dkfz-odcf / coworkflowsbaseplugin Goto Github PK
View Code? Open in Web Editor NEWA basic Roddy plugin for computational oncology workflows
License: MIT License
A basic Roddy plugin for computational oncology workflows
License: MIT License
Less errors, more success :D
Or extend the existing base workflow(s) to cover this as well.
NOTE that the cohort mechanism works different than the default pid based mechanism.
Not sure whether extractSampleNameFromXXX
scales. Did you consider using extractSampleNamesFrom
with possible values, like "bamFileName", "outputFileNames" (but this the latter example would be completely vague and intersecting with "bamFileName" -- so a better value would be needed). Also the concept of input and output directory is pretty vague for the plugin, because the output directory is often also used as input directory!
Maybe "extractSampleNamesFrom": "bamFileNames", "allFiles".
Method findFilenameFromOnScriptParameterPatterns
has a selectiontag parameter that is ignored. Fix this to allow restricting filename patterns (e.g. insert size files in WES align/merge vs. targetExtract job need different composition of filename that could efficiently be implemented with a selectiontag='shortBaseName' vs selectiontag='longBaseName' or similar)
E.g.:
Did your bam file names match the pattern: ?
Do you need to adapt possibleControlSampleNamePrefixes...
Working with many versions of the COWorkflows plugin is a mess.
Modify all plugins to use this version. Ensure all changes from non-public other COWorkflow repos into this repo.
function isControlWorkflow() {
test "${isControlWorkflow:-true}" == "true"
}
function isNoControlWorkflow() {
test "${isNoControlWorkflow:-false}" == "true"
}
[[ isControlWorkflow() ]] &&
Unfortunately, the sample extraction is not linked to the file search which results in unexpected behaviour, e.g.:
Time for a new metadata model.
We currently do have fastq loading code, but it is not in here.
assume to have xml file with
<cvalue name='possibleTumorSampleNamePrefixes' value='( metastasis tumor tumor02 tumor04 )' type='bashArray'/>
and the following bam files:
metastasis_PID_merged.mdup.bam
tumor_PID_merged.mdup.bam
Currently, metastasis is chosen as the tumor sample (tumor sample is simply neglected).
No warning/error is thrown to inform the user that several matching tumor bam files exist in the alignment folder.
Request: Throw an error (do not start worklow) and propose to set command line cvalue possibleTumorSampleNamePrefixes in order to explicitly choose one of both bam files.
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