Merge pull request #626 from maxulysse/dev_annotation

maxulysse · web-flow · commit 3fce8e253301 · 2022-07-08T10:22:28.000+02:00
Annotation code polish
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -108,7 +108,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#581](https://github.com/nf-core/sarek/pull/581) - `TIDDIT` is back
 - [#590](https://github.com/nf-core/sarek/pull/590) - Fix empty folders during scatter/gather
 - [#592](https://github.com/nf-core/sarek/pull/592) - Fix optional resources for Mutect2, GetPileupSummaries, and HaplotypeCaller: issue [#299](https://github.com/nf-core/sarek/issues/299), [#359](https://github.com/nf-core/sarek/issues/359), [#367](https://github.com/nf-core/sarek/issues/367)
-- [#598](https://github.com/nf-core/sarek/pull/598), [#614](https://github.com/nf-core/sarek/pull/614) - Remove WARNING message for config selector not matching
+- [#598](https://github.com/nf-core/sarek/pull/598), [#614](https://github.com/nf-core/sarek/pull/614), [#626](https://github.com/nf-core/sarek/pull/626) - Remove WARNING message for config selector not matching
 - [#599](https://github.com/nf-core/sarek/pull/599) - Add checks for correct data type for `params.step`
 - [#599](https://github.com/nf-core/sarek/pull/599) - Add checks for no empty `--tools` with `--step variant_calling` or `--step annotation`
 - [#600](https://github.com/nf-core/sarek/pull/600) - Remove `nf-core lint` warnings
diff --git a/conf/modules.config b/conf/modules.config
@@ -1191,7 +1191,9 @@ process{
                     pattern: "*{gz,gz.tbi}"
             ]
         }
+    }
 
+    if (params.tools && (params.tools.contains('snpeff') || params.tools.contains('merge'))) {
         withName: 'NFCORE_SAREK:SAREK:ANNOTATE:ANNOTATION_SNPEFF:TABIX_BGZIPTABIX' {
             publishDir       = [
                 mode: params.publish_dir_mode,

Original file line number	Diff line number	Diff line change
`@@ -1191,7 +1191,9 @@ process{`
`1191`	`1191`	`pattern: "*{gz,gz.tbi}"`
`1192`	`1192`	`]`
`1193`	`1193`	`}`
	`1194`	`+ }`
`1194`	`1195`
	`1196`	`+ if (params.tools && (params.tools.contains('snpeff') \|\| params.tools.contains('merge'))) {`
`1195`	`1197`	`withName: 'NFCORE_SAREK:SAREK:ANNOTATE:ANNOTATION_SNPEFF:TABIX_BGZIPTABIX' {`
`1196`	`1198`	`publishDir = [`
`1197`	`1199`	`mode: params.publish_dir_mode,`