I am running this pipeline from the sicilian_called_splice_juncs.tsv file which the sicilian pipeline delivers (https://github.com/salzman-lab/SICILIAN). When I do not run it with the "light" mode, and since I have the column "missing_domains" present in the input table, it raises an error on line 261 as there is no column named "posStart_group" or "posEnd_group", they have not been created before in the code of this script. However, there are two columns called posA_group and posB_group created upstream in this script using the start and end junction positions. I do not know if I am right with this change but I think that is possible that is pointing to this columns that already exist.
PR checklist
[x] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] Ensure the test suite passes (nextflow run . -profile test,docker).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[ ] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).
I am running this pipeline from the sicilian_called_splice_juncs.tsv file which the sicilian pipeline delivers (https://github.com/salzman-lab/SICILIAN). When I do not run it with the "light" mode, and since I have the column "missing_domains" present in the input table, it raises an error on line 261 as there is no column named "posStart_group" or "posEnd_group", they have not been created before in the code of this script. However, there are two columns called posA_group and posB_group created upstream in this script using the start and end junction positions. I do not know if I am right with this change but I think that is possible that is pointing to this columns that already exist.
PR checklist
nextflow run . -profile test,docker).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).