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s-andrews / nextflow_pipelines

The set of NGS processing pipelines used at Babraham
GNU General Public License v3.0
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Pipelines fail on filenames containing a + symbol #29

Open s-andrews opened 2 years ago

s-andrews commented 2 years ago

Not sure why, but all of the pipelines I ran completely ignored the files with a + in their name. This isn't a special character in unix so it's probably a nextflow thing.

s-andrews commented 2 years ago

Looks like this might be the same thing https://github.com/nextflow-io/nextflow/issues/219

s-andrews commented 2 years ago

Specifically it seems to be trim_galore which can't cope with this. FastQC and FastQ_Screen both seem to run OK.

s-andrews commented 2 years ago

Possibly it's to do with pairing?

FelixKrueger commented 2 years ago

that's quite possible...