User: alanh

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alanh10
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Posts by alanh

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Use filename found in an input Directory in a CommandLineTool
... We're writing CWL's for a couple of different tools that want a FASTA reference, but refer to them in different ways. For example, STAR wants a --genomeDir as the input and the tool searches for the files it expects in that directory, but BWA and Picard want the actual fasta filename as input, and ...
cwl written 11 months ago by alanh10 • updated 11 months ago by bogdan.gavrilovic210
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Comment: C: CWL: How do I use pipes?
... Can you provide an example that actually uses the ShellCommandRequirement and shellQuote:false? I know that the "right" way is using the "streamable: true" but what do you do if you CWL runner tool doesn't support that and you don't want to save the intermediate outputs? I am new to CWL, so I ...
written 12 months ago by alanh10
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Comment: C: Bam Header Edit
... Doesn't samtools reheader output the corrected bam to STDOUT, so you'll need to redirect the output to a file? i.e. the last line there should be something like: samtools reheader header.sam $BAM > ${BAM%.bam}.reheadered.bam ...
written 21 months ago by alanh10

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