Merge pull request #1465 from asp8200/fix_subworkflow_BAM_SENTIEON_DEDUP

Fix call to SENTIEON_DEDUP
nf-core · Apr 15, 2024 · aaf2151 · aaf2151
2 parents 63bc017 + dd0176e
commit aaf2151
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -56,6 +56,7 @@ Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the othe
 - [#1422](https://github.com/nf-core/sarek/pull/1422) - Fix `Cannot serialize context map` warning
 - [#1462](https://github.com/nf-core/sarek/pull/1462) - Fix ascat input channels
 - [#1463](https://github.com/nf-core/sarek/pull/1463) - Add `spark` profile to all gatk4spark tests
+- [#1465](https://github.com/nf-core/sarek/pull/1465) - Fix input channels for `SENTIEON_DEDUP`
 
 ### Removed
 

diff --git a/subworkflows/local/bam_sentieon_dedup/main.nf b/subworkflows/local/bam_sentieon_dedup/main.nf
@@ -19,7 +19,7 @@ workflow BAM_SENTIEON_DEDUP {
     bam = bam.map{ meta, bam -> [ meta - meta.subMap('data_type'), bam ] }
     bai = bai.map{ meta, bai -> [ meta - meta.subMap('data_type'), bai ] }
     bam_bai = bam.join(bai, failOnMismatch:true, failOnDuplicate:true)
-    SENTIEON_DEDUP(bam_bai, fasta.map{fa -> [[:], fa]}, fasta_fai.map{fai -> [[:], fai]})
+    SENTIEON_DEDUP(bam_bai, fasta, fasta_fai)
 
     // Join with the crai file
     cram = SENTIEON_DEDUP.out.cram.join(SENTIEON_DEDUP.out.crai, failOnDuplicate: true, failOnMismatch: true)