Merge pull request #320 from genomic-medicine-sweden/fix-bwa-output-bug

Fix bwa output bug
genomic-medicine-sweden · Jun 11, 2024 · c129653 · c129653
2 parents f16e5e6 + 32cab91
commit c129653
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,7 +19,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 
 - ShigaPass URL fixed
-- Fix qc channel regarding `mycobacterium_tuberculosis`
+- Fixed qc channel regarding `mycobacterium_tuberculosis`
+- Fixed bwa output file bug
 
 ### Changed
 

diff --git a/nextflow-modules/modules/bwa/main.nf b/nextflow-modules/modules/bwa/main.nf
@@ -68,7 +68,7 @@ process bwa_mem {
         -t $task.cpus \\
         \$INDEX \\
         ${reads.join(' ')} \\
-        | samtools sort $args2 --threads ${task.cpus} -o ${sampleName}.bam -
+        | samtools sort $args2 --threads ${task.cpus} -o $output -
 
     cat <<-END_VERSIONS > ${sampleName}_${task.process}_versions.yml
     ${task.process}: