diff --git a/CHANGELOG.md b/CHANGELOG.md index 429f463f..22560fce 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,6 @@ # nf-core/methylseq -## [v2.7.0](https://github.com/nf-core/methylseq/releases/tag/2.7.0) - [2024-10-23] +## [v2.7.0](https://github.com/nf-core/methylseq/releases/tag/2.7.0) - [2024-10-25] ### Bug fixes & refactoring diff --git a/modules/nf-core/bismark/coverage2cytosine/nextflow.config b/modules/nf-core/bismark/coverage2cytosine/nextflow.config index dc39a610..f593a1d1 100644 --- a/modules/nf-core/bismark/coverage2cytosine/nextflow.config +++ b/modules/nf-core/bismark/coverage2cytosine/nextflow.config @@ -1,22 +1,20 @@ process { withName: BISMARK_COVERAGE2CYTOSINE { ext.args = params.nomeseq ? '--nome-seq' : '' - publishDir = [ publishDir = [ path: { "${params.outdir}/bismark/coverage2cytosine/summaries" }, mode: params.publish_dir_mode, pattern: "*_summary.txt" - ], + ] publishDir = [ path: { "${params.outdir}/bismark/coverage2cytosine/reports" }, mode: params.publish_dir_mode, pattern: "*_report.txt.gz" - ], + ] publishDir = [ path: { "${params.outdir}/bismark/coverage2cytosine/coverage" }, mode: params.publish_dir_mode, pattern: "*cov.gz" ] - ] } } \ No newline at end of file diff --git a/subworkflows/local/bwameth/main.nf b/subworkflows/local/bwameth/main.nf index a90f7a8d..11c60eae 100644 --- a/subworkflows/local/bwameth/main.nf +++ b/subworkflows/local/bwameth/main.nf @@ -102,7 +102,7 @@ workflow BWAMETH { METHYLDACKEL_EXTRACT( alignments.join(bam_index), - fasta.map{ meta, fasta -> [fasta]}, + fasta.map{ meta, fasta_file -> [fasta_file]}, fasta_index ) METHYLDACKEL_EXTRACT.out.bedgraph.dump(tag: 'BWAMETH/METHYLDACKEL_EXTRACT: bedgraph') @@ -110,7 +110,7 @@ workflow BWAMETH { METHYLDACKEL_MBIAS( alignments.join(bam_index), - fasta.map{ meta, fasta -> [fasta]}, + fasta.map{ meta, fasta_file -> [fasta_file]}, fasta_index ) METHYLDACKEL_MBIAS.out.txt.dump(tag: 'BWAMETH/METHYLDACKEL_MBIAS: txt') diff --git a/workflows/methylseq/main.nf b/workflows/methylseq/main.nf index db0146f0..0cb93f59 100644 --- a/workflows/methylseq/main.nf +++ b/workflows/methylseq/main.nf @@ -16,15 +16,8 @@ include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfco 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' - -// Aligner: bismark or bismark_hisat -if( params.aligner =~ /bismark/ ){ - include { BISMARK } from '../../subworkflows/local/bismark/' -} -// Aligner: bwameth -else if ( params.aligner == 'bwameth' ){ - include { BWAMETH } from '../../subworkflows/local/bwameth' -} +include { BISMARK } from '../../subworkflows/local/bismark/' +include { BWAMETH } from '../../subworkflows/local/bwameth' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~