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fix usage of Fasta references for bwameth / samtools faidx #403

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merged 3 commits into from
May 28, 2024
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fix usage of Fasta references for bwameth / samtools faidx #403

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3f07b0f
fix usage of fasta references
maxulysse May 28, 2024
e72476b
update contributors
maxulysse May 28, 2024
d38c4b1
update CHANGELOG
maxulysse May 28, 2024
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9 changes: 9 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -2,6 +2,15 @@

## v2.7.0dev - [date]

### Bug fixes & refactoring

- 🔄 Updated template to nf-core/tools v2.12 [#377](https://github.com/nf-core/methylseq/pull/377)
- 🔄 Updated template to nf-core/tools v2.13 [#380](https://github.com/nf-core/methylseq/pull/380)
- 🔄 Updated template to nf-core/tools v2.13.1 [#384](https://github.com/nf-core/methylseq/pull/384)
- 🔄 Updated template to nf-core/tools v2.14.1 [#399](https://github.com/nf-core/methylseq/pull/399)
- 🐛 fix sample/replicate merge [#401](https://github.com/nf-core/methylseq/pull/401)
- 🐛 fix fasta reference usage [#403](https://github.com/nf-core/methylseq/pull/403)

## [v2.6.0](https://github.com/nf-core/methylseq/releases/tag/2.6.0) - 2024-01-05

### Bug fixes & refactoring
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -96,6 +96,7 @@ These scripts were originally written for use at the [National Genomics Infrastr
- Rickard Hammarén ([@Hammarn](https://github.com/Hammarn/))
- Alexander Peltzer ([@apeltzer](https://github.com/apeltzer/))
- Patrick Hüther ([@phue](https://github.com/phue/))
- Maxime U Garica ([@maxulysse](https://github.com/maxulysse/))

## Contributions and Support

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2 changes: 1 addition & 1 deletion subworkflows/local/prepare_genome.nf
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Expand Up @@ -64,7 +64,7 @@ workflow PREPARE_GENOME {
if (params.fasta_index) {
ch_fasta_index = Channel.value(file(params.fasta_index))
} else {
SAMTOOLS_FAIDX([[:], ch_fasta])
SAMTOOLS_FAIDX(ch_fasta.map{ fasta -> [[:], fasta]})
ch_fasta_index = SAMTOOLS_FAIDX.out.fai.map{ return(it[1])}
ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
}
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