diff --git a/CHANGELOG.md b/CHANGELOG.md index 8ff84358..49527461 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,7 @@ - 🐛 fix fasta gunzip output [#462](https://github.com/nf-core/methylseq/pull/457) - 🐛 fix bismark/align not resuming from cache [#461](https://github.com/nf-core/methylseq/pull/457) +- 🐛 disable gunzip publish by default (https://github.com/nf-core/methylseq/pull/474) ### Pipeline Updates diff --git a/conf/modules/gunzip.config b/conf/modules/gunzip.config new file mode 100644 index 00000000..3a03a67b --- /dev/null +++ b/conf/modules/gunzip.config @@ -0,0 +1,12 @@ +process { + withName: GUNZIP { + publishDir = [ + [ + path: { "${params.outdir}/gunzip/" }, + mode: params.publish_dir_mode, + pattern: "*.{fa,fasta}", + enabled: false + ] + ] + } +} diff --git a/main.nf b/main.nf index 636d0a80..f87f6d0e 100644 --- a/main.nf +++ b/main.nf @@ -72,9 +72,11 @@ workflow NFCORE_METHYLSEQ { FASTA_INDEX_BISMARK_BWAMETH.out.bismark_index, FASTA_INDEX_BISMARK_BWAMETH.out.bwameth_index, ) + ch_versions = ch_versions.mix(METHYLSEQ.out.versions) + emit: - multiqc_report = METHYLSEQ.out.multiqc_report // channel: /path/to/multiqc_report.html - versions = ch_versions // channel: [version1, version2, ...] + multiqc_report = METHYLSEQ.out.multiqc_report // channel: [ path(multiqc_report.html ) ] + versions = ch_versions // channel: [ path(versions.yml) ] } /* diff --git a/subworkflows/nf-core/fasta_index_bismark_bwameth/nextflow.config b/subworkflows/nf-core/fasta_index_bismark_bwameth/nextflow.config index c4bb551b..ee09ec49 100644 --- a/subworkflows/nf-core/fasta_index_bismark_bwameth/nextflow.config +++ b/subworkflows/nf-core/fasta_index_bismark_bwameth/nextflow.config @@ -1,4 +1,4 @@ - +includeConfig "../../../conf/modules/gunzip.config" includeConfig "../../../conf/modules/bismark_genomepreparation.config" includeConfig "../../../conf/modules/samtools_faidx.config" includeConfig "../../../conf/modules/bwameth_index.config" diff --git a/tests/bismark_emseq_clip_r1.nf.test.snap b/tests/bismark_emseq_clip_r1.nf.test.snap index 3f322d73..a4fddc15 100644 --- a/tests/bismark_emseq_clip_r1.nf.test.snap +++ b/tests/bismark_emseq_clip_r1.nf.test.snap @@ -111,8 +111,6 @@ "fastqc/zips/SRR389222_sub1_fastqc.zip", "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", - "gunzip", - "gunzip/genome.fa", "multiqc", "multiqc/bismark", "multiqc/bismark/multiqc_data", @@ -309,7 +307,6 @@ "SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,f64ef957cbd73eb084e00d72065f4d9e", "SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,c9263685b01da6d8ca5df0c0758dc220", "SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,747b1dfc8d64866106d9423e6fd34d91", - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "bismark-methylation-dp.txt:md5,670008662fcb3aeb28e1a83d79d30418", "bismark_alignment.txt:md5,9ea891969967030c3089b047f5a898fb", "bismark_deduplication.txt:md5,6be5ee75673e5dcc870d49fe938394c3", @@ -361,8 +358,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T16:48:43.85530348" + "timestamp": "2024-11-28T09:30:17.226120765" } } \ No newline at end of file diff --git a/tests/bismark_hisat.nf.test.snap b/tests/bismark_hisat.nf.test.snap index e6fde36d..157689c9 100644 --- a/tests/bismark_hisat.nf.test.snap +++ b/tests/bismark_hisat.nf.test.snap @@ -121,8 +121,6 @@ "fastqc/zips/SRR389222_sub1_fastqc.zip", "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", - "gunzip", - "gunzip/genome.fa", "multiqc", "multiqc/bismark_hisat", "multiqc/bismark_hisat/multiqc_data", @@ -319,7 +317,6 @@ "SRR389222_sub1_trimmed_bismark_hisat2.deduplicated_splitting_report.txt:md5,30d4e3aec9220b886a6ac17630f48ef3", "SRR389222_sub2_trimmed_bismark_hisat2.deduplicated_splitting_report.txt:md5,8519a3e58f6047f71e8cf09991482332", "SRR389222_sub3_trimmed_bismark_hisat2.deduplicated_splitting_report.txt:md5,e6144ca656936c6ee6e7281a1192fa78", - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "bismark-methylation-dp.txt:md5,233409b9665cb851aca3b6b4511ff757", "bismark_alignment.txt:md5,3acfd1a751bef6696b6fa095d0631bb6", "bismark_deduplication.txt:md5,c025b4368b08f9e623624908632e44a1", @@ -371,8 +368,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T16:50:33.026655728" + "timestamp": "2024-11-28T09:32:04.275412615" } } \ 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 9169ccc5..570e5afe 100644 --- a/tests/bismark_hisat_rrbs.nf.test.snap +++ b/tests/bismark_hisat_rrbs.nf.test.snap @@ -110,8 +110,6 @@ "fastqc/zips/SRR389222_sub1_fastqc.zip", "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", - "gunzip", - "gunzip/genome.fa", "multiqc", "multiqc/bismark_hisat", "multiqc/bismark_hisat/multiqc_data", @@ -300,7 +298,6 @@ "SRR389222_sub1_trimmed_bismark_hisat2_splitting_report.txt:md5,a3ea9994f88802972e25836058ea2b40", "SRR389222_sub2_trimmed_bismark_hisat2_splitting_report.txt:md5,4afad1d4dbe350b2d691561260018247", "SRR389222_sub3_trimmed_bismark_hisat2_splitting_report.txt:md5,bd4b6b3718a4270fc6844862da5c31a7", - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "bismark-methylation-dp.txt:md5,2ed19dff17c089738a62de166f44cf97", "bismark_alignment.txt:md5,0e1ef7bfb853be4fe2471ee1082865c0", "bismark_mbias_CHG_R1.txt:md5,cc89b38a24adcd51363a934964b03892", @@ -366,8 +363,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T16:54:45.712638793" + "timestamp": "2024-11-28T09:35:49.452970243" } } \ 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 841cff98..f6661ff6 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 @@ -143,8 +143,6 @@ "fastqc/zips/SRR389222_sub1_fastqc.zip", "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", - "gunzip", - "gunzip/genome.fa", "multiqc", "multiqc/bismark_hisat", "multiqc/bismark_hisat/multiqc_data", @@ -360,7 +358,6 @@ "BS_GA.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb", "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f", "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "bismark-methylation-dp.txt:md5,233409b9665cb851aca3b6b4511ff757", "bismark_alignment.txt:md5,3acfd1a751bef6696b6fa095d0631bb6", "bismark_deduplication.txt:md5,c025b4368b08f9e623624908632e44a1", @@ -444,8 +441,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T16:57:16.831873082" + "timestamp": "2024-11-28T09:37:31.824088531" } } \ No newline at end of file diff --git a/tests/bismark_nomeseq.nf.test.snap b/tests/bismark_nomeseq.nf.test.snap index 50bd058f..192b7644 100644 --- a/tests/bismark_nomeseq.nf.test.snap +++ b/tests/bismark_nomeseq.nf.test.snap @@ -135,8 +135,6 @@ "fastqc/zips/SRR389222_sub1_fastqc.zip", "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", - "gunzip", - "gunzip/genome.fa", "multiqc", "multiqc/bismark", "multiqc/bismark/multiqc_data", @@ -353,7 +351,6 @@ "SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,94f18ee855566ef9842b4909e3d3dd88", "SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,7c3526e022e97e49677f7428badef420", "SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,e8d2bf21731b6ed517c56385061b1dee", - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "bismark-methylation-dp.txt:md5,dcbe642c42e31d8e480a2e46b97bbd45", "bismark_alignment.txt:md5,544a74ea0f32005b0c886af79a6fad5b", "bismark_deduplication.txt:md5,db387240d46c09b0b952ed8b54855e76", @@ -405,8 +402,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T16:59:27.300398291" + "timestamp": "2024-11-28T09:39:19.824905083" } } \ No newline at end of file diff --git a/tests/bismark_rrbs.nf.test.snap b/tests/bismark_rrbs.nf.test.snap index 166d43da..1f53ba7f 100644 --- a/tests/bismark_rrbs.nf.test.snap +++ b/tests/bismark_rrbs.nf.test.snap @@ -110,8 +110,6 @@ "fastqc/zips/SRR389222_sub1_fastqc.zip", "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", - "gunzip", - "gunzip/genome.fa", "multiqc", "multiqc/bismark", "multiqc/bismark/multiqc_data", @@ -300,7 +298,6 @@ "SRR389222_sub1_trimmed_bismark_bt2_splitting_report.txt:md5,8bf9dc8dd2bb0bc918996edfd02d245e", "SRR389222_sub2_trimmed_bismark_bt2_splitting_report.txt:md5,faeff61aa8cb9d1ba6d67cd4fa7a8587", "SRR389222_sub3_trimmed_bismark_bt2_splitting_report.txt:md5,a5609edd39203f94c5e80dc619b94f68", - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "bismark-methylation-dp.txt:md5,0b7ac7f2e82a9cc4a3362bfcd66a3e26", "bismark_alignment.txt:md5,0a7b6ad94d54f24a91d5126a6acaa9de", "bismark_mbias_CHG_R1.txt:md5,1a54528651513f4bdfa223c22de60c30", @@ -366,8 +363,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T17:02:08.994971636" + "timestamp": "2024-11-28T09:41:20.064526318" } } \ No newline at end of file diff --git a/tests/bismark_run_preseq.nf.test.snap b/tests/bismark_run_preseq.nf.test.snap index ae60eb2e..682358fa 100644 --- a/tests/bismark_run_preseq.nf.test.snap +++ b/tests/bismark_run_preseq.nf.test.snap @@ -111,8 +111,6 @@ "fastqc/zips/SRR389222_sub1_fastqc.zip", "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", - "gunzip", - "gunzip/genome.fa", "multiqc", "multiqc/bismark", "multiqc/bismark/multiqc_data", @@ -309,7 +307,6 @@ "SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,94f18ee855566ef9842b4909e3d3dd88", "SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,7c3526e022e97e49677f7428badef420", "SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,e8d2bf21731b6ed517c56385061b1dee", - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "bismark-methylation-dp.txt:md5,dcbe642c42e31d8e480a2e46b97bbd45", "bismark_alignment.txt:md5,544a74ea0f32005b0c886af79a6fad5b", "bismark_deduplication.txt:md5,db387240d46c09b0b952ed8b54855e76", @@ -361,9 +358,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T17:04:32.299955979" + "timestamp": "2024-11-28T09:43:14.601958698" }, "Params: bismark | run_preseq with bowtie2-index": { "content": [ diff --git a/tests/bismark_run_qualimap.nf.test.snap b/tests/bismark_run_qualimap.nf.test.snap index 28102476..ba30b070 100644 --- a/tests/bismark_run_qualimap.nf.test.snap +++ b/tests/bismark_run_qualimap.nf.test.snap @@ -307,8 +307,6 @@ "fastqc/zips/SRR389222_sub1_fastqc.zip", "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", - "gunzip", - "gunzip/genome.fa", "multiqc", "multiqc/bismark", "multiqc/bismark/multiqc_data", @@ -558,7 +556,7 @@ "genome_mapping_quality_histogram.png:md5,74776b1e7e8c8876af1cf89d9dbb5f31", "genome_reads_content_per_read_position.png:md5,c6920dc357411880132c207c7d0aa68d", "genome_uniq_read_starts_histogram.png:md5,8f7549a63eee3d3f022699aaa5bb858d", - "qualimapReport.html:md5,2c25df556c43190d52453e76de692a13", + "qualimapReport.html:md5,bbc015c0d1f3c41a08c82fb7a6839039", "coverage_across_reference.txt:md5,2bb9eb828acfd71ace8f1e6a2ca124b4", "coverage_histogram.txt:md5,6ee761660a6072e5b6b75b7fe8d2c69e", "duplication_rate_histogram.txt:md5,d5f25ad3572b98880b6904dcf4b3ed25", @@ -603,7 +601,7 @@ "genome_mapping_quality_histogram.png:md5,7ba0db9375d09fd49946b9bca4ba92b4", "genome_reads_content_per_read_position.png:md5,1a6a7717ea948d2518808f72f58ffdef", "genome_uniq_read_starts_histogram.png:md5,395413ab1d0e10af72b116fd8cb12685", - "qualimapReport.html:md5,e87a83d69a3d001db49d57a92a7cf25e", + "qualimapReport.html:md5,1fe626f663d66a7ce0c6e1e0207d829d", "coverage_across_reference.txt:md5,081ddc3be3349b0c57d9676c03d84803", "coverage_histogram.txt:md5,47b75803a6925e883e254bb91d6220d2", "duplication_rate_histogram.txt:md5,3d06b34e40d1fdeb55c4ad19dc6ddad1", @@ -645,7 +643,7 @@ "genome_mapping_quality_histogram.png:md5,017451f46bc875ac58e7906bf7979956", "genome_reads_content_per_read_position.png:md5,fd94ec5bfe5ca4adfa6ebdeaebe25157", "genome_uniq_read_starts_histogram.png:md5,2f2555ef88c3bda05315469e684f5b19", - "qualimapReport.html:md5,91384759d5b7229060c7eea058f74fa1", + "qualimapReport.html:md5,af640b29bd28f80bdc0ab6fe7d9c97f4", "coverage_across_reference.txt:md5,a76b3da0ebb2f8bd6c36ec1902cf13f2", "coverage_histogram.txt:md5,ca854c05e9619233b7d95d44051cab80", "duplication_rate_histogram.txt:md5,530bb05c648d610227e121e1e74f41f8", @@ -687,7 +685,7 @@ "genome_mapping_quality_histogram.png:md5,a22ee10fcb9e34a84f607b089855fb92", "genome_reads_content_per_read_position.png:md5,9fa406f353148448f6b9ac11880bc6de", "genome_uniq_read_starts_histogram.png:md5,cf2fe3e30e11e7d6eb2db679cd12dc03", - "qualimapReport.html:md5,8753fb47fa86ef92999a0e6ed8b02fd6", + "qualimapReport.html:md5,c8114fbb2a63da68111f0d4cbb8a1973", "coverage_across_reference.txt:md5,fb9c989fc6c15d0a8fd0a58b8d3c20ce", "coverage_histogram.txt:md5,8a3f45461442657433914c6a5ecb1301", "duplication_rate_histogram.txt:md5,ec9a705fd3a300b126d556afa14c326b", @@ -697,7 +695,6 @@ "mapping_quality_across_reference.txt:md5,d9bafb5cc106bbd1dc7e31439c618f19", "mapping_quality_histogram.txt:md5,560e85b88f5f90e9ad7ad93ffef42d6f", "versions.yml:md5,bb8bc6f11e6ca441cdb653f077b870c2", - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "bismark-methylation-dp.txt:md5,dcbe642c42e31d8e480a2e46b97bbd45", "bismark_alignment.txt:md5,544a74ea0f32005b0c886af79a6fad5b", "bismark_deduplication.txt:md5,db387240d46c09b0b952ed8b54855e76", @@ -753,18 +750,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T17:08:57.318132441" - }, - "Params: bismark | run_preseq with bowtie2-index": { - "content": [ - 36 - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" - }, - "timestamp": "2024-11-27T17:10:56.214178009" + "timestamp": "2024-11-28T09:47:26.992492832" } -} \ 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 7d53a2e2..51196a93 100644 --- a/tests/bismark_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap @@ -139,8 +139,6 @@ "fastqc/zips/SRR389222_sub1_fastqc.zip", "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", - "gunzip", - "gunzip/genome.fa", "multiqc", "multiqc/bismark", "multiqc/bismark/multiqc_data", @@ -352,7 +350,6 @@ "BS_GA.rev.2.bt2:md5,fac2f8b39b0e15dec7aa79a0ecf12b49", "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f", "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "bismark-methylation-dp.txt:md5,dcbe642c42e31d8e480a2e46b97bbd45", "bismark_alignment.txt:md5,544a74ea0f32005b0c886af79a6fad5b", "bismark_deduplication.txt:md5,db387240d46c09b0b952ed8b54855e76", @@ -436,8 +433,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T17:13:14.566378345" + "timestamp": "2024-11-28T09:49:22.829291635" } } \ 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 fd4f619d..7406edb8 100644 --- a/tests/bismark_skip_deduplication.nf.test.snap +++ b/tests/bismark_skip_deduplication.nf.test.snap @@ -110,8 +110,6 @@ "fastqc/zips/SRR389222_sub1_fastqc.zip", "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", - "gunzip", - "gunzip/genome.fa", "multiqc", "multiqc/bismark", "multiqc/bismark/multiqc_data", @@ -300,7 +298,6 @@ "SRR389222_sub1_trimmed_bismark_bt2_splitting_report.txt:md5,15cd690a0366ff38703abf9dd1d5230c", "SRR389222_sub2_trimmed_bismark_bt2_splitting_report.txt:md5,90f7b7a242012045af7fccc5eb94fbf1", "SRR389222_sub3_trimmed_bismark_bt2_splitting_report.txt:md5,beda776b2f0e1faaeafd46f245d273f0", - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "bismark-methylation-dp.txt:md5,14edb46f1bc99ddc7f597cb4c6ac9e1c", "bismark_alignment.txt:md5,544a74ea0f32005b0c886af79a6fad5b", "bismark_mbias_CHG_R1.txt:md5,d92f984f52a98ee2943545dd2ae4b860", @@ -366,8 +363,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T17:15:37.365873735" + "timestamp": "2024-11-28T09:51:23.826120232" } } \ 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 407905d1..c8cd854a 100644 --- a/tests/bismark_skip_multiqc.nf.test.snap +++ b/tests/bismark_skip_multiqc.nf.test.snap @@ -111,8 +111,6 @@ "fastqc/zips/SRR389222_sub1_fastqc.zip", "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", - "gunzip", - "gunzip/genome.fa", "multiqc", "multiqc/bismark", "multiqc/bismark/multiqc_data", @@ -309,7 +307,6 @@ "SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,94f18ee855566ef9842b4909e3d3dd88", "SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,7c3526e022e97e49677f7428badef420", "SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,e8d2bf21731b6ed517c56385061b1dee", - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "bismark-methylation-dp.txt:md5,dcbe642c42e31d8e480a2e46b97bbd45", "bismark_alignment.txt:md5,544a74ea0f32005b0c886af79a6fad5b", "bismark_deduplication.txt:md5,db387240d46c09b0b952ed8b54855e76", @@ -361,8 +358,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T17:17:54.429778324" + "timestamp": "2024-11-28T09:53:44.275184035" } } \ 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 4cfa3b29..fb6bd21f 100644 --- a/tests/bismark_skip_trimming.nf.test.snap +++ b/tests/bismark_skip_trimming.nf.test.snap @@ -107,8 +107,6 @@ "fastqc/zips/SRR389222_sub1_fastqc.zip", "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", - "gunzip", - "gunzip/genome.fa", "multiqc", "multiqc/bismark", "multiqc/bismark/multiqc_data", @@ -270,7 +268,6 @@ "SRR389222_sub1_bismark_bt2.deduplicated_splitting_report.txt:md5,ec268cc572b8bcfea0959b47c7510f05", "SRR389222_sub2_bismark_bt2.deduplicated_splitting_report.txt:md5,ac550001718e22218294a6c16fa3cec4", "SRR389222_sub3_bismark_bt2.deduplicated_splitting_report.txt:md5,c015374e9b11c9eb7cb1359cb437f7be", - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "bismark-methylation-dp.txt:md5,475ce6b3c6f53158847d554ef22993db", "bismark_alignment.txt:md5,7d00ed2e752ebf0ee7baedc206c6572b", "bismark_deduplication.txt:md5,e319d929f7d2e163bafba0a48dda554e", @@ -318,8 +315,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T17:19:54.364856577" + "timestamp": "2024-11-28T09:55:44.514046309" } } \ No newline at end of file diff --git a/tests/bwameth.nf.test.snap b/tests/bwameth.nf.test.snap index 8b60392e..f2bbb9fb 100644 --- a/tests/bwameth.nf.test.snap +++ b/tests/bwameth.nf.test.snap @@ -65,8 +65,6 @@ "fastqc/zips/SRR389222_sub1_fastqc.zip", "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", - "gunzip", - "gunzip/genome.fa", "methyldackel", "methyldackel/Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph", "methyldackel/SRR389222_sub1.markdup.sorted_CpG.bedGraph", @@ -221,7 +219,6 @@ "SRR389222_sub2.stats:md5,9343b74f4d825bfb2a554be3d8bed432", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", "SRR389222_sub3.stats:md5,f41e135f71893e2a8b589c4a66cbfeec", - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph:md5,d3bce01078b6e7749f3906bf9faad5b5", "SRR389222_sub1.markdup.sorted_CpG.bedGraph:md5,0944ad0e3b05791bf6dfd06be7ca4af1", "SRR389222_sub2.markdup.sorted_CpG.bedGraph:md5,0a3c19af55d1625e91903ae25d1d2098", @@ -295,9 +292,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T17:22:51.548341521" + "timestamp": "2024-11-28T10:50:52.356626917" }, "Params: bwameth with bwameth-index": { "content": [ diff --git a/tests/bwameth_rrbs.nf.test.snap b/tests/bwameth_rrbs.nf.test.snap index 864af53f..4472fb73 100644 --- a/tests/bwameth_rrbs.nf.test.snap +++ b/tests/bwameth_rrbs.nf.test.snap @@ -52,8 +52,6 @@ "fastqc/zips/SRR389222_sub1_fastqc.zip", "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", - "gunzip", - "gunzip/genome.fa", "methyldackel", "methyldackel/Ecoli_10K_methylated.deduplicated.sorted_CpG.bedGraph", "methyldackel/SRR389222_sub1.deduplicated.sorted_CpG.bedGraph", @@ -197,7 +195,6 @@ "SRR389222_sub2.stats:md5,2fa170e542d799b47717984dc7c0a4a4", "SRR389222_sub3.flagstat:md5,73a5cb246f6388d5d449775d6e35f5fa", "SRR389222_sub3.stats:md5,89ccd73e9ed78f5102c5736f255e034a", - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "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", @@ -250,8 +247,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T17:26:51.658375122" + "timestamp": "2024-11-28T11:03:39.089301861" } } \ 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 521f3c55..2de87ce1 100644 --- a/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap @@ -85,8 +85,6 @@ "fastqc/zips/SRR389222_sub1_fastqc.zip", "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", - "gunzip", - "gunzip/genome.fa", "methyldackel", "methyldackel/Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph", "methyldackel/SRR389222_sub1.markdup.sorted_CpG.bedGraph", @@ -247,7 +245,6 @@ "genome.fa.bwameth.c2t.bwt:md5,4646f8ae6bd523b7f4106bbd32eff95e", "genome.fa.bwameth.c2t.pac:md5,a662d7add09698e25c8152fd2306ec66", "genome.fa.bwameth.c2t.sa:md5,4a1e905b828396a1909669bc9c573d8d", - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph:md5,d3bce01078b6e7749f3906bf9faad5b5", "SRR389222_sub1.markdup.sorted_CpG.bedGraph:md5,0944ad0e3b05791bf6dfd06be7ca4af1", "SRR389222_sub2.markdup.sorted_CpG.bedGraph:md5,0a3c19af55d1625e91903ae25d1d2098", @@ -353,8 +350,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T17:29:22.662705762" + "timestamp": "2024-11-28T10:54:55.04039479" } } \ 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 2ef79679..397d9be4 100644 --- a/tests/bwameth_skip_deduplication.nf.test.snap +++ b/tests/bwameth_skip_deduplication.nf.test.snap @@ -52,8 +52,6 @@ "fastqc/zips/SRR389222_sub1_fastqc.zip", "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", - "gunzip", - "gunzip/genome.fa", "methyldackel", "methyldackel/Ecoli_10K_methylated.sorted_CpG.bedGraph", "methyldackel/SRR389222_sub1.sorted_CpG.bedGraph", @@ -197,7 +195,6 @@ "SRR389222_sub2.stats:md5,9343b74f4d825bfb2a554be3d8bed432", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", "SRR389222_sub3.stats:md5,f41e135f71893e2a8b589c4a66cbfeec", - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "Ecoli_10K_methylated.sorted_CpG.bedGraph:md5,aa88f19284e63097e9abccac4d7c6669", "SRR389222_sub1.sorted_CpG.bedGraph:md5,4475a9462ce86a019015b69b82a9d5a2", "SRR389222_sub2.sorted_CpG.bedGraph:md5,18b8845d9d985d3c203ca6c9c40aab1b", @@ -250,8 +247,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T17:31:07.151965326" + "timestamp": "2024-11-28T10:56:17.383748035" } } \ 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 06ef9f7b..e7fb27c8 100644 --- a/tests/bwameth_skip_trimming.nf.test.snap +++ b/tests/bwameth_skip_trimming.nf.test.snap @@ -61,8 +61,6 @@ "fastqc/zips/SRR389222_sub1_fastqc.zip", "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", - "gunzip", - "gunzip/genome.fa", "methyldackel", "methyldackel/Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph", "methyldackel/SRR389222_sub1.markdup.sorted_CpG.bedGraph", @@ -182,7 +180,6 @@ "SRR389222_sub2.stats:md5,ce9216e71c0eb24371fb388429c59894", "SRR389222_sub3.flagstat:md5,e3e925a7b7356e93d14f5e9e102c55b7", "SRR389222_sub3.stats:md5,4f5336d853dfada24d9c34a754a7f0a8", - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph:md5,b43c4c8ff346ae865b2b5db996650942", "SRR389222_sub1.markdup.sorted_CpG.bedGraph:md5,0944ad0e3b05791bf6dfd06be7ca4af1", "SRR389222_sub2.markdup.sorted_CpG.bedGraph:md5,0a3c19af55d1625e91903ae25d1d2098", @@ -252,8 +249,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T17:33:10.51867221" + "timestamp": "2024-11-28T11:05:15.608887033" } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 138ffe08..774cfb9b 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -121,8 +121,6 @@ "fastqc/zips/SRR389222_sub1_fastqc.zip", "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", - "gunzip", - "gunzip/genome.fa", "multiqc", "multiqc/bismark", "multiqc/bismark/multiqc_data", @@ -319,7 +317,6 @@ "SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,94f18ee855566ef9842b4909e3d3dd88", "SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,7c3526e022e97e49677f7428badef420", "SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,e8d2bf21731b6ed517c56385061b1dee", - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "bismark-methylation-dp.txt:md5,dcbe642c42e31d8e480a2e46b97bbd45", "bismark_alignment.txt:md5,544a74ea0f32005b0c886af79a6fad5b", "bismark_deduplication.txt:md5,db387240d46c09b0b952ed8b54855e76", @@ -371,8 +368,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-27T17:35:35.454188918" + "timestamp": "2024-11-28T11:07:55.760553696" } } \ No newline at end of file diff --git a/workflows/methylseq/main.nf b/workflows/methylseq/main.nf index 51060687..15d5b70b 100644 --- a/workflows/methylseq/main.nf +++ b/workflows/methylseq/main.nf @@ -28,12 +28,12 @@ include { BWAMETH } from '../../subworkflows/local/bwameth' workflow METHYLSEQ { take: - samplesheet // channel: samplesheet read in from --input - ch_versions // channel: [ path(versions.yml) ] - ch_fasta // channel: path(genome.fasta) - ch_fasta_index // channel: path(star/index/) - ch_bismark_index // channel: path(star/index/) - ch_bwameth_index // channel: path(star/index/) + samplesheet // channel: [ path(samplesheet.csv) ] + ch_versions // channel: [ path(versions.yml) ] + ch_fasta // channel: [ path(fasta) ] + ch_fasta_index // channel: [ path(fasta index) ] + ch_bismark_index // channel: [ path(bismark index) ] + ch_bwameth_index // channel: [ path(bwameth index) ] main: @@ -42,40 +42,43 @@ workflow METHYLSEQ { // // Branch channels from input samplesheet channel // - samplesheet - .branch { meta, fastqs -> - single : fastqs.size() == 1 - return [ meta, fastqs.flatten() ] - multiple: fastqs.size() > 1 - return [ meta, fastqs.flatten() ] - } - .set { ch_samplesheet } + ch_samplesheet = samplesheet + .branch { meta, fastqs -> + single : fastqs.size() == 1 + return [ meta, fastqs.flatten() ] + multiple: fastqs.size() > 1 + return [ meta, fastqs.flatten() ] + } // // MODULE: Concatenate FastQ files from same sample if required // - CAT_FASTQ (ch_samplesheet.multiple) - .reads - .mix(ch_samplesheet.single) - .set {ch_fastq} + CAT_FASTQ ( + ch_samplesheet.multiple + ) + ch_fastq = CAT_FASTQ.out.reads.mix(ch_samplesheet.single) ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first()) // // MODULE: Run FastQC // - FASTQC (ch_fastq) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) - ch_versions = ch_versions.mix(FASTQC.out.versions.first()) + FASTQC ( + ch_fastq + ) + ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{ meta, zip -> zip }) + ch_versions = ch_versions.mix(FASTQC.out.versions.first()) // // MODULE: Run TrimGalore! // if (!params.skip_trimming) { - TRIMGALORE(ch_fastq) - reads = TRIMGALORE.out.reads + TRIMGALORE( + ch_fastq + ) + reads = TRIMGALORE.out.reads ch_versions = ch_versions.mix(TRIMGALORE.out.versions.first()) } else { - reads = ch_fastq + reads = ch_fastq } // @@ -83,7 +86,7 @@ workflow METHYLSEQ { // // Aligner: bismark or bismark_hisat - if( params.aligner =~ /bismark/ ){ + if ( params.aligner =~ /bismark/ ) { // // Run Bismark alignment + downstream processing // @@ -116,6 +119,7 @@ workflow METHYLSEQ { // // MODULE: Qualimap BamQC + // skipped by default. to use run with `--run_qualimap` param. // if(params.run_qualimap) { QUALIMAP_BAMQC ( @@ -126,23 +130,26 @@ workflow METHYLSEQ { } // - // MODULE: Run Preseq + // MODULE: Preseq LCEXTRAP + // skipped by default. to use run with `--run_preseq` param. // if(params.run_preseq) { - PRESEQ_LCEXTRAP (ch_bam) + PRESEQ_LCEXTRAP ( + ch_bam + ) ch_versions = ch_versions.mix(PRESEQ_LCEXTRAP.out.versions.first()) } // // Collate and save software versions // - softwareVersionsToYAML(ch_versions) - .collectFile( - storeDir: "${params.outdir}/pipeline_info", - name: 'nf_core_pipeline_software_mqc_versions.yml', - sort: true, - newLine: true - ).set { ch_collated_versions } + ch_collated_versions = softwareVersionsToYAML(ch_versions) + .collectFile( + storeDir: "${params.outdir}/pipeline_info", + name: 'nf_core_pipeline_software_mqc_versions.yml', + sort: true, + newLine: true + ) // // MODULE: MultiQC @@ -194,7 +201,7 @@ workflow METHYLSEQ { ) emit: - multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + multiqc_report = MULTIQC.out.report.toList() // channel: [ path(multiqc_report.html ) ] versions = ch_versions // channel: [ path(versions.yml) ] }