Closed ypriverol closed 1 year ago
Can you add a "--version" command so we dont have to hardcode the version in workflows everytime and everywhere? Would be awesome
parse_sdrf.py --version
give the version of the tool.
How can you specify that both raw and d are converted to mzml?
You mean having a conversion where you have more than one file type? Right now you will only have one file type to another, this is allowed: d:mzML
or raw:mzML
, d:d
, etc.
what if you have multiple file types in the initial design?
We don't allow that in quantms or even OpenMS. I guess is a really future use case.
It is allowed in quantms. I ran pipelines with raw and mzml before.
If you only allow one type of raw file, why a mapping at all? Then you just need an option "out_type".
Ok, what will be the expected behaviour, something like:
raw:mzml d:d
Which mean convert the raw to mzml and keep the d as d?
Yes exactly.
What should happen if the user gives contradictory changes, like d:d and d:raw ? Error?
I will put the following behavior: --extension_convert 'raw:mzml, d:mzml'
if multiple conversion options are provided for the same filetype: raw:mzml, raw:raw
the tool will through an error.
@jpfeuffer the following commit allows multiple file conversions: https://github.com/bigbio/sdrf-pipelines/pull/148/commits/9c304a7a4dac617f231c1f4f251c5fb9d506caf4
extension_convert
reflecting discussion in https://github.com/bigbio/sdrf-pipelines/issues/145 and PR in quantms https://github.com/bigbio/quantms/pull/275.