Merge pull request #162 from LouisLeNezet/fasta_index

Fix fasta index usage with `genomes` parameter

CHANGELOG.md

@@ -77,6 +77,7 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu) and [Mazza
 - [#158](https://github.com/nf-core/phaseimpute/pull/158) - Fix contigs usage when regions is only a subset of the given contigs (e.g. if panel file has the 22 chr and the region file only 2 then only the 2 common will be processed). Fix `multiQC` samples names for better comprehension. Fix `-resume` errors when `ch_fasta` is use by adding `cache = 'lenient'` in necessary processes. Fix `--window-size` of `GLIMPSE_CHUNK` from `4` to `4000000`.
 - [#153](https://github.com/nf-core/phaseimpute/pull/153) - Fix getFileExtension function. Fix image in `usage.md`. Fix small warnings and errors with updated language server. `def` has been added when necessary, `:` use instead of `,` in assertions, `_` added to variables not used in closures, `for` loop replaced by `.each{}`, remove unused code / input.
 - [#161](https://github.com/nf-core/phaseimpute/pull/161) - Fix `VCF_SPLIT_BCFTOOLS` when only one sample present by updating `BCFTOOLS_PLUGINSPLIT` and adding `BCFTOOLS_QUERY` to get truth samples names for renaming the resulting files.
+- [#162](https://github.com/nf-core/phaseimpute/pull/162) - Fix `fai` usage when provided by `genomes` parameter.
 
 ### `Dependencies`
 

subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf

@@ -84,6 +84,8 @@ workflow PIPELINE_INITIALISATION {
             SAMTOOLS_FAIDX(ch_fasta, Channel.of([[], []]))
             ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions.first())
             fai         = SAMTOOLS_FAIDX.out.fai.map{ it[1] }
+        } else {
+            fai = Channel.of(file(fai, checkIfExists:true))
         }
     } else if (params.fasta) {
         genome = file(params.fasta, checkIfExists:true).getBaseName()