sdrf-pipelines
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bigbio
A repository to convert SDRF proteomics files into pipelines config files
``` Command output: /usr/local/lib/python3.12/site-packages/sdrf_pipelines/sdrf/sdrf_schema.py:355: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead. validation_results = panda_sdrf.applymap(validate_string) /usr/local/lib/python3.12/site-packages/sdrf_pipelines/sdrf/sdrf_schema.py:355: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead. validation_results = panda_sdrf.applymap(validate_string) Multiple columns found...
This release will be a major release including multiple features and bug fixes. Issues: - [ ] #155 - [ ] #154 - [x] #153 - [ ] #152 -...
Hey, I noticed the SDRF validator is a bit difficult to maintain and to understand in it's current state, as it is one long python script. To make it more...
Hi! Would it be possible to include a free text validation for SDRF? This would smooth out the link between lesSDRF and the PRIDE submission pipeline. Always happy to help...
If you want to convert to openms or mq, there might be more restrictions on certain columns and entries like modifications or TMT channel nomenclature. We should make sure that...
In this example, we have the same file repated, the SDRF validatior should fails because not multiplexing is in place. https://github.com/bigbio/quantms/issues/328
When a file has an empty cell, would be great that the validator give the name of the column + the row index + the source name.
Hi ! I have made a sdrf file to use as input in the nf-core/quantms pipeline (v.1.2.0). But I encounter an error related to the tmt labels (or so I...
https://github.com/bigbio/sdrf-pipelines/blob/96e2a69faaa2e2636020f612bd7507d614460403/sdrf_pipelines/maxquant/maxquant.py#L78 Sorting the default label results in `label_list` being `['2', 'M', 'T', 'T']` with a length of 4 which then probably leads to [leads ](https://github.com/bigbio/sdrf-pipelines/blob/96e2a69faaa2e2636020f612bd7507d614460403/sdrf_pipelines/maxquant/maxquant.py#L62) being true and we have...
Variables with failed assignment in a try block are not available in the corresponding exception. https://github.com/bigbio/sdrf-pipelines/blob/cf2425d5767cddfaaae1b31d0385eef51eff6171/sdrf_pipelines/zooma/ols.py#L175 The logging here needs to either compose the url separately or use the variables...