Stav Grossfeld

Results 2 comments of Stav Grossfeld

Sarek parabricks gpu test_full: A USER ERROR has occurred: Bad input: Sample HCC1395_HCC1395N is not in BAM header: [sample]

[nextflow_log_sarek_gpu_july_1.txt](https://github.com/user-attachments/files/21008176/nextflow_log_sarek_gpu_july_1.txt) Hi @famosab , thank you for working on this! I ran your changes, interestingly it didn't hit Mutect2 but instead ran ascat and hit this error ``` INFO: Environment...

Sarek parabricks gpu test_full: A USER ERROR has occurred: Bad input: Sample HCC1395_HCC1395N is not in BAM header: [sample]

Hey @famosab with --tools mutect2 your fix worked.. so seems like theres an unrelated error in the test_full still relating to Ascat command ``` nextflow run famosab/sarek -r fix/fq2bam -profile...