Merge pull request #31 from jemten/publish_intervals

publish gens intervals by default
nf-core · Jun 12, 2024 · 92d1f46 · 92d1f46
2 parents a0333ea + 8711079
commit 92d1f46
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -22,6 +22,7 @@ Initial release of nf-core/createpanelrefs, created with the [nf-core](https://n
 - [#24](https://github.com/nf-core/createpanelrefs/pull/24) - Updates germlinecnvcaller subworkflow to use mappability and segmental duplications track
 - [#24](https://github.com/nf-core/createpanelrefs/pull/24) - Updates germlinecnvcaller and gens subworkflows to use custom names for panel of normals.
 - [#28](https://github.com/nf-core/createpanelrefs/pull/28) - Updates default args for gens subworkflow and made the parameters available from the command line.
+- [#31](https://github.com/nf-core/createpanelrefs/pull/31) - Publish interval_list file from gens subworkflow by default.
 
 ### `Fixed`
 

diff --git a/conf/modules/gens_pon.config b/conf/modules/gens_pon.config
@@ -40,6 +40,11 @@ process {
         ext.args = { ["--imr OVERLAPPING_ONLY",
                         "--bin-length ${params.gens_bin_length}"].join(" ")
                     }
+        publishDir = [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/gens_pon/intervals" },
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
     }
 
     withName: '.*GENS_PON:GATK4_COLLECTREADCOUNTS' {