Merge pull request #1217 from maxulysse/joint_mutect2_tumor_only_fix

FIX: Final fix for joint_mutect2 tumor_only in mutect2 subworkflow
nf-core · Sep 8, 2023 · c59cd0b · c59cd0b
2 parents 75829ff + 6336cf6
commit c59cd0b
Show file tree

Hide file tree

Showing 3 changed files with 9 additions and 10 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -62,6 +62,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas
 - [#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
 - [#1216](https://github.com/nf-core/sarek/pull/1216) - Better test coverage for variant calling `*_all` subworkflows
+- [#1217](https://github.com/nf-core/sarek/pull/1217) - Fix `groupTuple` statement 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
@@ -113,12 +113,7 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
     if (tools.split(',').contains('mutect2')) {
         BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2(
             // Adjust meta.map to simplify joining channels
-            // 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', 'data_type', 'patient') , cram, crai ] :
-                [ meta + [ id:meta.sample ] - meta.subMap('sample', 'status', 'data_type'), cram, crai ]
-            },
+            cram.map{ meta, 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 ] },
             // Remap channel to match module/subworkflow

diff --git a/subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf b/subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf
@@ -41,12 +41,15 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2 {
     if (joint_mutect2) {
         // Perform variant calling using mutect2 module in tumor single mode
         // Group cram files by patient
-        patient_crams = input.groupTuple()
+        input_joint = input
+            .map{ meta, input, index -> [ meta + [ id:meta.patient ], input, index ] }
+            .groupTuple()
+
         // Add intervals for scatter-gather scaling
-        patient_cram_intervals = patient_crams.combine(intervals)
+        input_joint_intervals = input_joint.combine(intervals)
         // Move num_intervals to meta map and reorganize channel for MUTECT2 module
-            .map{ meta, t_cram, t_crai, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], t_cram, t_crai, intervals ] }
-        MUTECT2(patient_cram_intervals, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi)
+            .map{ meta, cram, crai, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], cram, crai, intervals ] }
+        MUTECT2(input_joint_intervals, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi)
     }
     else {
         // Perform variant calling using mutect2 module in tumor single mode