Maxime U Garcia

Hi, Sorry, I did not notice this question before, so I'm only replying now. Sarek was at the beginning designed to analyse tumor/normal pairs (and additional relapses), but we realised...

In Sarek, we have one BWA-mem | samtools sort process cf: https://github.com/SciLifeLab/Sarek/blob/master/main.nf#L166-L187 Then we're grouping samples by the read groups: https://github.com/SciLifeLab/Sarek/blob/master/main.nf#L199-L205 And then merging the BAMs: https://github.com/SciLifeLab/Sarek/blob/master/main.nf#L207-L222

We have a similar idea that we use for germline sample: https://github.com/SciLifeLab/Sarek/blob/master/main.nf#L738-L766

Not sure about the `s` to `z` but apart from that, it looks ok to me

looks ok to me, just need to be sure that it's working, if I remember well, that was our whole issue there

@Shaun-Regenbaum sorry about that, but I'd reckon we'd need to fix the conflicts

Fully agreeing on that, need to refactor the whole references genome handling

any chance adding that make this work: ``` dbsnp: "s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz" dbsnp_tbi: "s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi" known_indels: "[s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz](s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/%7BMills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels%7D.vcf.gz)" known_indels_tbi: "[s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi](s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/%7BMills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels%7D.vcf.gz.tbi)" ```

Can you share your samplesheet?

Nevermind, saw it