This PR changes the FILTER_DIFFTABLE module to python with pandas; I noticed while working on #257 that the previous module sometimes filters out all the genes, not just the non-DE ones. I was not able to find where the issue is with AWK after a lot of trying out, so the module now uses python.
The module now also applies log2 to the threshold parameter so that the DE gene results are the same as in the report tables; I checked this and the tables now agree with each other (see attached zip).
This PR changes the FILTER_DIFFTABLE module to python with pandas; I noticed while working on #257 that the previous module sometimes filters out all the genes, not just the non-DE ones. I was not able to find where the issue is with AWK after a lot of trying out, so the module now uses python. The module now also applies log2 to the threshold parameter so that the DE gene results are the same as in the report tables; I checked this and the tables now agree with each other (see attached zip).
filtered_results.zip
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).