1aa2021ec3360d0deccd0f6e97240551", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", + "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/samtools/index/nextflow.config b/modules/nf-core/samtools/index/nextflow.config new file mode 100644 index 00000000..5131f953 --- /dev/null +++ b/modules/nf-core/samtools/index/nextflow.config @@ -0,0 +1,19 @@ +process { + withName: SAMTOOLS_INDEX { + ext.prefix = "" + publishDir = [ + [ + path: { "${params.outdir}/${params.aligner}/deduplicated/" }, + mode: params.publish_dir_mode, + pattern: "*.bai", + enabled: !params.skip_deduplication + ], + [ + path: { "${params.outdir}/${params.aligner}/alignments/" }, + mode: params.publish_dir_mode, + pattern: "*.bai", + enabled: params.skip_deduplication + ] + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/nextflow.config b/modules/nf-core/samtools/sort/nextflow.config index 1918458c..bfb6eb1e 100644 --- a/modules/nf-core/samtools/sort/nextflow.config +++ b/modules/nf-core/samtools/sort/nextflow.config @@ -1,7 +1,18 @@ process { withName: SAMTOOLS_SORT { - ext.prefix = { "${meta.id}.sorted" } + ext.prefix = params.skip_deduplication ? { "${meta.id}.sorted" } : { "${meta.id}.deduplicated.sorted" } publishDir = [ + [ + path: { "${params.outdir}/${params.aligner}/deduplicated/" }, + mode: params.publish_dir_mode, + pattern: "*.deduplicated.sorted.bam" + ], + [ + path: { "${params.outdir}/${params.aligner}/alignments/" }, + mode: params.publish_dir_mode, + pattern: "*.sorted.bam", + enabled: params.skip_deduplication + ], [ path: { "${params.outdir}/${params.aligner}/deduplicated/" }, mode: params.publish_dir_mode, diff --git a/nf-test.config b/nf-test.config index b7a7023a..5cc9c78a 100644 --- a/nf-test.config +++ b/nf-test.config @@ -16,7 +16,7 @@ config { // load the necessary plugins plugins { - load "nft-bam@0.3.0" + load "nft-bam@0.5.0" load "nft-utils@0.0.3" } } diff --git a/subworkflows/local/bismark/main.nf b/subworkflows/local/bismark/main.nf deleted file mode 100644 index e94c0692..00000000 --- a/subworkflows/local/bismark/main.nf +++ /dev/null @@ -1,159 +0,0 @@ -/* - * Bismark subworkflow - */ -include { BISMARK_ALIGN } from '../../../modules/nf-core/bismark/align/main' -include { SAMTOOLS_SORT as SAMTOOLS_SORT_ALIGNED } from '../../../modules/nf-core/samtools/sort/main' -include { SAMTOOLS_SORT as SAMTOOLS_SORT_DEDUPLICATED } from '../../../modules/nf-core/samtools/sort/main' -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_DEDUPLICATED } from '../../../modules/nf-core/samtools/index/main' -include { BISMARK_DEDUPLICATE } from '../../../modules/nf-core/bismark/deduplicate/main' -include { BISMARK_METHYLATIONEXTRACTOR } from '../../../modules/nf-core/bismark/methylationextractor/main' -include { BISMARK_COVERAGE2CYTOSINE } from '../../../modules/nf-core/bismark/coverage2cytosine/main' -include { BISMARK_REPORT } from '../../../modules/nf-core/bismark/report/main' -include { BISMARK_SUMMARY } from '../../../modules/nf-core/bismark/summary/main' - -workflow BISMARK { - take: - reads // channel: [ val(meta), [ reads ] ] - fasta // channel: /path/to/genome.fasta - bismark_index // channel: /path/to/BismarkIndex/ - skip_deduplication // boolean: whether to deduplicate alignments - cytosine_report // boolean: whether the run coverage2cytosine - - main: - - ch_versions = Channel.empty() - /* - * Align with bismark - */ - BISMARK_ALIGN ( - reads, - fasta, - bismark_index - ) - BISMARK_ALIGN.out.bam.dump(tag: 'BISMARK_ALIGN: bam') - BISMARK_ALIGN.out.report.dump(tag: 'BISMARK_ALIGN: report') - - ch_versions = ch_versions.mix(BISMARK_ALIGN.out.versions) - - /* - * Sort raw output BAM - */ - SAMTOOLS_SORT_ALIGNED( - BISMARK_ALIGN.out.bam, - [[:],[]] // Empty map and list as is optional input but required for nextflow - ) - SAMTOOLS_SORT_ALIGNED.out.bam.dump(tag: 'BISMARK/SAMTOOLS_SORT_ALIGNED: bam') - - ch_versions = ch_versions.mix(SAMTOOLS_SORT_ALIGNED.out.versions) - - if (skip_deduplication) { - alignments = BISMARK_ALIGN.out.bam - alignment_reports = BISMARK_ALIGN.out.report.map{ meta, report -> [ meta, report, [] ] } - - alignments.dump(tag: 'BISMARK/skip_deduplication: alignments') - alignment_reports.dump(tag: 'BISMARK/skip_deduplication: alignment_reports') - } else { - /* - * Run deduplicate_bismark - */ - BISMARK_DEDUPLICATE(BISMARK_ALIGN.out.bam) - - alignments = BISMARK_DEDUPLICATE.out.bam - alignment_reports = BISMARK_ALIGN.out.report.join(BISMARK_DEDUPLICATE.out.report) - ch_versions = ch_versions.mix(BISMARK_DEDUPLICATE.out.versions) - - alignments.dump(tag: 'BISMARK_DEDUPLICATE: alignments') - alignment_reports.dump(tag: 'BISMARK_DEDUPLICATE: alignment_reports') - } - - /* - * Run bismark_methylation_extractor - */ - BISMARK_METHYLATIONEXTRACTOR ( - alignments, - bismark_index - ) - BISMARK_METHYLATIONEXTRACTOR.out.report.dump(tag: 'BISMARK_METHYLATIONEXTRACTOR: report') - BISMARK_METHYLATIONEXTRACTOR.out.mbias.dump(tag: 'BISMARK_METHYLATIONEXTRACTOR: mbias') - - ch_versions = ch_versions.mix(BISMARK_METHYLATIONEXTRACTOR.out.versions) - - /* - * Run coverage2cytosine - */ - if (cytosine_report) { - BISMARK_COVERAGE2CYTOSINE ( - BISMARK_METHYLATIONEXTRACTOR.out.coverage, - fasta, - bismark_index - ) - BISMARK_COVERAGE2CYTOSINE.out.report.dump(tag: 'BISMARK_COVERAGE2CYTOSINE: report') - BISMARK_COVERAGE2CYTOSINE.out.coverage.dump(tag: 'BISMARK_COVERAGE2CYTOSINE: coverage') - BISMARK_COVERAGE2CYTOSINE.out.summary.dump(tag: 'BISMARK_COVERAGE2CYTOSINE: summary') - - ch_versions = ch_versions.mix(BISMARK_COVERAGE2CYTOSINE.out.versions) - } - - /* - * Generate bismark sample reports - */ - BISMARK_REPORT ( - alignment_reports - .join(BISMARK_METHYLATIONEXTRACTOR.out.report) - .join(BISMARK_METHYLATIONEXTRACTOR.out.mbias) - ) - BISMARK_REPORT.out.report.dump(tag: 'BISMARK_REPORT: report') - - ch_versions = ch_versions.mix(BISMARK_REPORT.out.versions) - - /* - * Generate bismark summary report - */ - BISMARK_SUMMARY ( - BISMARK_ALIGN.out.bam.collect{ it[1].name }.ifEmpty([]), - alignment_reports.collect{ it[1] }.ifEmpty([]), - alignment_reports.collect{ it[2] }.ifEmpty([]), - BISMARK_METHYLATIONEXTRACTOR.out.report.collect{ it[1] }.ifEmpty([]), - BISMARK_METHYLATIONEXTRACTOR.out.mbias.collect{ it[1] }.ifEmpty([]) - ) - BISMARK_SUMMARY.out.summary.dump(tag: 'BISMARK_REPORT: summary') - - ch_versions = ch_versions.mix(BISMARK_SUMMARY.out.versions) - - /* - * MODULE: Run samtools sort - */ - SAMTOOLS_SORT_DEDUPLICATED ( - alignments, - [[:],[]] // Empty map and list as is optional input but required for nextflow - ) - SAMTOOLS_SORT_DEDUPLICATED.out.bam.dump(tag: 'BISMARK/SAMTOOLS_SORT_DEDUPLICATED: bam') - - ch_versions = ch_versions.mix(SAMTOOLS_SORT_DEDUPLICATED.out.versions) - - /* - * MODULE: Run samtools index on dedup bam - */ - SAMTOOLS_INDEX_DEDUPLICATED(SAMTOOLS_SORT_DEDUPLICATED.out.bam) - - SAMTOOLS_INDEX_DEDUPLICATED.out.bai.dump(tag: 'BISMARK/SAMTOOLS_INDEX_DEDUPLICATED: bai') - - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_DEDUPLICATED.out.versions) - - /* - * Collect MultiQC inputs - */ - BISMARK_SUMMARY.out.summary.ifEmpty([]) - .mix(alignment_reports.collect{ it[1] }) - .mix(alignment_reports.collect{ it[2] }) - .mix(BISMARK_METHYLATIONEXTRACTOR.out.report.collect{ it[1] }) - .mix(BISMARK_METHYLATIONEXTRACTOR.out.mbias.collect{ it[1] }) - .mix(BISMARK_REPORT.out.report.collect{ it[1] }) - .set{ multiqc_files } - - emit: - bam = SAMTOOLS_SORT_ALIGNED.out.bam // channel: [ val(meta), [ bam ] ] ## sorted, non-deduplicated (raw) BAM from aligner - dedup = SAMTOOLS_SORT_DEDUPLICATED.out.bam // channel: [ val(meta), [ bam ] ] ## sorted, possibly deduplicated BAM - mqc = multiqc_files // path: *{html,txt} - versions = ch_versions // path: *.version.txt -} diff --git a/subworkflows/local/bismark/nextflow.config b/subworkflows/local/bismark/nextflow.config deleted file mode 100644 index d58d65ad..00000000 --- a/subworkflows/local/bismark/nextflow.config +++ /dev/null @@ -1,32 +0,0 @@ - -includeConfig "../../../modules/nf-core/bismark/align/nextflow.config" -includeConfig "../../../modules/nf-core/samtools/sort/nextflow.config" -includeConfig "../../../modules/nf-core/bismark/deduplicate/nextflow.config" -includeConfig "../../../modules/nf-core/bismark/methylationextractor/nextflow.config" -includeConfig "../../../modules/nf-core/bismark/coverage2cytosine/nextflow.config" -includeConfig "../../../modules/nf-core/bismark/report/nextflow.config" -includeConfig "../../../modules/nf-core/bismark/summary/nextflow.config" - -process { - withName: SAMTOOLS_SORT_DEDUPLICATED { - ext.prefix = { "${meta.id}.deduplicated.sorted" } - publishDir = [ - [ - path: { "${params.outdir}/${params.aligner}/deduplicated/" }, - mode: params.publish_dir_mode, - pattern: "*.deduplicated.sorted.bam" - ] - ] - } - - withName: SAMTOOLS_INDEX_DEDUPLICATED { - ext.args = "" - publishDir = [ - [ - path: { "${params.outdir}/${params.aligner}/deduplicated/" }, - mode: params.publish_dir_mode, - pattern: "*.bai" - ] - ] - } -} diff --git a/subworkflows/local/bismark/tests/bismark_hisat.nf.test b/subworkflows/local/bismark/tests/bismark_hisat.nf.test deleted file mode 100644 index 1f1070b3..00000000 --- a/subworkflows/local/bismark/tests/bismark_hisat.nf.test +++ /dev/null @@ -1,70 +0,0 @@ -nextflow_workflow { - - name "Test Workflow BISMARK_HISAT" - script "../main.nf" - workflow "BISMARK" - config "../nextflow.config" - - setup { - run("UNTAR") { - script "../../../../modules/nf-core/untar/main.nf" - process { - """ - input[0] = [ - [:], - file(params.pipelines_testdata_base_path + 'reference/Hisat2_Index.tar.gz', checkIfExists: true) - ] - """ - } - } - } - - test("Bismark_Hisat | save_reference") { - - when { - params { - aligner = "bismark_hisat" - publish_dir_mode = 'copy' - unmapped = false - save_align_intermeds = false - skip_deduplication = false - cytosine_report = false - rrbs = false - nomeseq = false - slamseq = false - save_reference = true - outdir = "results" - } - 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] = 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 - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - workflow.out.bam.collect { bam(it[1]).getReadsMD5() }, - workflow.out.dedup.collect { bam(it[1]).getReadsMD5() }, - //workflow.out.mqc, - workflow.out.versions - ).match() } - ) - } - - } - -} diff --git a/subworkflows/local/bismark/tests/bismark_hisat.nf.test.snap b/subworkflows/local/bismark/tests/bismark_hisat.nf.test.snap deleted file mode 100644 index a531a2e7..00000000 --- a/subworkflows/local/bismark/tests/bismark_hisat.nf.test.snap +++ /dev/null @@ -1,27 +0,0 @@ -{ - "Bismark_Hisat | save_reference": { - "content": [ - [ - "3a6485d719fcaf868c7f95c8f10a3f3c" - ], - [ - "dae445da532c973dc9149f3ceba2d2c5" - ], - [ - "versions.yml:md5,2273d537ccb64f2260adeb6844523d73", - "versions.yml:md5,6a04613f312dd68246d992a7f6fa03a5", - "versions.yml:md5,c06f3e25000330e948f7a35708270f3f", - "versions.yml:md5,c2ad6c469b4d15c963f03b2228376a80", - "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": "2024-10-20T11:17:46.351442694" - } -} diff --git a/subworkflows/local/bismark/tests/main.nf.test b/subworkflows/local/bismark/tests/main.nf.test deleted file mode 100644 index b38cbdbc..00000000 --- a/subworkflows/local/bismark/tests/main.nf.test +++ /dev/null @@ -1,70 +0,0 @@ -nextflow_workflow { - - name "Test Workflow BISMARK" - script "../main.nf" - workflow "BISMARK" - config "../nextflow.config" - - setup { - run("UNTAR") { - script "../../../../modules/nf-core/untar/main.nf" - process { - """ - input[0] = [ - [:], - file(params.pipelines_testdata_base_path + 'reference/Bowtie2_Index.tar.gz', checkIfExists: true) - ] - """ - } - } - } - - test("Bismark | save_reference") { - - when { - params { - aligner = "bismark" - publish_dir_mode = 'copy' - unmapped = false - save_align_intermeds = false - skip_deduplication = false - cytosine_report = false - rrbs = false - nomeseq = false - slamseq = false - save_reference = true - outdir = "results" - } - 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] = 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 - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - workflow.out.bam.collect { bam(it[1]).getReadsMD5() }, - workflow.out.dedup.collect { bam(it[1]).getReadsMD5() }, - //workflow.out.mqc, - workflow.out.versions - ).match() } - ) - } - - } - -} diff --git a/subworkflows/local/bismark/tests/main.nf.test.snap b/subworkflows/local/bismark/tests/main.nf.test.snap deleted file mode 100644 index 6757ea79..00000000 --- a/subworkflows/local/bismark/tests/main.nf.test.snap +++ /dev/null @@ -1,27 +0,0 @@ -{ - "Bismark | save_reference": { - "content": [ - [ - "d6951f6d3381e22becf62553a37c0f3f" - ], - [ - "35d55bee1ca653931716e40dac4aba30" - ], - [ - "versions.yml:md5,2273d537ccb64f2260adeb6844523d73", - "versions.yml:md5,6a04613f312dd68246d992a7f6fa03a5", - "versions.yml:md5,c06f3e25000330e948f7a35708270f3f", - "versions.yml:md5,c2ad6c469b4d15c963f03b2228376a80", - "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": "2024-10-20T11:14:29.732866935" - } -} diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf b/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf new file mode 100644 index 00000000..e5f2ffe5 --- /dev/null +++ b/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf @@ -0,0 +1,154 @@ +include { BISMARK_ALIGN } from '../../../modules/nf-core/bismark/align/main' +include { BISMARK_DEDUPLICATE } from '../../../modules/nf-core/bismark/deduplicate/main' +include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' +include { BISMARK_METHYLATIONEXTRACTOR } from '../../../modules/nf-core/bismark/methylationextractor/main' +include { BISMARK_COVERAGE2CYTOSINE } from '../../../modules/nf-core/bismark/coverage2cytosine/main' +include { BISMARK_REPORT } from '../../../modules/nf-core/bismark/report/main' +include { BISMARK_SUMMARY } from '../../../modules/nf-core/bismark/summary/main' + +workflow FASTQ_ALIGN_DEDUP_BISMARK { + + take: + ch_reads // channel: [ val(meta), [ reads ] ] + ch_fasta // channel: [ val(meta), [ fasta ] ] + ch_bismark_index // channel: [ val(meta), [ bismark index ] ] + skip_deduplication // boolean: whether to deduplicate alignments + cytosine_report // boolean: whether the run coverage2cytosine + + main: + ch_alignments = Channel.empty() + ch_alignment_reports = Channel.empty() + ch_methylation_bedgraph = Channel.empty() + ch_methylation_calls = Channel.empty() + ch_methylation_coverage = Channel.empty() + ch_methylation_report = Channel.empty() + ch_methylation_mbias = Channel.empty() + ch_coverage2cytosine_coverage = Channel.empty() + ch_coverage2cytosine_report = Channel.empty() + ch_coverage2cytosine_summary = Channel.empty() + ch_bismark_report = Channel.empty() + ch_bismark_summary = Channel.empty() + ch_multiqc_files = Channel.empty() + ch_versions = Channel.empty() + + /* + * Align with bismark + */ + BISMARK_ALIGN ( + ch_reads, + ch_fasta, + ch_bismark_index + ) + ch_alignments = BISMARK_ALIGN.out.bam + ch_alignment_reports = BISMARK_ALIGN.out.report.map{ meta, report -> [ meta, report, [] ] } + ch_versions = ch_versions.mix(BISMARK_ALIGN.out.versions) + + if (!skip_deduplication) { + /* + * Run deduplicate_bismark + */ + BISMARK_DEDUPLICATE ( + BISMARK_ALIGN.out.bam + ) + ch_alignments = BISMARK_DEDUPLICATE.out.bam + ch_alignment_reports = BISMARK_ALIGN.out.report.join(BISMARK_DEDUPLICATE.out.report) + ch_versions = ch_versions.mix(BISMARK_DEDUPLICATE.out.versions) + } + + /* + * MODULE: Run samtools sort on aligned or deduplicated bam + */ + SAMTOOLS_SORT ( + ch_alignments, + [[:],[]] // [ [meta], [fasta]] + ) + ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions) + + /* + * MODULE: Run samtools index on aligned or deduplicated bam + */ + SAMTOOLS_INDEX ( + SAMTOOLS_SORT.out.bam + ) + ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions) + + /* + * Run bismark_methylation_extractor + */ + BISMARK_METHYLATIONEXTRACTOR ( + ch_alignments, + ch_bismark_index + ) + ch_methylation_bedgraph = BISMARK_METHYLATIONEXTRACTOR.out.bedgraph + ch_methylation_calls = BISMARK_METHYLATIONEXTRACTOR.out.methylation_calls + ch_methylation_coverage = BISMARK_METHYLATIONEXTRACTOR.out.coverage + ch_methylation_report = BISMARK_METHYLATIONEXTRACTOR.out.report + ch_methylation_mbias = BISMARK_METHYLATIONEXTRACTOR.out.mbias + ch_versions = ch_versions.mix(BISMARK_METHYLATIONEXTRACTOR.out.versions) + + /* + * Run bismark coverage2cytosine + */ + if (cytosine_report) { + BISMARK_COVERAGE2CYTOSINE ( + ch_methylation_coverage, + ch_fasta, + ch_bismark_index + ) + ch_coverage2cytosine_coverage = BISMARK_COVERAGE2CYTOSINE.out.coverage + ch_coverage2cytosine_report = BISMARK_COVERAGE2CYTOSINE.out.report + ch_coverage2cytosine_summary = BISMARK_COVERAGE2CYTOSINE.out.summary + ch_versions = ch_versions.mix(BISMARK_COVERAGE2CYTOSINE.out.versions) + } + + /* + * Generate bismark sample reports + */ + BISMARK_REPORT ( + ch_alignment_reports + .join(ch_methylation_report) + .join(ch_methylation_mbias) + ) + ch_bismark_report = BISMARK_REPORT.out.report + ch_versions = ch_versions.mix(BISMARK_REPORT.out.versions) + + /* + * Generate bismark summary report + */ + BISMARK_SUMMARY ( + BISMARK_ALIGN.out.bam.collect{ meta, bam -> bam.name }, + ch_alignment_reports.collect{ meta, align_report, dedup_report -> align_report }, + ch_alignment_reports.collect{ meta, align_report, dedup_report -> dedup_report }.ifEmpty([]), + ch_methylation_report.collect{ meta, report -> report }, + ch_methylation_mbias.collect{ meta, mbias -> mbias } + ) + ch_bismark_summary = BISMARK_SUMMARY.out.summary + ch_versions = ch_versions.mix(BISMARK_SUMMARY.out.versions) + + /* + * Collect MultiQC inputs + */ + ch_multiqc_files = ch_bismark_summary + .mix(ch_alignment_reports.collect{ meta, align_report, dedup_report -> align_report }) + .mix(ch_alignment_reports.collect{ meta, align_report, dedup_report -> dedup_report }) + .mix(ch_methylation_report.collect{ meta, report -> report }) + .mix(ch_methylation_mbias.collect{ meta, mbias -> mbias }) + .mix(ch_bismark_report.collect{ meta, report -> report }) + + emit: + bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), [ bam ] ] + bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), [ bai ] ] + coverage2cytosine_coverage = ch_coverage2cytosine_coverage // channel: [ val(meta), [ coverage ] ] + coverage2cytosine_report = ch_coverage2cytosine_report // channel: [ val(meta), [ report ] ] + coverage2cytosine_summary = ch_coverage2cytosine_summary // channel: [ val(meta), [ summary ] ] + methylation_bedgraph = ch_methylation_bedgraph // channel: [ val(meta), [ bedgraph ] ] + methylation_calls = ch_methylation_calls // channel: [ val(meta), [ methylation_calls ] ] + methylation_coverage = ch_methylation_coverage // channel: [ val(meta), [ coverage ] ] + methylation_report = ch_methylation_report // channel: [ val(meta), [ report ] ] + methylation_mbias = ch_methylation_mbias // channel: [ val(meta), [ mbias ] ] + bismark_report = ch_bismark_report // channel: [ val(meta), [ report ] ] + bismark_summary = ch_bismark_summary // channel: [ val(meta), [ summary ] ] + multiqc = ch_multiqc_files // path: *{html,txt} + versions = ch_versions // path: *.version.txt +} diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/meta.yml b/subworkflows/nf-core/fastq_align_dedup_bismark/meta.yml new file mode 100644 index 00000000..7622b98e --- /dev/null +++ b/subworkflows/nf-core/fastq_align_dedup_bismark/meta.yml @@ -0,0 +1,136 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "fastq_align_dedup_bismark" +description: Align BS-Seq reads to a reference genome using bismark, deduplicate and sort +keywords: + - bismark + - 3-letter genome + - map + - methylation + - 5mC + - methylseq + - bisulphite + - bisulfite + - bam +components: + - bismark/align + - samtools/sort + - samtools/index + - bismark/deduplicate + - bismark/methylationextractor + - bismark/coverage2cytosine + - bismark/report + - bismark/summary +input: + - ch_reads: + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + Structure: [ val(meta), [ path(reads) ] ] + pattern: "*.{fastq,fastq.gz}" + - ch_fasta: + type: file + description: | + Structure: [ val(meta), path(fasta) ] + pattern: "*.{fa,fa.gz}" + - ch_bismark_index: + description: | + Bismark genome index files + Structure: [ val(meta), path(index) ] + pattern: "BismarkIndex" + - skip_deduplication: + type: boolean + description: | + Skip deduplication of aligned reads + - cytosine_report: + type: boolean + description: | + Produce coverage2cytosine reports that relates methylation calls back to genomic cytosine contexts +output: + - bam: + type: file + description: | + Channel containing aligned or deduplicated BAM files. + Structure: [ val(meta), path(bam) ] + pattern: "*.bam" + - bai: + type: file + description: | + Channel containing aligned or deduplicated BAM index files. + Structure: [ val(meta), path(bam.bai) ] + pattern: "*.bai" + - coverage2cytosine_coverage: + type: file + description: | + Channel containing coverage information from coverage2cytosine. + Structure: [ val(meta), path(coverage.txt) ] + pattern: "*.cov.gz" + - coverage2cytosine_report: + type: file + description: | + Channel containing report from coverage2cytosine summarizing cytosine methylation coverage. + Structure: [ val(meta), path(report.txt) ] + pattern: "*report.txt.gz" + - coverage2cytosine_summary: + type: file + description: | + Channel containing summary information from coverage2cytosine. + Structure: [ val(meta), path(summary.txt) ] + pattern: "*cytosine_context_summary.txt" + - methylation_bedgraph: + type: file + description: | + Channel containing methylation data in bedGraph format. + Structure: [ val(meta), path(methylation.bedgraph) ] + pattern: "*.bedGraph.gz" + - methylation_calls: + type: file + description: | + Channel containing methylation call data. + Structure: [ val(meta), path(calls.txt) ] + pattern: "*.txt.gz" + - methylation_coverage: + type: file + description: | + Channel containing methylation coverage data. + Structure: [ val(meta), path(coverage.txt) ] + pattern: "*.cov.gz" + - methylation_report: + type: file + description: | + Channel containing methylation report detailing methylation patterns. + Structure: [ val(meta), path(report.txt) ] + pattern: "*_splitting_report.txt" + - methylation_mbias: + type: file + description: | + Channel containing M-bias report showing methylation bias across read positions. + Structure: [ val(meta), path(mbias.txt) ] + pattern: "*.M-bias.txt" + - bismark_report: + type: file + description: | + Channel containing Bismark report with mapping and methylation statistics. + Structure: [ val(meta), path(bismark_report.txt) ] + pattern: "*report.{html,txt}" + - bismark_summary: + type: file + description: | + Channel containing Bismark summary report. + Structure: [ val(meta), path(bismark_summary.txt) ] + pattern: "*report.{html,txt}" + - multiqc: + type: file + description: | + Channel containing MultiQC report aggregating results across samples. + Structure: [ val(meta), path(multiqc_report.html) ] + pattern: "*.html" + - versions: + type: file + description: | + File containing software versions. + Structure: [ path(versions.yml) ] + pattern: "versions.yml" +authors: + - "@sateeshperi" +maintainers: + - "@sateeshperi" diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/nextflow.config b/subworkflows/nf-core/fastq_align_dedup_bismark/nextflow.config new file mode 100644 index 00000000..03e07673 --- /dev/null +++ b/subworkflows/nf-core/fastq_align_dedup_bismark/nextflow.config @@ -0,0 +1,8 @@ +includeConfig "../../../modules/nf-core/bismark/align/nextflow.config" +includeConfig "../../../modules/nf-core/bismark/deduplicate/nextflow.config" +includeConfig "../../../modules/nf-core/samtools/sort/nextflow.config" +includeConfig "../../../modules/nf-core/samtools/index/nextflow.config" +includeConfig "../../../modules/nf-core/bismark/methylationextractor/nextflow.config" +includeConfig "../../../modules/nf-core/bismark/coverage2cytosine/nextflow.config" +includeConfig "../../../modules/nf-core/bismark/report/nextflow.config" +includeConfig "../../../modules/nf-core/bismark/summary/nextflow.config" \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test new file mode 100644 index 00000000..27bf692a --- /dev/null +++ b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test @@ -0,0 +1,440 @@ +nextflow_workflow { + + name "Test Subworkflow FASTQ_ALIGN_DEDUP_BISMARK" + script "../main.nf" + workflow "FASTQ_ALIGN_DEDUP_BISMARK" + config "./nextflow.config" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/fastq_align_dedup_bismark" + tag "bismark/align" + tag "samtools/sort" + tag "samtools/index" + tag "bismark/deduplicate" + tag "bismark/methylationextractor" + tag "bismark/coverage2cytosine" + tag "bismark/report" + tag "bismark/summary" + tag "untar" + + setup { + run("UNTAR", alias: "BOWTIE2") { + script "../../../../modules/nf-core/untar/main.nf" + process { + """ + input[0] = [ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz', checkIfExists: true) + ] + """ + } + } + + run("UNTAR", alias: "HISAT2") { + script "../../../../modules/nf-core/untar/main.nf" + process { + """ + input[0] = [ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz', checkIfExists: true) + ] + """ + } + } + } + + test("Params: bismark single-end | default") { + + when { + params { + aligner = "bismark" + cytosine_report = false + skip_deduplication = false + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = BOWTIE2.