move custom samplesheet parsing code out of driver script

BIMSBbioinfo / pigx_bsseq

bisulfite sequencing pipeline from fastq to methylation reports

https://bioinformatics.mdc-berlin.de/pigx/

GNU General Public License v3.0

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move custom samplesheet parsing code out of driver script #66

Open rekado opened 6 years ago

rekado commented 6 years ago

The driver script should be usable by all pipelines and be moved to the pigx repository. Before that can be done, we need to move all custom samplesheet parsing code out of the script.

rekado commented 6 years ago

in particular it's these procedures:

parse_diff_meth
get_filenames
get_extension
fq_suffix
is_zipped
splitext_fqgz
parse_samples

This also includes special diffmeth processing in generate_config.

rekado commented 6 years ago

parse_diff_meth is gone since c5d38e7.

rekado commented 6 years ago

This depends on #89

Blosberg commented 6 years ago

This depends on #89

So, then wishlist for now?

rekado commented 6 years ago

yes. Done.