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I resolved the error. The Issue arose from how fastp handles fastq.gz files. I believe the .gz extension si necessary for the tool to process it as a gz. |
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I have a nextflow process that takes fastqs from multiple lanes. Each lane can be extremely large, so merging them and writing the merged file to temp is time consuming. I wanted to perform something akin to a function substitution so I could read the files directly into the tool I am using.
The fastqs is a channel containing paths to my fastq files.
e.g:
minimap2 <(${fastqs}) ...
And
fastp -i <(${fastqs1}) ...
However this throws and error. It's there a way to do this correctly in nextflow, or an alternative that avoids creating temp files?
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