Tibanna #144
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Tibanna #144
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The output of "translate_sample_sheet_for_report" is generated in the current working directory with respect to the script. Depending on how it is executed, the file may end up in an unexpected location, causing Snakemake to wonder where the file went. The confusion disappears when writing to standard output and redirecting explicitly to the output file. This ensures that the working directory is irrelevant.
Adjust salmon_quant to use that tar file instead of just the index file. This ensures that the scheduler can arrange for all needed files to be available when the salmon_quant rule is processed.
We need this for counts_from_SALMON, which operates on the whole output directory of the salmon_quant rule.
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These are some of the changes that we found necessary for using PiGx RNAseq with Tibanna.
make distcheckpasses.While these changes include tar-wrapping for salmon rules, they do not include the same for STAR rules. In both cases the scripts access the whole directory instead of just a single file. We use tar to add the whole directory as an input. This complicates the script somewhat as the tar archive needs to be unpacked before use.
It's possible that more changes are necessary, but we haven't tested this variant with Tibanna yet.