Merge pull request #188 from MaxUlysse/Bee

fix input/output for IndexBamFile
nf-core · Apr 17, 2020 · ae4a2b0 · ae4a2b0
2 parents 411c2d5 + 60437f1
commit ae4a2b0
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -79,6 +79,7 @@ Piellorieppe is one of the main massif in the Sarek National Park.
 - [#164](https://github.com/nf-core/sarek/pull/164) - Fix issues when running with `Sentieon`
 - [#164](https://github.com/nf-core/sarek/pull/164) - Add more VCFs to annotation
 - [#167](https://github.com/nf-core/sarek/pull/167) - Add `--markdup_java_options` documentation to fix [#166](https://github.com/nf-core/sarek/issues/166)
+- [#188](https://github.com/nf-core/sarek/pull/188) - Fix input/output channels for process `IndexBamFile` to match actual files in the `mapped.tsv` files
 
 ### Deprecated - [2.6dev]
 

diff --git a/main.nf b/main.nf
@@ -1205,10 +1205,10 @@ process IndexBamMergedForSentieon {
     tag {idPatient + "-" + idSample}
 
     input:
-        set idPatient, idSample, file(bam) from mergedBamForSentieon
+        set idPatient, idSample, file("${idSample}.bam") from mergedBamForSentieon
 
     output:
-        set idPatient, idSample, file(bam), file("${idSample}.bam.bai") into bamForSentieonDedup
+        set idPatient, idSample, file("${idSample}.bam"), file("${idSample}.bam.bai") into bamForSentieonDedup
 
     script:
     """
@@ -1226,18 +1226,17 @@ process IndexBamFile {
     publishDir "${params.outdir}/Preprocessing/${idSample}/Mapped", mode: params.publish_dir_mode
 
     input:
-        set idPatient, idSample, file(bam) from bam_mapped_merged_to_index
+        set idPatient, idSample, file("${idSample}.bam") from bam_mapped_merged_to_index
 
     output:
-        set idPatient, idSample, file(bam), file("*.bai") into bam_mapped_merged_indexed
+        set idPatient, idSample, file("${idSample}.bam"), file("${idSample}.bam.bai") into bam_mapped_merged_indexed
         set idPatient, idSample into tsv_bam_indexed
 
     when: !(params.known_indels)
 
     script:
     """
-    samtools index ${bam}
-    mv ${bam}.bai ${bam.baseName}.bai
+    samtools index ${idSample}.bam
     """
 }