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apply suggestions from nextflow vscode formatter + update date in cha… #445

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Oct 25, 2024
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Merged

apply suggestions from nextflow vscode formatter + update date in cha… #445

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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -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

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6 changes: 2 additions & 4 deletions modules/nf-core/bismark/coverage2cytosine/nextflow.config
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4 changes: 2 additions & 2 deletions subworkflows/local/bwameth/main.nf
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Expand Up @@ -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')
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11 changes: 2 additions & 9 deletions workflows/methylseq/main.nf
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Expand Up @@ -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'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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