FastQC args error with GNU parallel

[biobenkj]

Hi Felix,

For reasons I can't quite figure out, when I run TrimGalore! with GNU parallel it will give me an inappropriate number of input files error when I include the --fastqc_args option specifying an alternate output directory location.

I have 28 file pairs and have made sure that they do indeed pair correctly. If I remove the --fastqc_args option, it will operate normally.

Here is the command:

parallel trim_galore --illumina --paired --fastqc --fastqc_args "-o /path/to/my/folder" {} {=s/_1/_2/=} ::: *_1.fastq.gz

Thanks for your time!

[FelixKrueger]

Hi Ben,

I have to admit that I don't know an answer to why it doesn't work but I am guessing that it somehow has to do with the pattern recognition of GNU parallel (which I am not at all familiar with). Taken on its own, the command: trim_galore --illumina --paired --fastqc --fastqc_args "-o /path/to/my/folder" seems to work as intended in my hands.

I just realised that the original message I got from Github showed this command:

parallel trim_galore --illumina --paired --fastqc --fastqc_args "/path/to/my/folder" {} {=s/_1/_2/=} ::: *_1.fastq.gz

In this command, the -o was missing, so maybe that was the reason? Or does the folder name contain a pattern match as well?

[biobenkj]

Hi Felix,

Thanks for your reply! It may very well be based on parallel's way of handling things. The original command that I attached was edited because I forgot the -o option before the path. Interestingly, it does work fine in the absence of the -o (just gave it a shot - though FastQC will break since it goes to look for a folder that doesn't contain any files to run on). I keep trying to think of why it is doing this, but can't come up with anything reasonable. Feel free to close the issue and can edit if I come to any sort of conclusion. Thanks!

[FelixKrueger]

That sounds like a plan, maybe a GNU parallel developer would like to chip in? Cheers, Felix