create index on "markduplicates" output BAM

[ahwanpandey]

rnafusion/modules/nf-core/gatk4/markduplicates/main.nf

Line 47 in 4e5de7d

gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\

Hello,

I am using v4.0.0

Can you please add "--CREATE_INDEX true" to the marduplicates process and also perhaps rename the output file to SAMPLE_ID.Aligned.sortedByCoord.dupsMarked.bam ?

I think you could also remove the extra BAM files in the following folders and just keep the one from the "markduplicates" output?

KEEP = ./picard/66893_Tumor_RNA.bam
DELETE = ./samtools/66893_Tumor_RNA.Aligned.sortedByCoord.bam
DELETE = ./star/66893_Tumor_RNA.Aligned.sortedByCoord.out.bam

I can delete these later but seems like a waste of space and probably could be deleted by the pipeline itself?

Thanks!
Ahwan

[ahwanpandey]

Hello,

Just checking if you were able to look into this?

Thanks!