Gatk pipeline wdl on multiples sample input

Question

[quentin54520]

Hello all,

i would like to use gatk pipelines with cromwell on our hpc, however for germline single sample pipeline i wanted to know if there is a way to run it directly on multiple samples? I can't see myself writing more than a hundred input.json files with one sample per file ...

according to my research there is a read tsv function but I don't see how to integrate it into the pipeline (the idea being to have a tsv file with the name of the sample, the path of the file, etc. )

Thanks in advance.