Longread coverage workflow #82
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muffato
reviewed
Apr 4, 2023
DLBPointon
previously approved these changes
Apr 4, 2023
We will be reviewing test data for automated testing shortly. Currently tested locally with both S and L size parameters. |
What's the command-line for running the tests ? |
muffato
reviewed
Apr 7, 2023
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Why did you replace sort with bedtools sort ? The authors themselves say it's not very useful, cf the disclaimer at the bottom of https://bedtools.readthedocs.io/en/latest/content/tools/sort.html
bin/findHalfcoverage.py
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| action="store", type="string", dest="depth", | ||
| help="depthgraph file, bp count at each depth") | ||
| parser.add_option("-w", "--wiggle", | ||
| action="store", type="string", dest="wig", default=5, |
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So that the value is kept as a float, not a string
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| action="store", type="string", dest="wig", default=5, | |
| action="store", type="float", dest="wig", default=5, |
bin/findHalfcoverage.py
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| action="store", type="string", dest="wig", default=5, | ||
| help="wiggle room to add to depth cutoff ie 30X + wiggleroom. Default is 5X") | ||
| parser.add_option("--cut", | ||
| action="store", type="string", dest="covcut", default=60, |
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| action="store", type="string", dest="covcut", default=60, | |
| action="store", type="float", dest="covcut", default=60, |
bin/findHalfcoverage.py
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| if options.wig == None: | ||
| options.wig = 5 | ||
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| if options.covcut == None: | ||
| options.covcut = 60 | ||
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Not needed anymore
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| if options.wig == None: | |
| options.wig = 5 | |
| if options.covcut == None: | |
| options.covcut = 60 | |
bin/findHalfcoverage.py
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| action="store", type="string", dest="covcut", default=60, | ||
| help="%Number for coverage cutoff to include in results. ie 50% of scaffold needs to be under diploid peak etc. Default is 60%") | ||
| parser.add_option("-t", "--totalsize", | ||
| action="store", type="string", dest="totsize", default=250000, |
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Suggested change
| action="store", type="string", dest="totsize", default=250000, | |
| action="store", type="int", dest="totsize", default=250000, |
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Updated findHalfCoverage.py with corrections. |
muffato
approved these changes
Apr 19, 2023
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Added long read coverage workflow and required modules for it.
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).