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Fix vcf #465

Merged
merged 5 commits into from Feb 5, 2024
Merged

Fix vcf #465

merged 5 commits into from Feb 5, 2024

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rannick
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@rannick rannick commented Feb 2, 2024 •
edited

fix VCF_COLLECT for cases when fusioninspector filters out fusions detected and fed in via fusionreport (fusioninspector empty but fusionreport not empty). Closes #460

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  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
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  • If necessary, also make a PR on the nf-core/rnafusion branch on the nf-core/test-datasets repository.
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  • Output Documentation in docs/output.md is updated.
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github-actions bot commented Feb 2, 2024

Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install black: pip install black
  • Fix formatting errors in your pipeline: black .

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github-actions bot commented Feb 2, 2024 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 017d6da

+| ✅ 171 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • pipeline_todos - TODO string in WorkflowRnafusion.groovy: Optionally add in-text citation tools to this list.

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-05 09:19:35

@rannick rannick requested a review from fevac February 2, 2024 10:27
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rannick commented Feb 2, 2024 •
edited

VCF_COLLECT script tested successfully with outputs from vwucher

@rannick rannick closed this Feb 5, 2024
@rannick rannick reopened this Feb 5, 2024
@rannick rannick merged commit 8440a2c into dev Feb 5, 2024
18 checks passed
@rannick rannick deleted the fix_vcf branch February 5, 2024 09:27
fevac
fevac approved these changes Feb 5, 2024
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lgtm!

bin/vcf_collect.py
Comment on lines +276 to +284
df[["ChromosomeA", "PosA", "Strand1"]] = df["LeftBreakpoint"].str.split(":", expand=True)
df[["ChromosomeB", "PosB", "Strand2"]] = df["RightBreakpoint"].str.split(":", expand=True)
df[["LeftGeneName", "Left_ensembl_gene_id"]] = df["LeftGene"].str.split("^", expand=True)
df[["RightGeneName", "Right_ensembl_gene_id"]] = df["RightGene"].str.split("^", expand=True)
df["annots"] = (
df["annots"]
.apply(convert_to_list)
.apply(lambda x: ",".join(map(str, x)) if isinstance(x, list) else str(x) if pd.notna(x) else "")
)
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would be nice to move this into a function

bin/vcf_collect.py
Comment on lines +286 to +302
for i in [
"ChromosomeA",
"Strand1",
"ChromosomeB",
"Strand2",
"LeftGeneName",
"Left_ensembl_gene_id",
"RightGeneName",
"Right_ensembl_gene_id",
"annots",
]:
df[i] = ""
for j in [
"PosA",
"PosB",
]:
df[j] = np.nan
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would be nice to move this to a function

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@apeltzer apeltzer apeltzer approved these changes

@fevac fevac fevac approved these changes

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@rannick @apeltzer @fevac