From a38adfad7d523bfa9fdf425dc961b7dd6eda3198 Mon Sep 17 00:00:00 2001 From: LouisBzh Date: Mon, 25 Nov 2024 10:30:26 +0100 Subject: [PATCH 1/2] Fix fasta index usage with igenome --- subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf | 2 ++ 1 file changed, 2 insertions(+) diff --git a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf index 23da802d..a8a6e6f6 100644 --- a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf +++ b/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() From aa55dfba8982cc3be7534831dddcfd5432d34f85 Mon Sep 17 00:00:00 2001 From: LouisBzh Date: Mon, 25 Nov 2024 11:17:39 +0100 Subject: [PATCH 2/2] Update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c5d51369..3422d470 100644 --- a/CHANGELOG.md +++ b/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`