diff --git a/CHANGELOG.md b/CHANGELOG.md index b16d6abfb2..d678bf7abb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -58,6 +58,8 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a - [#143](https://github.com/nf-core/sarek/pull/143) - Fix annotation CI testing with `snpEff` and `VEP` - [#144](https://github.com/nf-core/sarek/pull/144) - Fix CircleCI for building `VEP` containers - [#146](https://github.com/nf-core/sarek/pull/146) - Fix `--no_intervals` for `Mutect2` cf [#135](https://github.com/nf-core/sarek/issues/135) +- [#156](https://github.com/nf-core/sarek/pull/156) - Fix typos +- [#156](https://github.com/nf-core/sarek/pull/156) - Fix issues with `dbsnp` files while using only `Sention` tools ### `Deprecated` diff --git a/main.nf b/main.nf index 08e9876c22..788301b250 100644 --- a/main.nf +++ b/main.nf @@ -285,8 +285,8 @@ if (params.chrDir) exit 1, "The params `--chrDir` has been removed.\n\tPlease ch params.chrLength = null if (params.chrLength) exit 1, "The params `--chrLength` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--chr_length" -params.dnsnpIndex = null -if (params.dnsnpIndex) exit 1, "The params `--dnsnpIndex` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--dnsnp_index" +params.dbsnpIndex = null +if (params.dbsnpIndex) exit 1, "The params `--dbsnpIndex` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--dbsnp_index" params.fastaFai = null if (params.fastaFai) exit 1, "The params `--fastaFai` has been removed.\n\tPlease check: https://nf-co.re/sarek/docs/usage.md#--fasta_fai" @@ -438,7 +438,7 @@ params.ac_loci_gc = params.genome && 'ascat' in tools ? params.genomes[params.ge params.bwa = params.genome && params.fasta && 'mapping' in step ? params.genomes[params.genome].bwa ?: null : null params.chr_dir = params.genome && 'controlfreec' in tools ? params.genomes[params.genome].chr_dir ?: null : null params.chr_length = params.genome && 'controlfreec' in tools ? params.genomes[params.genome].chr_length ?: null : null -params.dbsnp = params.genome && ('mapping' in step || 'controlfreec' in tools || 'haplotypecaller' in tools || 'mutect2' in tools) ? params.genomes[params.genome].dbsnp ?: null : null +params.dbsnp = params.genome && ('mapping' in step || 'controlfreec' in tools || 'haplotypecaller' in tools || 'mutect2' in tools || params.sentieon) ? params.genomes[params.genome].dbsnp ?: null : null params.dbsnp_index = params.genome && params.dbsnp ? params.genomes[params.genome].dbsnp_index ?: null : null params.dict = params.genome && params.fasta ? params.genomes[params.genome].dict ?: null : null params.fasta_fai = params.genome && params.fasta ? params.genomes[params.genome].fasta_fai ?: null : null @@ -456,7 +456,7 @@ ch_ac_loci = params.ac_loci && 'ascat' in tools ? Channel.value(file(params.ac_l ch_ac_loci_gc = params.ac_loci_gc && 'ascat' in tools ? Channel.value(file(params.ac_loci_gc)) : "null" ch_chr_dir = params.chr_dir && 'controlfreec' in tools ? Channel.value(file(params.chr_dir)) : "null" ch_chr_length = params.chr_length && 'controlfreec' in tools ? Channel.value(file(params.chr_length)) : "null" -ch_dbsnp = params.dbsnp && ('mapping' in step || 'controlfreec' in tools || 'haplotypecaller' in tools || 'mutect2' in tools) ? Channel.value(file(params.dbsnp)) : "null" +ch_dbsnp = params.dbsnp && ('mapping' in step || 'controlfreec' in tools || 'haplotypecaller' in tools || 'mutect2' in tools || params.sentieon) ? Channel.value(file(params.dbsnp)) : "null" ch_fasta = params.fasta && !('annotate' in step) ? Channel.value(file(params.fasta)) : "null" ch_fai = params.fasta_fai && !('annotate' in step) ? Channel.value(file(params.fasta_fai)) : "null" ch_germline_resource = params.germline_resource && 'mutect2' in tools ? Channel.value(file(params.germline_resource)) : "null"