User

Matthias De Smet

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Recent activity by Matthias De Smet

  • Cromwell question: localization of reference files

    Hi, First of all, sorry for asking a question thats already been asked 100's of times, but I can't seem to find an answer that applies. I'm trying to run an alignment task in docker using bwa-mem2,...

    • 2 followers
    • 3 comments
    • 0 votes

  • Using fofn files in docker

    Hi, I've got a task that runs in docker and creates a fofn file. This fofn is then to be used as input for another task (not in docker). However, the filepaths in the fofn are relative to the cromw...

    • 2 followers
    • 5 comments
    • 0 votes

  • map Array[File] to Object[samplename, Array[Files] based on filename

    Hi, We're creating a workflow to demultiplex Illumina bcl's to uBam using Picard. The downside here is that Picard creates files per lane. I'm trying to merge the uBam's/sample/lane into 1 uBam/sam...

    • 6 followers
    • 7 comments
    • 1 vote