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.coverage2cytosine_coverage, + workflow.out.coverage2cytosine_report, + workflow.out.coverage2cytosine_summary, + workflow.out.methylation_bedgraph, + workflow.out.methylation_calls, + workflow.out.methylation_coverage, + workflow.out.methylation_report, + workflow.out.methylation_mbias, + workflow.out.bismark_report.collect { meta, report -> file(report).name }, + workflow.out.bismark_summary[0][1], + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark paired-end | default") { + + when { + params { + aligner = "bismark" + cytosine_report = false + skip_deduplication = false + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = BOWTIE2.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.coverage2cytosine_coverage, + workflow.out.coverage2cytosine_report, + workflow.out.coverage2cytosine_summary, + workflow.out.methylation_bedgraph, + workflow.out.methylation_calls, + workflow.out.methylation_coverage, + workflow.out.methylation_report, + workflow.out.methylation_mbias, + workflow.out.bismark_report.collect { meta, report -> file(report).name }, + workflow.out.bismark_summary[0][1], + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark paired-end | skip_deduplication") { + + when { + params { + aligner = "bismark" + skip_deduplication = true + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = BOWTIE2.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.coverage2cytosine_coverage, + workflow.out.coverage2cytosine_report, + workflow.out.coverage2cytosine_summary, + workflow.out.methylation_bedgraph, + workflow.out.methylation_calls, + workflow.out.methylation_coverage, + workflow.out.methylation_report, + workflow.out.methylation_mbias, + workflow.out.bismark_report.collect { meta, report -> file(report).name }, + workflow.out.bismark_summary[0][1], + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark paired-end | cytosine_report") { + + when { + params { + aligner = "bismark" + cytosine_report = true + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = BOWTIE2.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.coverage2cytosine_coverage, + workflow.out.coverage2cytosine_report, + workflow.out.coverage2cytosine_summary, + workflow.out.methylation_bedgraph, + workflow.out.methylation_calls, + workflow.out.methylation_coverage, + workflow.out.methylation_report, + workflow.out.methylation_mbias, + workflow.out.bismark_report.collect { meta, report -> file(report).name }, + workflow.out.bismark_summary[0][1], + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark_hisat single-end | default") { + + when { + params { + aligner = "bismark_hisat" + cytosine_report = false + skip_deduplication = false + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = HISAT2.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.coverage2cytosine_coverage, + workflow.out.coverage2cytosine_report, + workflow.out.coverage2cytosine_summary, + workflow.out.methylation_bedgraph, + workflow.out.methylation_calls, + workflow.out.methylation_coverage, + workflow.out.methylation_report, + workflow.out.methylation_mbias, + workflow.out.bismark_report.collect { meta, report -> file(report).name }, + workflow.out.bismark_summary[0][1], + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark_hisat paired-end | default") { + + when { + params { + aligner = "bismark_hisat" + cytosine_report = false + skip_deduplication = false + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = HISAT2.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.coverage2cytosine_coverage, + workflow.out.coverage2cytosine_report, + workflow.out.coverage2cytosine_summary, + workflow.out.methylation_bedgraph, + workflow.out.methylation_calls, + workflow.out.methylation_coverage, + workflow.out.methylation_report, + workflow.out.methylation_mbias, + workflow.out.bismark_report.collect { meta, report -> file(report).name }, + workflow.out.bismark_summary[0][1], + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark_hisat paired-end | skip_deduplication") { + + when { + params { + aligner = "bismark_hisat" + skip_deduplication = true + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = HISAT2.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.coverage2cytosine_coverage, + workflow.out.coverage2cytosine_report, + workflow.out.coverage2cytosine_summary, + workflow.out.methylation_bedgraph, + workflow.out.methylation_calls, + workflow.out.methylation_coverage, + workflow.out.methylation_report, + workflow.out.methylation_mbias, + workflow.out.bismark_report.collect { meta, report -> file(report).name }, + workflow.out.bismark_summary[0][1], + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark_hisat paired-end | cytosine_report") { + + when { + params { + aligner = "bismark_hisat" + cytosine_report = true + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = HISAT2.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.coverage2cytosine_coverage, + workflow.out.coverage2cytosine_report, + workflow.out.coverage2cytosine_summary, + workflow.out.methylation_bedgraph, + workflow.out.methylation_calls, + workflow.out.methylation_coverage, + workflow.out.methylation_report, + workflow.out.methylation_mbias, + workflow.out.bismark_report.collect { meta, report -> file(report).name }, + workflow.out.bismark_summary[0][1], + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap new file mode 100644 index 00000000..a4d82189 --- /dev/null +++ b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap @@ -0,0 +1,808 @@ +{ + "Params: bismark_hisat paired-end | default": { + "content": [ + [ + "4bf31467bec7b5d5669aa4ac16f6f93f" + ], + [ + "test.sorted.bam.bai" + ], + [ + + ], + [ + + ], + [ + + ], + [ + [ + { 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"id": "test", + "single_end": true + }, + "Ecoli_10K_methylated_R1_bismark_bt2.deduplicated.M-bias.txt:md5,857b28589351f2c63f587a2c040db748" + ] + ], + [ + "Ecoli_10K_methylated_R1_bismark_bt2_SE_report.html" + ], + "bismark_summary_report.txt:md5,855dfc95b1dbb0876aff2831380bba99", + [ + "Ecoli_10K_methylated_R1_bismark_bt2.deduplicated.M-bias.txt", + "Ecoli_10K_methylated_R1_bismark_bt2.deduplicated_splitting_report.txt", + "Ecoli_10K_methylated_R1_bismark_bt2.deduplication_report.txt", + "Ecoli_10K_methylated_R1_bismark_bt2_SE_report.html", + "Ecoli_10K_methylated_R1_bismark_bt2_SE_report.txt", + "bismark_summary_report.html", + "bismark_summary_report.txt" + ], + [ + "versions.yml:md5,46e043d0037e7446544ae1e25b65536c", + "versions.yml:md5,6b5bf82c070f4410ead76cc9a363529c", + "versions.yml:md5,6f2f867f534bb0ae0ffbdc52d036afce", + "versions.yml:md5,9b480db277eebeb6265cbd003553c22c", + "versions.yml:md5,a675051417ba65700b5db32d98aa65b6", + "versions.yml:md5,aa64d431e6cfc5ffcbd5012a76b0c1a3", + "versions.yml:md5,c2438ca96ec6728b06c8706639eb233c" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-17T05:10:47.730967756" + }, + "Params: bismark_hisat paired-end | skip_deduplication": { + "content": [ + [ + "4bf31467bec7b5d5669aa4ac16f6f93f" + ], + [ + "test.sorted.bam.bai" + ], + [ + + ], + [ + + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "Ecoli_10K_methylated_R1_bismark_hisat2.bedGraph.gz:md5,036f675959865a43f49899108d53b546" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + [ + "CHG_OB_Ecoli_10K_methylated_R1_bismark_hisat2.txt.gz:md5,2c1285905b97b35a9088f811e2bda70e", + "CHG_OT_Ecoli_10K_methylated_R1_bismark_hisat2.txt.gz:md5,473499e02bab8a14f8c804746bc98486", + "CHH_OB_Ecoli_10K_methylated_R1_bismark_hisat2.txt.gz:md5,dda9a584b2a9bc7b84d39fe6210f8bfc", + "CHH_OT_Ecoli_10K_methylated_R1_bismark_hisat2.txt.gz:md5,265670d72805a8689afe35ace9a7148a", + "CpG_OB_Ecoli_10K_methylated_R1_bismark_hisat2.txt.gz:md5,d2912083fda7c2b4ad5916fe9cd8acf7", + "CpG_OT_Ecoli_10K_methylated_R1_bismark_hisat2.txt.gz:md5,3f1d464af4efb77956f06546eabf8f1a" + ] + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "Ecoli_10K_methylated_R1_bismark_hisat2.bismark.cov.gz:md5,63511c46275713088957950285acd653" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "Ecoli_10K_methylated_R1_bismark_hisat2_splitting_report.txt:md5,7767e575a343a9b077dcd03e594550f1" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "Ecoli_10K_methylated_R1_bismark_hisat2.M-bias.txt:md5,857b28589351f2c63f587a2c040db748" + ] + ], + [ + "Ecoli_10K_methylated_R1_bismark_hisat2_SE_report.html" + ], + "bismark_summary_report.txt:md5,dd73bb37e3116c25480990bd37f3f99f", + [ + "Ecoli_10K_methylated_R1_bismark_hisat2.M-bias.txt", + "Ecoli_10K_methylated_R1_bismark_hisat2_SE_report.html", + "Ecoli_10K_methylated_R1_bismark_hisat2_SE_report.txt", + "Ecoli_10K_methylated_R1_bismark_hisat2_splitting_report.txt", + "bismark_summary_report.html", + "bismark_summary_report.txt" + ], + [ + "versions.yml:md5,46e043d0037e7446544ae1e25b65536c", + "versions.yml:md5,6b5bf82c070f4410ead76cc9a363529c", + "versions.yml:md5,6f2f867f534bb0ae0ffbdc52d036afce", + "versions.yml:md5,9b480db277eebeb6265cbd003553c22c", + "versions.yml:md5,aa64d431e6cfc5ffcbd5012a76b0c1a3", + "versions.yml:md5,c2438ca96ec6728b06c8706639eb233c" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-17T05:13:57.892659443" + }, + "Params: bismark paired-end | skip_deduplication": { + "content": [ + [ + "4bf31467bec7b5d5669aa4ac16f6f93f" + ], + [ + "test.sorted.bam.bai" + ], + [ + + ], + [ + + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "Ecoli_10K_methylated_R1_bismark_bt2.bedGraph.gz:md5,036f675959865a43f49899108d53b546" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + [ + "CHG_OB_Ecoli_10K_methylated_R1_bismark_bt2.txt.gz:md5,2c1285905b97b35a9088f811e2bda70e", + "CHG_OT_Ecoli_10K_methylated_R1_bismark_bt2.txt.gz:md5,473499e02bab8a14f8c804746bc98486", + "CHH_OB_Ecoli_10K_methylated_R1_bismark_bt2.txt.gz:md5,dda9a584b2a9bc7b84d39fe6210f8bfc", + "CHH_OT_Ecoli_10K_methylated_R1_bismark_bt2.txt.gz:md5,265670d72805a8689afe35ace9a7148a", + "CpG_OB_Ecoli_10K_methylated_R1_bismark_bt2.txt.gz:md5,d2912083fda7c2b4ad5916fe9cd8acf7", + "CpG_OT_Ecoli_10K_methylated_R1_bismark_bt2.txt.gz:md5,3f1d464af4efb77956f06546eabf8f1a" + ] + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "Ecoli_10K_methylated_R1_bismark_bt2.bismark.cov.gz:md5,63511c46275713088957950285acd653" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "Ecoli_10K_methylated_R1_bismark_bt2_splitting_report.txt:md5,39c7721863c121645d68a4827e57ec77" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "Ecoli_10K_methylated_R1_bismark_bt2.M-bias.txt:md5,857b28589351f2c63f587a2c040db748" + ] + ], + [ + "Ecoli_10K_methylated_R1_bismark_bt2_SE_report.html" + ], + "bismark_summary_report.txt:md5,9f639cca6fe43c0461d2da88d931a036", + [ + "Ecoli_10K_methylated_R1_bismark_bt2.M-bias.txt", + "Ecoli_10K_methylated_R1_bismark_bt2_SE_report.html", + "Ecoli_10K_methylated_R1_bismark_bt2_SE_report.txt", + "Ecoli_10K_methylated_R1_bismark_bt2_splitting_report.txt", + "bismark_summary_report.html", + "bismark_summary_report.txt" + ], + [ + "versions.yml:md5,46e043d0037e7446544ae1e25b65536c", + "versions.yml:md5,6b5bf82c070f4410ead76cc9a363529c", + "versions.yml:md5,6f2f867f534bb0ae0ffbdc52d036afce", + "versions.yml:md5,9b480db277eebeb6265cbd003553c22c", + "versions.yml:md5,aa64d431e6cfc5ffcbd5012a76b0c1a3", + "versions.yml:md5,c2438ca96ec6728b06c8706639eb233c" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-17T05:11:19.884389766" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/tests/nextflow.config b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/nextflow.config new file mode 100644 index 00000000..8d94d8ff --- /dev/null +++ b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/nextflow.config @@ -0,0 +1,15 @@ +params { + aligner = "bismark" + cytosine_report = false + skip_deduplication = false +} + +process { + withName: 'BISMARK_ALIGN' { + ext.args = { params.aligner == 'bismark_hisat' ? ' --hisat2' : ' --bowtie2' } + } + + withName: 'SAMTOOLS_SORT' { + ext.prefix = { "${meta.id}.sorted" } + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 0fcbf7b3..d6e593e8 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -92,10 +92,12 @@ def checkCondaChannels() { channels = config.channels } catch (NullPointerException e) { + log.debug(e) log.warn("Could not verify conda channel configuration.") return null } catch (IOException e) { + log.debug(e) log.warn("Could not verify conda channel configuration.") return null } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index ca964ce8..02dbf094 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -52,10 +52,12 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } - ) + expect { + with(workflow) { + assert success + assert "nextflow_workflow v9.9.9" in stdout + } + } } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 5cb7bafe..4cd33626 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -261,7 +261,8 @@ def attachMultiqcReport(multiqc_report) { } } } - catch (Exception all) { + catch (Exception msg) { + log.debug(msg) if (multiqc_report) { log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email") } @@ -358,7 +359,9 @@ new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') ['sendmail', '-t'].execute() << sendmail_html log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") } - catch (Exception all) { + catch (Exception msg) { + log.debug(msg) + log.debug("Trying with mail instead of sendmail") // Catch failures and try with plaintext def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] mail_cmd.execute() << email_html diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test index 842dc432..8fb30164 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -42,7 +42,7 @@ nextflow_workflow { params { test_data = '' - outdir = 1 + outdir = null } workflow { @@ -94,7 +94,7 @@ nextflow_workflow { params { test_data = '' - outdir = 1 + outdir = null } workflow { diff --git a/tests/bismark_emseq_clip_r1.nf.test.snap b/tests/bismark_emseq_clip_r1.nf.test.snap index 8cf448f0..2fbc0269 100644 --- a/tests/bismark_emseq_clip_r1.nf.test.snap +++ b/tests/bismark_emseq_clip_r1.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bismark | em_seq | clip_r1": { "content": [ - 44, + 40, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -580,6 +580,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-26T05:15:58.208167729" + "timestamp": "2024-11-26T08:52:00.954651917" } } \ No newline at end of file diff --git a/tests/bismark_hisat.nf.test.snap b/tests/bismark_hisat.nf.test.snap index 31bb8153..ff12de0b 100644 --- a/tests/bismark_hisat.nf.test.snap +++ b/tests/bismark_hisat.nf.test.snap @@ -1,17 +1,17 @@ { "Params: bismark_hisat with hisat2-index": { "content": [ - 44 + 40 ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-26T05:19:59.406677987" + "timestamp": "2024-11-26T08:55:42.808484694" }, "Params: bismark_hisat": { "content": [ - 44, + 40, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -592,6 +592,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-26T05:18:01.013706514" + "timestamp": "2024-11-26T08:53:51.469200211" } } \ 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 ef51f756..45251d0e 100644 --- a/tests/bismark_hisat_rrbs.nf.test.snap +++ b/tests/bismark_hisat_rrbs.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bismark_hisat | rrbs": { "content": [ - 40, + 36, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -585,6 +585,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-26T05:22:36.565902084" + "timestamp": "2024-11-26T08:57:57.525885941" } } \ 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 d4d047c2..2e94e52c 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 @@ -1,7 +1,7 @@ { "Params: bismark_hisat | save_reference | save_align_intermeds": { "content": [ - 44, + 40, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -29,13 +29,13 @@ [ "bismark_hisat", "bismark_hisat/alignments", - "bismark_hisat/alignments/Ecoli_10K_methylated.sorted.bam", + "bismark_hisat/alignments/Ecoli_10K_methylated.deduplicated.sorted.bam", "bismark_hisat/alignments/Ecoli_10K_methylated_1_val_1_bismark_hisat2_pe.bam", - "bismark_hisat/alignments/SRR389222_sub1.sorted.bam", + "bismark_hisat/alignments/SRR389222_sub1.deduplicated.sorted.bam", "bismark_hisat/alignments/SRR389222_sub1_trimmed_bismark_hisat2.bam", - "bismark_hisat/alignments/SRR389222_sub2.sorted.bam", + "bismark_hisat/alignments/SRR389222_sub2.deduplicated.sorted.bam", "bismark_hisat/alignments/SRR389222_sub2_trimmed_bismark_hisat2.bam", - "bismark_hisat/alignments/SRR389222_sub3.sorted.bam", + "bismark_hisat/alignments/SRR389222_sub3.deduplicated.sorted.bam", "bismark_hisat/alignments/SRR389222_sub3_trimmed_bismark_hisat2.bam", "bismark_hisat/alignments/logs", "bismark_hisat/alignments/logs/Ecoli_10K_methylated_1_val_1_bismark_hisat2_PE_report.txt", @@ -612,7 +612,7 @@ ], [ [ - "Ecoli_10K_methylated.sorted.bam", + "Ecoli_10K_methylated.deduplicated.sorted.bam", "a1bd6455ebe3ecb43fe55e02d149d98" ], [ @@ -620,24 +620,24 @@ "534293d598c34366bcde057d3972b60" ], [ - "SRR389222_sub1.sorted.bam", - "b203a3936158c51706e56c3a4e16191e" + "SRR389222_sub1.deduplicated.sorted.bam", + "8d735d1f6337b2cf2fa720773ce34b60" ], [ "SRR389222_sub1_trimmed_bismark_hisat2.bam", "4ee84a71b73e58161226cc4d8ca1f9b9" ], [ - "SRR389222_sub2.sorted.bam", - "6f8b0d6f085cc6a3d597b8839ba94b8b" + "SRR389222_sub2.deduplicated.sorted.bam", + "45d53a598b4e59d173e32ea1f0558083" ], [ "SRR389222_sub2_trimmed_bismark_hisat2.bam", "3e3ccc351ed92abdced1edb24fbb94ed" ], [ - "SRR389222_sub3.sorted.bam", - "c03e8e797936ca18a7e286977c7cf16" + "SRR389222_sub3.deduplicated.sorted.bam", + "ddb15c5ef0686837616d73f45c154b8d" ], [ "SRR389222_sub3_trimmed_bismark_hisat2.bam", @@ -665,6 +665,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-26T05:24:34.153448411" + "timestamp": "2024-11-26T08:59:39.226471235" } } \ No newline at end of file diff --git a/tests/bismark_nomeseq.nf.test.snap b/tests/bismark_nomeseq.nf.test.snap index c24d5a6d..20408d1c 100644 --- a/tests/bismark_nomeseq.nf.test.snap +++ b/tests/bismark_nomeseq.