organism = [org_name, org_label, org_yaml] #104
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Looks good and much simpler - thank you. I also still need to see how dissectBCL would cope with the new organism list from Parkour |
adRn-s
commented
Nov 28, 2024
| @@ -689,14 +657,14 @@ def GetResults(config, project, libraries): | |||
| reruncount += 1 | |||
| outputDir, rv, sambaUpdate = globals()[pipeline](config, group, project, organism, libraryType, tuples) | |||
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Here we are passing over the organism variable, which is the list of 3 strings. This is because the pipeline-calling functions (e.g. scRNAseq()) won't work with just one.
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Jan 17, 2025
| if tuples[0][2].startswith("Smart-Seq2"): | ||
| # SMART-seq isn't a dUTP-based method! | ||
| CMD.extend(['--libraryType', '0']) | ||
| elif tuples[0][2].startswith("NEBNext Low Input RNA Library"): | ||
| # Unstranded | ||
| CMD.extend(['--libraryType', '0']) | ||
| CMD.extend(['--libraryType', '0', r"--trimmerOptions '-a AGATCGGAAGAGC -A AGATCGGAAGAGC'"]) |
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This comment is only to highlight that I sneaked in a change that should probably have had its own PR.
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Basically, we pass the list of 3 strings to any pipeline function (e.g.
ATAC()), and use org_name for logs or emails, org_label for directories, and org_yaml for commands.Extra maps (
BRB.ET.getOffSpeciesRate()and10X_snakepipe) are not changed (yet). I hope we don't need more strings for these. In any case, I would leave those changes for a latter release.