Merge branch 'dev' into controlfreec_bug

nf-core · Sep 7, 2023 · 58457e8 · 58457e8
2 parents 29eb2d6 + c695d25
commit 58457e8
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -59,6 +59,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas
 - [#1204](https://github.com/nf-core/sarek/pull/1204) - Fix issue with nf-validation: lane can be a requirement of bam too now
 - [#1205](https://github.com/nf-core/sarek/pull/1205) - Less tests triggered
 - [#1214](https://github.com/nf-core/sarek/pull/1214) - Don't pass in intervals file to ControlFREEC for WGS analysis
+- [#1215](https://github.com/nf-core/sarek/pull/1215) - Fix `meta.id` for mutect2 tumor_only subworkflows
 
 ### Dependencies
 

diff --git a/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf b/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
@@ -116,8 +116,8 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
             // joint_mutect2 mode needs different meta.map than regular mode
             cram.map{ meta, cram, crai ->
                 joint_mutect2 ?
-                [ meta + [ id:meta.patient ] - meta.subMap('sample', 'status', 'num_intervals', 'data_type', 'patient') , cram, crai ] :
-                [ meta - meta.subMap('sample', 'status', 'num_intervals', 'data_type'), cram, crai ]
+                [ meta + [ id:meta.patient ] - meta.subMap('sample', 'status', 'data_type', 'patient') , cram, crai ] :
+                [ meta + [ id:meta.sample ] - meta.subMap('sample', 'status', 'data_type'), cram, crai ]
             },
             // Remap channel to match module/subworkflow
             fasta.map{ it -> [ [ id:'fasta' ], it ] },