Merge pull request #13 from TRON-Bioinformatics/remove_star_bam_sorting

Remove outSAMtype parameter
TRON-Bioinformatics · Jul 19, 2024 · ccbdb3e · ccbdb3e
2 parents 8ec8065 + cc31d59
commit ccbdb3e
Showing 1 changed file with 0 additions and 2 deletions.
diff --git a/modules/02_star.nf b/modules/02_star.nf
@@ -28,7 +28,6 @@ process STAR {
     --outReadsUnmapped Fastx \
     --outFilterMismatchNoverLmax 0.02 \
     --runThreadN ${task.cpus} \
-    --outSAMtype BAM SortedByCoordinate \
     --outFileNamePrefix ${name}.
 
     mv ${name}.Aligned.sortedByCoord.out.bam ${name}.bam
@@ -67,7 +66,6 @@ process STAR_SE {
     --outReadsUnmapped Fastx \
     --outFilterMismatchNoverLmax 0.02 \
     --runThreadN ${task.cpus} \
-    --outSAMtype BAM SortedByCoordinate \
     --outFileNamePrefix ${name}.
 
     mv ${name}.Aligned.sortedByCoord.out.bam ${name}.bam