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bismark | nomeseq": { "content": [ - 48, + 44, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -626,6 +626,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-26T05:26:36.822643371" + "timestamp": "2024-11-26T09:01:53.215628858" } } \ No newline at end of file diff --git a/tests/bismark_rrbs.nf.test.snap b/tests/bismark_rrbs.nf.test.snap index c01db616..5c429c06 100644 --- a/tests/bismark_rrbs.nf.test.snap +++ b/tests/bismark_rrbs.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bismark | rrbs": { "content": [ - 40, + 36, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -585,6 +585,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-26T05:28:59.98842641" + "timestamp": "2024-11-26T09:04:59.71267952" } } \ 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 8cdb3e73..8aec9139 100644 --- a/tests/bismark_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bismark | save_reference | save_align_intermeds": { "content": [ - 44, + 40, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -29,13 +29,13 @@ [ "bismark", "bismark/alignments", - "bismark/alignments/Ecoli_10K_methylated.sorted.bam", + "bismark/alignments/Ecoli_10K_methylated.deduplicated.sorted.bam", "bismark/alignments/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.bam", - "bismark/alignments/SRR389222_sub1.sorted.bam", + "bismark/alignments/SRR389222_sub1.deduplicated.sorted.bam", "bismark/alignments/SRR389222_sub1_trimmed_bismark_bt2.bam", - "bismark/alignments/SRR389222_sub2.sorted.bam", + "bismark/alignments/SRR389222_sub2.deduplicated.sorted.bam", "bismark/alignments/SRR389222_sub2_trimmed_bismark_bt2.bam", - "bismark/alignments/SRR389222_sub3.sorted.bam", + "bismark/alignments/SRR389222_sub3.deduplicated.sorted.bam", "bismark/alignments/SRR389222_sub3_trimmed_bismark_bt2.bam", "bismark/alignments/logs", "bismark/alignments/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_PE_report.txt", @@ -604,7 +604,7 @@ ], [ [ - "Ecoli_10K_methylated.sorted.bam", + "Ecoli_10K_methylated.deduplicated.sorted.bam", "a54ab7c96f9523a4ccd25fd69f6905f8" ], [ @@ -612,24 +612,24 @@ "fad4414ebdaafdb15e0584b393400b27" ], [ - "SRR389222_sub1.sorted.bam", - "fa0f34c0d0d4d321b89973f23e033aa1" + "SRR389222_sub1.deduplicated.sorted.bam", + "3f11ef5fbbda3797fd6217728e4f00d3" ], [ "SRR389222_sub1_trimmed_bismark_bt2.bam", "934288bfc59d40ff7e73706d07815fb" ], [ - "SRR389222_sub2.sorted.bam", - "d347232a4fc5b1e02e98254b6ce97ae6" + "SRR389222_sub2.deduplicated.sorted.bam", + "b01f29fc1d8d46922a69df09c636b4c4" ], [ "SRR389222_sub2_trimmed_bismark_bt2.bam", "a94aeadc2acebd0a46647bb95acf2d55" ], [ - "SRR389222_sub3.sorted.bam", - "29648af285a183ae2194790b5a325186" + "SRR389222_sub3.deduplicated.sorted.bam", + "347195c04c9ffd2a2b10967a6682fc69" ], [ "SRR389222_sub3_trimmed_bismark_bt2.bam", @@ -657,6 +657,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-26T05:31:07.656922689" + "timestamp": "2024-11-26T09:07:38.571423231" } } \ 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 69de2e25..118dfd7b 100644 --- a/tests/bismark_skip_deduplication.nf.test.snap +++ b/tests/bismark_skip_deduplication.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bismark | skip_deduplication": { "content": [ - 40, + 36, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -29,9 +29,17 @@ [ "bismark", "bismark/alignments", + "bismark/alignments/Ecoli_10K_methylated.sorted.bam", + "bismark/alignments/Ecoli_10K_methylated.sorted.bam.bai", "bismark/alignments/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.bam", + "bismark/alignments/SRR389222_sub1.sorted.bam", + "bismark/alignments/SRR389222_sub1.sorted.bam.bai", "bismark/alignments/SRR389222_sub1_trimmed_bismark_bt2.bam", + "bismark/alignments/SRR389222_sub2.sorted.bam", + "bismark/alignments/SRR389222_sub2.sorted.bam.bai", "bismark/alignments/SRR389222_sub2_trimmed_bismark_bt2.bam", + "bismark/alignments/SRR389222_sub3.sorted.bam", + "bismark/alignments/SRR389222_sub3.sorted.bam.bai", "bismark/alignments/SRR389222_sub3_trimmed_bismark_bt2.bam", "bismark/alignments/logs", "bismark/alignments/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_PE_report.txt", @@ -39,14 +47,6 @@ "bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", "bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", "bismark/deduplicated", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai", "bismark/methylation_calls", "bismark/methylation_calls/bedGraph", "bismark/methylation_calls/bedGraph/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.bedGraph.gz", @@ -543,43 +543,43 @@ "qualimap_gc_content.txt:md5,55baed387d09b5a0583ce2b5abfc0d12", "qualimap_genome_fraction.txt:md5,bde4b1a12ad8ad0420b44fa3f1ed0512", "qualimap_insert_size.txt:md5,8327f805cbaf1c61ca3128b6c16c7dfd", - "genome_results.txt:md5,e2a57140a56e0e4a1905c70084ccbb41", - "genome_results.txt:md5,e26877c78ca30a559d5697938181c786", - "genome_results.txt:md5,7cfeccc601bb4a823e0ccf6bd32b4fb4", - "genome_results.txt:md5,2dd07533db9b09442aa391aea7b9a91f" + "genome_results.txt:md5,7886cc1a96ee892e49898b0d69ed66f2", + "genome_results.txt:md5,520b434b304ccc96b2a9b8d2c7af5653", + "genome_results.txt:md5,50321f6d8ab88ef91a11b651ba0ec735", + "genome_results.txt:md5,9c2018ca775cbd5457d429f29718201b" ], [ [ - "Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.bam", - "fad4414ebdaafdb15e0584b393400b27" + "Ecoli_10K_methylated.sorted.bam", + "a54ab7c96f9523a4ccd25fd69f6905f8" ], [ - "SRR389222_sub1_trimmed_bismark_bt2.bam", - "934288bfc59d40ff7e73706d07815fb" + "Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.bam", + "fad4414ebdaafdb15e0584b393400b27" ], [ - "SRR389222_sub2_trimmed_bismark_bt2.bam", - "a94aeadc2acebd0a46647bb95acf2d55" + "SRR389222_sub1.sorted.bam", + "fa0f34c0d0d4d321b89973f23e033aa1" ], [ - "SRR389222_sub3_trimmed_bismark_bt2.bam", - "6579ca7e49b9d7760ea5b3f3456739a1" + "SRR389222_sub1_trimmed_bismark_bt2.bam", + "934288bfc59d40ff7e73706d07815fb" ], [ - "Ecoli_10K_methylated.deduplicated.sorted.bam", - "a54ab7c96f9523a4ccd25fd69f6905f8" + "SRR389222_sub2.sorted.bam", + "d347232a4fc5b1e02e98254b6ce97ae6" ], [ - "SRR389222_sub1.deduplicated.sorted.bam", - "fa0f34c0d0d4d321b89973f23e033aa1" + "SRR389222_sub2_trimmed_bismark_bt2.bam", + "a94aeadc2acebd0a46647bb95acf2d55" ], [ - "SRR389222_sub2.deduplicated.sorted.bam", - "d347232a4fc5b1e02e98254b6ce97ae6" + "SRR389222_sub3.sorted.bam", + "29648af285a183ae2194790b5a325186" ], [ - "SRR389222_sub3.deduplicated.sorted.bam", - "29648af285a183ae2194790b5a325186" + "SRR389222_sub3_trimmed_bismark_bt2.bam", + "6579ca7e49b9d7760ea5b3f3456739a1" ] ] ], @@ -587,6 +587,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-26T05:33:23.283562704" + "timestamp": "2024-11-26T09:09:57.750043344" } } \ 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 edcbc313..5af23d73 100644 --- a/tests/bismark_skip_multiqc.nf.test.snap +++ b/tests/bismark_skip_multiqc.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bismark | skip_multiqc": { "content": [ - 44, + 40, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -582,6 +582,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-26T05:35:27.933113343" + "timestamp": "2024-11-26T09:12:08.282174331" } } \ No newline at end of file diff --git a/tests/bismark_skip_trimming.nf.test.snap b/tests/bismark_skip_trimming.nf.test.snap index b5da93f3..1c1218f9 100644 --- a/tests/bismark_skip_trimming.nf.test.snap +++ b/tests/bismark_skip_trimming.