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Add tellread #149
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Add tellread #149
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Version 2.0 of TellSeq support removes the master tellread.sh script and the drop-in replacement TRConvertJob.py for Job()s that wrap individual steps in the original script. These steps can be used in whole or in part in varying order in the refactored SPP plugin (qp-klp).
Added optional parameter to Pipeline() class that overwrites the values in the lane column of a sample-sheet's data section. This functionality used to reside in the qp-klp plugin and is a common usage pattern. This allows SPP to override the value in a sample-sheet's lane column with the value provided by the user at submission time.
Fixes error found when post-processing adapter-trimmed fastq files. All files were being moved into one of the project sub-folders, rather than into their associated folders. This appears to be due to recent implementation change. All files are now moved into their correct folder.
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@antgonza There are 36 files to review, which is quite large, but a number are new files in the contrib directory that don't need reviewing. There's also new Jinja2 template files and they're fairly easy to read. Many files just contain small changes. There is also some new code to test processing squeue output and a simulated squeue python script. |
antgonza
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Nov 25, 2024
sequence_processing_pipeline/templates/compute_sequence_counts_for_normalization.sbatch
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Request from Antonio to make TRNormCountsJob more generalized for current and upcoming work. TRNormCountsJob replaced w/SeqCountsJob: * takes a list of paths to fastq and/or fastq.gz files. * runs seqtk to count sequences and bases in parallel. * aggregator code produces a json file of counts from log output.
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@antgonza Ready for review! Thanks again! |
This was referenced Dec 2, 2024
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Changes and additions to support tellseq.