This adds the options to run PMDtools only on a specific part of the genome within the damage manipulation subworkflow. Input options are the mapping reference, an already masked fasta file and a bed file for masking of the mapping reference.
This closes #1029.
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).
[x] Usage Documentation in docs/usage.md is updated.
[x] Output Documentation in docs/output.md is updated.
[ ] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).
This adds the options to run PMDtools only on a specific part of the genome within the damage manipulation subworkflow. Input options are the mapping reference, an already masked fasta file and a bed file for masking of the mapping reference. This closes #1029.
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).