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bismark | skip_trimming": { "content": [ - 40, + 36, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -539,6 +539,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-26T05:37:44.553089799" + "timestamp": "2024-11-26T09:13:42.068141055" } } \ No newline at end of file diff --git a/tests/bwameth.nf.test.snap b/tests/bwameth.nf.test.snap index b4616040..5e74c0f6 100644 --- a/tests/bwameth.nf.test.snap +++ b/tests/bwameth.nf.test.snap @@ -39,12 +39,16 @@ "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", "bwameth/deduplicated", + "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", "bwameth/deduplicated/picard_metrics", @@ -416,24 +420,40 @@ "samtools-flagstat-dp_Read_counts.txt:md5,6a5332e2ad59f7da00b5a9a1a25fd2f8", "samtools-stats-dp.txt:md5,52021b9a9455b39b39dd357bc2e8d346", "samtools_alignment_plot.txt:md5,39f42e039f96cc2b17248b44ccaf425b", - "genome_results.txt:md5,1ee2e29ac41c2cd7e6a0f00741e8d16e", - "genome_results.txt:md5,2c755b15ae5ad4a1d29395320a6264ca", - "genome_results.txt:md5,2294badeccd2e8870fd6c60d115687b0", - "genome_results.txt:md5,4da1144933d094185d02f7482c120804" + "genome_results.txt:md5,5e6ff1f186689e9d5128725e003d6224", + "genome_results.txt:md5,6ba4b4d1d2299ee67094cf8cc3b038b5", + "genome_results.txt:md5,ab83bbae50e739ce32ace6ecc4e57591", + "genome_results.txt:md5,fda50629865f661d97c8dc57072baab2" ], [ + [ + "Ecoli_10K_methylated.deduplicated.sorted.bam", + "a2921f761f431ede522016f83f75c12d" + ], [ "Ecoli_10K_methylated.markdup.sorted.bam", "a2921f761f431ede522016f83f75c12d" ], + [ + "SRR389222_sub1.deduplicated.sorted.bam", + "e50275d6d44138f19d65ee479444d5ce" + ], [ "SRR389222_sub1.markdup.sorted.bam", "e50275d6d44138f19d65ee479444d5ce" ], + [ + "SRR389222_sub2.deduplicated.sorted.bam", + "d365b8b2662b2abffb51dd67a1f463b4" + ], [ "SRR389222_sub2.markdup.sorted.bam", "d365b8b2662b2abffb51dd67a1f463b4" ], + [ + "SRR389222_sub3.deduplicated.sorted.bam", + "a9fd2900b9d759f8f4f62cbbb2744fde" + ], [ "SRR389222_sub3.markdup.sorted.bam", "a9fd2900b9d759f8f4f62cbbb2744fde" @@ -444,7 +464,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-26T05:41:22.192924801" + "timestamp": "2024-11-26T09:15:31.060582786" }, "Params: bwameth with bwameth-index": { "content": [ diff --git a/tests/bwameth_rrbs.nf.test.snap b/tests/bwameth_rrbs.nf.test.snap index 1d7acc84..70449f34 100644 --- a/tests/bwameth_rrbs.nf.test.snap +++ b/tests/bwameth_rrbs.nf.test.snap @@ -38,6 +38,11 @@ "bwameth/alignments/samtools_stats/SRR389222_sub2.stats", "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", + "bwameth/deduplicated", + "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", + "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", + "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", + "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "fastqc", "fastqc/Ecoli_10K_methylated_1_fastqc.html", "fastqc/Ecoli_10K_methylated_2_fastqc.html", @@ -53,10 +58,10 @@ "gunzip", "gunzip/genome.fa", "methyldackel", - "methyldackel/Ecoli_10K_methylated.sorted_CpG.bedGraph", - "methyldackel/SRR389222_sub1.sorted_CpG.bedGraph", - "methyldackel/SRR389222_sub2.sorted_CpG.bedGraph", - "methyldackel/SRR389222_sub3.sorted_CpG.bedGraph", + "methyldackel/Ecoli_10K_methylated.deduplicated.sorted_CpG.bedGraph", + "methyldackel/SRR389222_sub1.deduplicated.sorted_CpG.bedGraph", + "methyldackel/SRR389222_sub2.deduplicated.sorted_CpG.bedGraph", + "methyldackel/SRR389222_sub3.deduplicated.sorted_CpG.bedGraph", "methyldackel/mbias", "methyldackel/mbias/Ecoli_10K_methylated.mbias.txt", "methyldackel/mbias/SRR389222_sub1.mbias.txt", @@ -352,10 +357,10 @@ "SRR389222_sub3.flagstat:md5,73a5cb246f6388d5d449775d6e35f5fa", "SRR389222_sub3.stats:md5,89ccd73e9ed78f5102c5736f255e034a", "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", - "Ecoli_10K_methylated.sorted_CpG.bedGraph:md5,5e0bf8c8bb3162de75203784414a6399", - "SRR389222_sub1.sorted_CpG.bedGraph:md5,4475a9462ce86a019015b69b82a9d5a2", - "SRR389222_sub2.sorted_CpG.bedGraph:md5,18b8845d9d985d3c203ca6c9c40aab1b", - "SRR389222_sub3.sorted_CpG.bedGraph:md5,70dcc3836dc9721c2de367d1cf05e815", + "Ecoli_10K_methylated.deduplicated.sorted_CpG.bedGraph:md5,aa55074c144aa6eaa184480038c75932", + "SRR389222_sub1.deduplicated.sorted_CpG.bedGraph:md5,9e9e6922a8d99881874d299bfd7af5de", + "SRR389222_sub2.deduplicated.sorted_CpG.bedGraph:md5,d6c973d9fa7c6bc5f47141d14c18a105", + "SRR389222_sub3.deduplicated.sorted_CpG.bedGraph:md5,0ce36f42cc865eb59c7c6fd43d016d2c", "Ecoli_10K_methylated.mbias.txt:md5,7fb217502c2f3ae955bdfd744b6cbb72", "SRR389222_sub1.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81", "SRR389222_sub2.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81", @@ -386,19 +391,34 @@ "samtools-flagstat-dp_Read_counts.txt:md5,1491440de94dc58b28ca8f61d893a710", "samtools-stats-dp.txt:md5,deab74e7245766aab6b2284492959fed", "samtools_alignment_plot.txt:md5,e10b792693e5a69776f623f5f7de647e", - "genome_results.txt:md5,1473f581e4d67696c1948f5523211cab", - "genome_results.txt:md5,07b8ef58f6c6bb40c0c9c4704b50e0b3", - "genome_results.txt:md5,1466a5585ad5887f8fea7af2732efcba", - "genome_results.txt:md5,58d212848ac7b7650e3bd6812a4064af" + "genome_results.txt:md5,e30cbb971a3bc235624c7899bdce6e62", + "genome_results.txt:md5,e3f94b55db3953d774727a89adb954e2", + "genome_results.txt:md5,a5178e697b27759c1ce7112e9e3b6d63", + "genome_results.txt:md5,0d3ba7f76583dc8ffd9247f7d4032adc" ], [ - + [ + "Ecoli_10K_methylated.deduplicated.sorted.bam", + "8039fd2db60f8ca71daa444e62411f53" + ], + [ + "SRR389222_sub1.deduplicated.sorted.bam", + "a75ccc7cde779aac54662b03e5c01fe0" + ], + [ + "SRR389222_sub2.deduplicated.sorted.bam", + "82d2a7df2d4cb1ed2ea1e0456aff1cb" + ], + [ + "SRR389222_sub3.deduplicated.sorted.bam", + "7856b5549c566fb795c46f0674e069e1" + ] ] ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-26T05:46:18.431989802" + "timestamp": "2024-11-26T09:19:08.400099306" } } \ 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 a2b97b7f..3ae26c7b 100644 --- a/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap @@ -30,17 +30,17 @@ "bwameth", "bwameth/alignments", "bwameth/alignments/Ecoli_10K_methylated.bam", - "bwameth/alignments/Ecoli_10K_methylated.sorted.bam", - "bwameth/alignments/Ecoli_10K_methylated.sorted.bam.bai", + "bwameth/alignments/Ecoli_10K_methylated.deduplicated.sorted.bam", + "bwameth/alignments/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", "bwameth/alignments/SRR389222_sub1.bam", - "bwameth/alignments/SRR389222_sub1.sorted.bam", - "bwameth/alignments/SRR389222_sub1.sorted.bam.bai", + "bwameth/alignments/SRR389222_sub1.deduplicated.sorted.bam", + "bwameth/alignments/SRR389222_sub1.deduplicated.sorted.bam.bai", "bwameth/alignments/SRR389222_sub2.bam", - "bwameth/alignments/SRR389222_sub2.sorted.bam", - "bwameth/alignments/SRR389222_sub2.sorted.bam.bai", + "bwameth/alignments/SRR389222_sub2.deduplicated.sorted.bam", + "bwameth/alignments/SRR389222_sub2.deduplicated.sorted.bam.bai", "bwameth/alignments/SRR389222_sub3.bam", - "bwameth/alignments/SRR389222_sub3.sorted.bam", - "bwameth/alignments/SRR389222_sub3.sorted.bam.bai", + "bwameth/alignments/SRR389222_sub3.deduplicated.sorted.bam", + "bwameth/alignments/SRR389222_sub3.deduplicated.sorted.bam.bai", "bwameth/alignments/samtools_stats", "bwameth/alignments/samtools_stats/Ecoli_10K_methylated.flagstat", "bwameth/alignments/samtools_stats/Ecoli_10K_methylated.stats", @@ -51,12 +51,16 @@ "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", "bwameth/deduplicated", + "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", "bwameth/deduplicated/picard_metrics", @@ -442,10 +446,10 @@ "samtools-flagstat-dp_Read_counts.txt:md5,6a5332e2ad59f7da00b5a9a1a25fd2f8", "samtools-stats-dp.txt:md5,52021b9a9455b39b39dd357bc2e8d346", "samtools_alignment_plot.txt:md5,39f42e039f96cc2b17248b44ccaf425b", - "genome_results.txt:md5,1ee2e29ac41c2cd7e6a0f00741e8d16e", - "genome_results.txt:md5,2c755b15ae5ad4a1d29395320a6264ca", - "genome_results.txt:md5,2294badeccd2e8870fd6c60d115687b0", - "genome_results.txt:md5,4da1144933d094185d02f7482c120804" + "genome_results.txt:md5,5e6ff1f186689e9d5128725e003d6224", + "genome_results.txt:md5,6ba4b4d1d2299ee67094cf8cc3b038b5", + "genome_results.txt:md5,ab83bbae50e739ce32ace6ecc4e57591", + "genome_results.txt:md5,fda50629865f661d97c8dc57072baab2" ], [ [ @@ -453,7 +457,7 @@ "4a9ba2169facef4ed3d92d539c8c78af" ], [ - "Ecoli_10K_methylated.sorted.bam", + "Ecoli_10K_methylated.deduplicated.sorted.bam", "a2921f761f431ede522016f83f75c12d" ], [ @@ -461,7 +465,7 @@ "e50275d6d44138f19d65ee479444d5ce" ], [ - "SRR389222_sub1.sorted.bam", + "SRR389222_sub1.deduplicated.sorted.bam", "e50275d6d44138f19d65ee479444d5ce" ], [ @@ -469,7 +473,7 @@ "d365b8b2662b2abffb51dd67a1f463b4" ], [ - "SRR389222_sub2.sorted.bam", + "SRR389222_sub2.deduplicated.sorted.bam", "d365b8b2662b2abffb51dd67a1f463b4" ], [ @@ -477,21 +481,37 @@ "a9fd2900b9d759f8f4f62cbbb2744fde" ], [ - "SRR389222_sub3.sorted.bam", + "SRR389222_sub3.deduplicated.sorted.bam", "a9fd2900b9d759f8f4f62cbbb2744fde" ], + [ + "Ecoli_10K_methylated.deduplicated.sorted.bam", + "a2921f761f431ede522016f83f75c12d" + ], [ "Ecoli_10K_methylated.markdup.sorted.bam", "a2921f761f431ede522016f83f75c12d" ], + [ + "SRR389222_sub1.deduplicated.sorted.bam", + "e50275d6d44138f19d65ee479444d5ce" + ], [ "SRR389222_sub1.markdup.sorted.bam", "e50275d6d44138f19d65ee479444d5ce" ], + [ + "SRR389222_sub2.deduplicated.sorted.bam", + "d365b8b2662b2abffb51dd67a1f463b4" + ], [ "SRR389222_sub2.markdup.sorted.bam", "d365b8b2662b2abffb51dd67a1f463b4" ], + [ + "SRR389222_sub3.deduplicated.sorted.bam", + "a9fd2900b9d759f8f4f62cbbb2744fde" + ], [ "SRR389222_sub3.markdup.sorted.bam", "a9fd2900b9d759f8f4f62cbbb2744fde" @@ -502,6 +522,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-26T05:48:36.54774249" + "timestamp": "2024-11-26T09:21:00.149331298" } } \ 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 92427def..451e9ffe 100644 --- a/tests/bwameth_skip_deduplication.nf.test.snap +++ b/tests/bwameth_skip_deduplication.nf.test.snap @@ -29,6 +29,10 @@ [ "bwameth", "bwameth/alignments", + "bwameth/alignments/Ecoli_10K_methylated.sorted.bam", + "bwameth/alignments/SRR389222_sub1.sorted.bam", + "bwameth/alignments/SRR389222_sub2.sorted.bam", + "bwameth/alignments/SRR389222_sub3.sorted.bam", "bwameth/alignments/samtools_stats", "bwameth/alignments/samtools_stats/Ecoli_10K_methylated.flagstat", "bwameth/alignments/samtools_stats/Ecoli_10K_methylated.stats", @@ -38,6 +42,7 @@ "bwameth/alignments/samtools_stats/SRR389222_sub2.stats", "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", + "bwameth/deduplicated", "fastqc", "fastqc/Ecoli_10K_methylated_1_fastqc.html", "fastqc/Ecoli_10K_methylated_2_fastqc.html", @@ -392,13 +397,28 @@ "genome_results.txt:md5,478f711b8ef22e094e4d0ff7fa0dfda0" ], [ - + [ + "Ecoli_10K_methylated.sorted.bam", + "a2921f761f431ede522016f83f75c12d" + ], + [ + "SRR389222_sub1.sorted.bam", + "e50275d6d44138f19d65ee479444d5ce" + ], + [ + "SRR389222_sub2.sorted.bam", + "d365b8b2662b2abffb51dd67a1f463b4" + ], + [ + "SRR389222_sub3.sorted.bam", + "a9fd2900b9d759f8f4f62cbbb2744fde" + ] ] ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-26T05:50:14.727789889" + "timestamp": "2024-11-26T09:22:38.368456822" } } \ No newline at end of file diff --git a/tests/bwameth_skip_trimming.nf.test.snap b/tests/bwameth_skip_trimming.nf.test.snap index 3cfac2c0..69f9dbb6 100644 --- a/tests/bwameth_skip_trimming.nf.test.snap +++ b/tests/bwameth_skip_trimming.nf.test.snap @@ -35,12 +35,16 @@ "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", "bwameth/deduplicated", + "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", "bwameth/deduplicated/picard_metrics", @@ -373,24 +377,40 @@ "samtools-flagstat-dp_Read_counts.txt:md5,2d5434b646dac99397d86bd31731df01", "samtools-stats-dp.txt:md5,e1290c4b0ad11142147f69f4256c4524", "samtools_alignment_plot.txt:md5,fe4c9af19d69c3982b75ad458a1a9148", - "genome_results.txt:md5,2a1a374d5b1e3884c57d2d5333db54a6", - "genome_results.txt:md5,c4a9a1a76ba36cf770bf8be9a7fe5b55", - "genome_results.txt:md5,ac65d95bd5c7fd40b90d53d233c7b511", - "genome_results.txt:md5,b7376228bb23c9133fed45b95c60d082" + "genome_results.txt:md5,f85cc6e4d1935710e7cc7471afafe58b", + "genome_results.txt:md5,20dba8ac3965d75c244c24a3ab1f23f3", + "genome_results.txt:md5,6662db015b4c3565ec0738fba4af5e62", + "genome_results.txt:md5,a6c5e3d933b8b63d524bc7ec375251fa" ], [ + [ + "Ecoli_10K_methylated.deduplicated.sorted.bam", + "5b485bcabdb1ad5955cfa061741fad31" + ], [ "Ecoli_10K_methylated.markdup.sorted.bam", "5b485bcabdb1ad5955cfa061741fad31" ], + [ + "SRR389222_sub1.deduplicated.sorted.bam", + "37ec1c6338cc3fee7ab1cb2d48dba38" + ], [ "SRR389222_sub1.markdup.sorted.bam", "37ec1c6338cc3fee7ab1cb2d48dba38" ], + [ + "SRR389222_sub2.deduplicated.sorted.bam", + "783d3be6b5bfa58142c3dbe864f6d8c5" + ], [ "SRR389222_sub2.markdup.sorted.bam", "783d3be6b5bfa58142c3dbe864f6d8c5" ], + [ + "SRR389222_sub3.deduplicated.sorted.bam", + "4bbaef9917f4ff0248d1f5853f583fd0" + ], [ "SRR389222_sub3.markdup.sorted.bam", "4bbaef9917f4ff0248d1f5853f583fd0" @@ -401,6 +421,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-26T05:52:01.995851054" + "timestamp": "2024-11-26T09:24:32.999255506" } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 0668a6eb..c644577e 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,17 +1,17 @@ { "Params: default with bowtie2-index": { "content": [ - 44 + 40 ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-26T05:57:22.965324385" + "timestamp": "2024-11-26T09:28:51.135397834" }, "Params: default": { "content": [ - 44, + 40, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -592,6 +592,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.1" }, - "timestamp": "2024-11-26T05:54:48.597834845" + "timestamp": "2024-11-26T09:26:44.606360547" } } \ No newline at end of file diff --git a/workflows/methylseq/main.nf b/workflows/methylseq/main.nf index 0cb93f59..847d25b7 100644 --- a/workflows/methylseq/main.nf +++ b/workflows/methylseq/main.nf @@ -5,19 +5,19 @@ */ -include { FASTQC } from '../../modules/nf-core/fastqc/main' -include { TRIMGALORE } from '../../modules/nf-core/trimgalore/main' -include { QUALIMAP_BAMQC } from '../../modules/nf-core/qualimap/bamqc/main' -include { PRESEQ_LCEXTRAP } from '../../modules/nf-core/preseq/lcextrap/main' -include { MULTIQC } from '../../modules/nf-core/multiqc/main' -include { CAT_FASTQ } from '../../modules/nf-core/cat/fastq/main' -include { paramsSummaryMap } from 'plugin/nf-schema' -include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline' -include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' -include { methodsDescriptionText } from '../../subworkflows/local/utils_nfcore_methylseq_pipeline' -include { validateInputSamplesheet } from '../../subworkflows/local/utils_nfcore_methylseq_pipeline' -include { BISMARK } from '../../subworkflows/local/bismark/' -include { BWAMETH } from '../../subworkflows/local/bwameth' +include { FASTQC } from '../../modules/nf-core/fastqc/main' +include { TRIMGALORE } from '../../modules/nf-core/trimgalore/main' +include { QUALIMAP_BAMQC } from '../../modules/nf-core/qualimap/bamqc/main' +include { PRESEQ_LCEXTRAP } from '../../modules/nf-core/preseq/lcextrap/main' +include { MULTIQC } from '../../modules/nf-core/multiqc/main' +include { CAT_FASTQ } from '../../modules/nf-core/cat/fastq/main' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline' +include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' +include { methodsDescriptionText } from '../../subworkflows/local/utils_nfcore_methylseq_pipeline' +include { validateInputSamplesheet } from '../../subworkflows/local/utils_nfcore_methylseq_pipeline' +include { FASTQ_ALIGN_DEDUP_BISMARK } from '../../subworkflows/nf-core/fastq_align_dedup_bismark/main' +include { BWAMETH } from '../../subworkflows/local/bwameth' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -87,17 +87,16 @@ workflow METHYLSEQ { // // Run Bismark alignment + downstream processing // - BISMARK ( + FASTQ_ALIGN_DEDUP_BISMARK ( reads, ch_fasta, ch_bismark_index, params.skip_deduplication || params.rrbs, params.cytosine_report || params.nomeseq ) - ch_versions = ch_versions.mix(BISMARK.out.versions.unique{ it.baseName }) - ch_bam = BISMARK.out.bam - ch_dedup = BISMARK.out.dedup - ch_aligner_mqc = BISMARK.out.mqc + ch_versions = ch_versions.mix(FASTQ_ALIGN_DEDUP_BISMARK.out.versions.unique{ it.baseName }) + ch_bam = FASTQ_ALIGN_DEDUP_BISMARK.out.bam + ch_aligner_mqc = FASTQ_ALIGN_DEDUP_BISMARK.out.multiqc } // Aligner: bwameth else if ( params.aligner == 'bwameth' ){ @@ -119,7 +118,7 @@ workflow METHYLSEQ { // MODULE: Qualimap BamQC // QUALIMAP_BAMQC ( - ch_dedup, + ch_bam, params.bamqc_regions_file ? Channel.fromPath( params.bamqc_regions_file, checkIfExists: true ).toList() : [] ) ch_versions = ch_versions.mix(QUALIMAP_BAMQC.out.versions.first()) diff --git a/workflows/methylseq/nextflow.config b/workflows/methylseq/nextflow.config index e1ee85ad..3eb53510 100644 --- a/workflows/methylseq/nextflow.config +++ b/workflows/methylseq/nextflow.config @@ -1,14 +1,15 @@ - -includeConfig "../../subworkflows/local/bismark/nextflow.config" -includeConfig "../../subworkflows/local/bwameth/nextflow.config" -includeConfig "../../subworkflows/local/prepare_genome/nextflow.config" - +// module configs includeConfig "../../modules/nf-core/fastqc/nextflow.config" includeConfig "../../modules/nf-core/trimgalore/nextflow.config" includeConfig "../../modules/nf-core/multiqc/nextflow.config" includeConfig "../../modules/nf-core/preseq/lcextrap/nextflow.config" includeConfig "../../modules/nf-core/qualimap/bamqc/nextflow.config" +// subworkflow configs +includeConfig "../../subworkflows/nf-core/fastq_align_dedup_bismark/nextflow.config" +includeConfig "../../subworkflows/local/bwameth/nextflow.config" +includeConfig "../../subworkflows/local/prepare_genome/nextflow.config" + process { publishDir = [