Merge pull request #403 from maxulysse/fasta_references

fix usage of Fasta references for bwameth / samtools faidx

CHANGELOG.md

@@ -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

README.md

@@ -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
 

subworkflows/local/prepare_genome.nf

@@ -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)
         }