Major update of latest template from nf-core #262
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modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
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Most of this is done in nf-core#70 |
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I like it better if we have one PR for template merge. And one PR for version update. |
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@ypriverol @jpfeuffer In all DIA test, the identification and quantification work was skipped, and Dia-NN did not work, which caused pmultiqc not to receive the diann_report and mistook it for the DDA type. |
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We should run the identification and quant steps. Can you fix it @WangHong007 |
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@ypriverol can you maybe do a new PR where you are just changing the version numbers. a) this will have a much cleaner commit history and b) we can be more sure about errors caused by this |
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@jpfeuffer @WangHong007 @daichengxin are working already in the PR. |
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Ok. I just think you would save some time. Because most of the errors are not present on nf-core. |
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So I think the reason is the very complicated merge in this PR. |
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Hi @jpfeuffer, All issues are solved except for TMT. I tested TMT locally, it also reported same problems. But I tested it using previous version, it's ok. These are two proteininference input files from before openms updating and 2.9.0. Could you review? Thanks a lot. |
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That was very helpful @daichengxin . We probably also need the idXMLs that were used in IDMapper. Do you have them? |
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TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210_.zip ConsensusXML and idXML |
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thanks I will look into it immediately |
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fixed in OpenMS/OpenMS#6758 |
jpfeuffer
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Mar 13, 2023
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@jpfeuffer we are ready. You can merge the PR. |
jpfeuffer
approved these changes
Mar 13, 2023
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PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).