Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix typo #293

Merged
merged 2 commits into from
Oct 16, 2020
Merged

Fix typo #293

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
589048e
fix: typo CamelCase -> snake_case
maxulysse Oct 16, 2020
29d66a5
chores: update CHANGELOG
maxulysse Oct 16, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
- [#272](https://github.com/nf-core/sarek/pull/272) - Fix annotation `--tools merge` issue
- [#279](https://github.com/nf-core/sarek/pull/279) - Fix issue with `--step prepare_recalibration` [#267](https://github.com/nf-core/sarek/issues/267)
- [#280](https://github.com/nf-core/sarek/pull/280) - Use HTML codes instead of `<` and `>` in docs
- [#293](https://github.com/nf-core/sarek/pull/293) - Fix typo issue when printing infos [#292](https://github.com/nf-core/sarek/issues/292)

### Removed

Expand Down
8 changes: 4 additions & 4 deletions main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -214,8 +214,8 @@ skipQC = params.skip_qc ? params.skip_qc == 'all' ? skipQClist : params.skip_qc.
if (!checkParameterList(skipQC, skipQClist)) exit 1, 'Unknown QC tool(s), see --help for more information'

annoList = defineAnnoList()
annotateTools = params.annotate_tools ? params.annotate_tools.split(',').collect{it.trim().toLowerCase().replaceAll('-', '')} : []
if (!checkParameterList(annotateTools,annoList)) exit 1, 'Unknown tool(s) to annotate, see --help for more information'
annotate_tools = params.annotate_tools ? params.annotate_tools.split(',').collect{it.trim().toLowerCase().replaceAll('-', '')} : []
if (!checkParameterList(annotate_tools,annoList)) exit 1, 'Unknown tool(s) to annotate, see --help for more information'

// Check parameters
if ((params.ascat_ploidy && !params.ascat_purity) || (!params.ascat_ploidy && params.ascat_purity)) exit 1, 'Please specify both --ascat_purity and --ascat_ploidy, or none of them'
Expand Down Expand Up @@ -3500,9 +3500,9 @@ if (step == 'annotate') {
Channel.fromPath("${params.outdir}/VariantCalling/*/TIDDIT/*.vcf.gz")
.flatten().map{vcf -> ['TIDDIT', vcf.minus(vcf.fileName)[-2].toString(), vcf]}
).choice(vcfToAnnotate, vcfNoAnnotate) {
annotateTools == [] || (annotateTools != [] && it[0] in annotateTools) ? 0 : 1
annotate_tools == [] || (annotate_tools != [] && it[0] in annotate_tools) ? 0 : 1
}
} else if (annotateTools == []) {
} else if (annotate_tools == []) {
// Annotate user-submitted VCFs
// If user-submitted, Sarek assume that the idSample should be assumed automatically
vcfToAnnotate = Channel.fromPath(tsvPath)
Expand Down