Removed the meta from input and output for print_contamination module, so output of multiple samples is printed. This closes #1000 .
The output from print_contamination.py now prints "null" in the json and "None" in the txt output, as mentioned in #995 . Downstream behaviour in MultiQC needs to be assessed in the future.
PR checklist
[x] This comment contains a description of changes (with reason).
[x] If you've fixed a bug or added code that should be tested, add tests!
[ ] If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
[ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[ ] If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repository.
[x] Make sure your code lints (nf-core lint .).
[x] 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).
Removed the meta from input and output for print_contamination module, so output of multiple samples is printed. This closes #1000 . The output from print_contamination.py now prints "null" in the json and "None" in the txt output, as mentioned in #995 . Downstream behaviour in MultiQC needs to be assessed in the future.
PR checklist
scrape_software_versions.py
nf-core lint .
).nextflow run . -profile test,docker
).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).