User: dami

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dami10
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Posts by dami

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Comment: C: bedtools sort -faidx in CWL
... You are right, the bed file to be sorted needs to be added to the command at the top with the -i flag so that you get: bedtools sort -header -faidx ref.fasta.fai -i some.bed ...
written 5 months ago by dami10
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Comment: C: bedtools sort -faidx in CWL
... Thanks for your response! What you are saying is true, However, if this is part of a bigger pipeline where the .fai is also needed as a fasta index file its repetitive to add it everywhere manually. So I was hoping that there was a way to access the secondary files directly. ...
written 5 months ago by dami10
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bedtools sort -faidx in CWL
... How does one uses a secondairy file as the input to a command in CWL? I try to do : bedtools sort -header -faidx hg38.fasta.fai So in CWL i got to #!/usr/bin/env cwl-runner cwlVersion: v1.0 class: CommandLineTool label: "sort a bed file based on occurrence in fasta" ...
bedtools cwl sort written 7 months ago by dami10 • updated 3 months ago by kaushik.ghose60

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