Merge pull request #445 from sateeshperi/dev

apply suggestions from nextflow vscode formatter + update date in cha…
nf-core · Oct 25, 2024 · cd1a02f · cd1a02f
2 parents 0bbf07f + 58219d5
commit cd1a02f
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Showing 4 changed files with 7 additions and 16 deletions.
diff --git 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
diff --git a/subworkflows/local/bwameth/main.nf b/subworkflows/local/bwameth/main.nf
@@ -102,15 +102,15 @@ 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')
     METHYLDACKEL_EXTRACT.out.methylkit.dump(tag: 'BWAMETH/METHYLDACKEL_EXTRACT: methylkit')
 
     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
@@ -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'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~