CGI results get overwritten if two of mutations, cnas, translocations are specified

[HomoPolyethylen]

Description of the bug

When specifying two or more of mutations, cnas, translocations, for the same sample (each in one row in the samplesheet), they get queried individually, overwriting the previous results.

Probably due to output files having the same name.

potential fixes:

• join channels / group by sample so that a single query containing all variant types can be submitted
• set output names depending on variant type
• ...

Command used and terminal output

nextflow run qbic-pipelines/variantmtb -r dev -profile docker -params-file params.yml

Relevant files

input_SNPs-CNAs.csv

params.yml

input             : "input_SNPs-CNAs.csv"
outdir            : "variantmtb_debug_out"
genome            : "GRCh37"
databases         : "cgi"
cgi_cancer_type   : "Any cancer type"

System information

No response