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FelixKrueger / TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
GNU General Public License v3.0
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specify output file for pipelines ? #102

Closed colindaven closed 4 years ago

colindaven commented 4 years ago

Hi,

using this to trim Nextera transposase seqs, which works great, I found it very strange that I can't specify an output file.

This is not great for a pipeline which I am adding it to (or did I overlook something?).

Is there any reason an output file / files option would be unworkable ?

Thanks

FelixKrueger commented 4 years ago

Hi Colin,

Instead of allowing users to specify completely arbitrary names, you can choose to use a basename instead of letting Trim Galore derive the name from the input filenames. This is from the --help:

--basename <PREFERRED_NAME>

Use PREFERRED_NAME as the basename for output files, instead of deriving the filenames from the input files.
Single-end data would be called PREFERRED_NAME_trimmed.fq(.gz), or PREFERRED_NAME_val_1.fq(.gz) and
PREFERRED_NAME_val_2.fq(.gz) for paired-end data. --basename only works when 1 file (single-end) or 2
files (paired-end) are specified, but not for longer lists.

Since the filenames are completely predicable, this behaviour should be fairly easy to implement in a pipeline, or simply use rename afterwards. I hope this is acceptable?

colindaven commented 4 years ago

Hi Felix,

thanks for the prompt reply. I prefer to have complete control over the name to keep is short. I solved this with an additional mv command in the pipeline.

Colin