Enabling stdinput in the style of FastQC#89
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kerrycobb wants to merge 1 commit intosmithlabcode:masterfrom
Open
Enabling stdinput in the style of FastQC#89kerrycobb wants to merge 1 commit intosmithlabcode:masterfrom
kerrycobb wants to merge 1 commit intosmithlabcode:masterfrom
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A feature of FastQC that is missing from falco is the ability to use stdin as input. I made a few changes to allow it to be done in the style of FastQC like
cat <fastq files> | falco stdin:<prefix>.I haven't tested it extensively but at a glance it looks like it's working with fastqc files. It assumes fastq format. I'm not sure how FastQC accomodates other formats as stdin. Perhaps with the --format flag.
I don't have much time right now to keep working on this. My fork is doing what I needed. Maybe this can inspire or help you to implement this feature. If you are receptive, I may be able to put some more effort in at some point to make this more robust and add some tests.