diff --git a/CHANGELOG.md b/CHANGELOG.md index 8dd90e75..7a315401 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,7 +12,8 @@ - 🔧 Install `fastq_align_dedup_bismark` subworkflow from nf-core/subworkflows [#453](https://github.com/nf-core/methylseq/pull/457) - 🔧 Install `fasta_index_bismark_bwameth` subworkflow from nf-core/subworkflows [#466](https://github.com/nf-core/methylseq/pull/) - 🔧 Install `fastq_align_dedup_bwameth` subworkflow from nf-core/subworkflows [#467](https://github.com/nf-core/methylseq/pull/) -- 🔧 reorg individual configs to `conf/modules/` named configs [#459](https://github.com/nf-core/methylseq/pull/) +- 🔧 reorg individual configs to `conf/modules/` named configs [#459](https://github.com/nf-core/methylseq/pull/469) +- 🔧 `run_preseq` param + skip preseq/lcextrap module by default [#458](https://github.com/nf-core/methylseq/pull/470) ## [v2.7.1](https://github.com/nf-core/methylseq/releases/tag/2.7.1) - [2024-10-27] diff --git a/conf/modules/preseq_lcextrap.config b/conf/modules/preseq_lcextrap.config index 09e4768e..efc2a888 100644 --- a/conf/modules/preseq_lcextrap.config +++ b/conf/modules/preseq_lcextrap.config @@ -5,12 +5,14 @@ process { [ path: { "${params.outdir}/${params.aligner}/preseq" }, mode: params.publish_dir_mode, - pattern: "*.txt" + pattern: "*.txt", + enabled: params.run_preseq ], [ path: { "${params.outdir}/${params.aligner}/preseq/log" }, mode: params.publish_dir_mode, - pattern: "*.log" + pattern: "*.log", + enabled: params.run_preseq ] ] } diff --git a/nextflow.config b/nextflow.config index 4cf66cba..7f80d1e0 100644 --- a/nextflow.config +++ b/nextflow.config @@ -87,6 +87,9 @@ params { skip_deduplication = false skip_multiqc = false + // Run options + run_preseq = false + // Boilerplate options outdir = null publish_dir_mode = 'copy' diff --git a/nextflow_schema.json b/nextflow_schema.json index ca54aada..c5dddf12 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -442,6 +442,20 @@ }, "fa_icon": "fas fa-fast-forward" }, + "run_pipeline_steps": { + "title": "Run pipeline steps", + "type": "object", + "description": "", + "default": "", + "properties": { + "run_preseq": { + "type": "boolean", + "description": "Run preseq/lcextrap tool", + "fa_icon": "fas fa-fast-forward" + } + }, + "fa_icon": "fas fa-fast-forward" + }, "institutional_config_options": { "title": "Institutional config options", "type": "object", @@ -613,6 +627,9 @@ { "$ref": "#/$defs/skip_pipeline_steps" }, + { + "$ref": "#/$defs/run_pipeline_steps" + }, { "$ref": "#/$defs/generic_options" }, diff --git a/tests/bismark_run_preseq.nf.test b/tests/bismark_run_preseq.nf.test new file mode 100644 index 00000000..229e6ea5 --- /dev/null +++ b/tests/bismark_run_preseq.nf.test @@ -0,0 +1,59 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + + test("Params: bismark | run_preseq") { + when { + params { + outdir = "$outputDir" + run_preseq = true + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + + test("Params: bismark | run_preseq with bowtie2-index") { + when { + params { + bismark_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz" + outdir = "$outputDir" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size() + ).match() } + ) + } + } + +} diff --git a/tests/bismark_run_preseq.nf.test.snap b/tests/bismark_run_preseq.nf.test.snap new file mode 100644 index 00000000..7e72da6f --- /dev/null +++ b/tests/bismark_run_preseq.nf.test.snap @@ -0,0 +1,597 @@ +{ + "Params: bismark | run_preseq": { + "content": [ + 40, + { + "BISMARK_ALIGN": { + "bismark": "0.24.2" + }, + "BISMARK_GENOMEPREPARATION": { + "bismark": "0.24.2" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GUNZIP": { + "gunzip": 1.1 + }, + "QUALIMAP_BAMQC": { + "qualimap": 2.3 + }, + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.9 + }, + "Workflow": { + "nf-core/methylseq": "v2.8.0dev" + } + }, + [ + "bismark", + "bismark/alignments", + "bismark/alignments/logs", + "bismark/alignments/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_PE_report.txt", + "bismark/alignments/logs/SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt", + "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", 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"genome_results.txt:md5,235830239cfc43d8e84c049b1e9b180a" + ], + [ + [ + "Ecoli_10K_methylated.deduplicated.sorted.bam", + "a54ab7c96f9523a4ccd25fd69f6905f8" + ], + [ + "SRR389222_sub1.deduplicated.sorted.bam", + "3f11ef5fbbda3797fd6217728e4f00d3" + ], + [ + "SRR389222_sub2.deduplicated.sorted.bam", + "b01f29fc1d8d46922a69df09c636b4c4" + ], + [ + "SRR389222_sub3.deduplicated.sorted.bam", + "347195c04c9ffd2a2b10967a6682fc69" + ] + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.1" + }, + "timestamp": "2024-11-27T09:41:36.634432131" + }, + "Params: bismark | run_preseq with bowtie2-index": { + "content": [ + 40 + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.1" + }, + "timestamp": "2024-11-27T09:43:31.675901802" + } +} \ No newline at end of file diff --git a/workflows/methylseq/main.nf b/workflows/methylseq/main.nf index 847d25b7..5247cd8f 100644 --- a/workflows/methylseq/main.nf +++ b/workflows/methylseq/main.nf @@ -126,8 +126,10 @@ workflow METHYLSEQ { // // MODULE: Run Preseq // - PRESEQ_LCEXTRAP (ch_bam) - ch_versions = ch_versions.mix(PRESEQ_LCEXTRAP.out.versions.first()) + if(params.run_preseq) { + PRESEQ_LCEXTRAP (ch_bam) + ch_versions = ch_versions.mix(PRESEQ_LCEXTRAP.out.versions.first()) + } // // Collate and save software versions @@ -169,7 +171,9 @@ workflow METHYLSEQ { ) ch_multiqc_files = ch_multiqc_files.mix(QUALIMAP_BAMQC.out.results.collect{ it[1] }.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(PRESEQ_LCEXTRAP.out.log.collect{ it[1] }.ifEmpty([])) + if (params.run_preseq) { + ch_multiqc_files = ch_multiqc_files.mix(PRESEQ_LCEXTRAP.out.log.collect{ it[1] }.ifEmpty([])) + } ch_multiqc_files = ch_multiqc_files.mix(ch_aligner_mqc.ifEmpty([])) if (!params.skip_trimming) { ch_multiqc_files = ch_multiqc_files.mix(TRIMGALORE.out.log.collect{ it[1] })