DSL2: Add mapAD #1072
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DSL2: Add mapAD #1072
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apeltzer
approved these changes
Sep 21, 2024
TCLamnidis
requested changes
Sep 27, 2024
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Very good! Just some small changes! 😄
- Rename parameters to match formatting of other params. (they should follow the schema
section_tool_paramatername. i.e.mapping_mapad_gap_read_end_distanceshould bemapping_mapad_gapreadenddistance) - Could you give
mapping_mapad_Da long-form name? I worry that_Dand_dwill be confused by users. - You don't need to run
SAMTOOLS_SORT_MAPADat all. We do a samtools sort after merging all lanes/shards together anyway.
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Thank you both for the reviews! |
TCLamnidis
approved these changes
Oct 4, 2024
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Great work! Just one small edit to the parameter helptext.
I see you have another PR test left unchecked (ssDNA library). Is that still pending?
Re point 3 of my last review:
I see no SORT calls in the subworkflows of other mappers, but it is entirely possible that they output already sorted bams. I'm happy to take your call on this, was just checking it was intentional and not a forgotten module addition used for testing 👍
Co-authored-by: Thiseas C. Lamnidis <[email protected]>
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Oh, good catch. I've verified that. |
jfy133
approved these changes
Oct 11, 2024
| "mapping_mapad_stacklimitabort": { | ||
| "type": "boolean", | ||
| "description": "Set the --stack_limit_abort flag, which instructs mapAD to not try and recover from a full backtracking stack.", | ||
| "help_text": "Without this flag, mapAD tries to recover from a full backtracking stack by removing low-scoring sub-alignments. This can help to recover from difficult to map reads, at the cost of a slower alignment. Setting this flag will speed up the alignment process.\n\n> Modifies mapAD map parameter: `--stack_limit_abort`", |
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I don't really follow what exactly the behaviour does here, and I think the 'backtracking stack' jargon might not be help either.
Suggested change
| "help_text": "Without this flag, mapAD tries to recover from a full backtracking stack by removing low-scoring sub-alignments. This can help to recover from difficult to map reads, at the cost of a slower alignment. Setting this flag will speed up the alignment process.\n\n> Modifies mapAD map parameter: `--stack_limit_abort`", | |
| "help_text": "By default, mapAD will remove low-scoring sub-alignments, helping to recover from difficult to map reads, at the cost of a slower alignment. Setting this flag will speed up the alignment process by not removing these.\n\n> Modifies mapAD map parameter: `--stack_limit_abort`", |
Is that what you mean?
| ch_input_for_mapping.index, | ||
| params.mapping_mapad_p, | ||
| ch_input_for_mapping.strandedness, | ||
| params.mapping_mapad_f, |
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Just to check, all of these parameters would make sense to apply across all samples/genomes in a run?
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@jch-13 What is the state of this PR? |
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PR checklist
scrape_software_versions.pynf-core lint .).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).PR TODO
version.ymlgeneration