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feat: Mutect2 additional parameters #516

Merged
merged 30 commits into from Mar 22, 2023
Merged

feat: Mutect2 additional parameters #516

merged 30 commits into from Mar 22, 2023

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tdayris
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@tdayris tdayris commented Jul 8, 2022 •
edited

Description

This PR handles bed intervals, germline vcf, panel of normals input files and f1r2 output file.

I also introduced how to enable multi threading in some special cases, since I have witnessed issues on several computing clusters last year.

QC

For all wrappers added by this PR, I made sure that

  • there is a test case which covers any introduced changes,
  • input: and output: file paths in the resulting rule can be changed arbitrarily,
  • either the wrapper can only use a single core, or the example rule contains a threads: x statement with x being a reasonable default,
  • rule names in the test case are in snake_case and somehow tell what the rule is about or match the tools purpose or name (e.g., map_reads for a step that maps reads),
  • all environment.yaml specifications follow the respective best practices,
  • wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:),
  • all fields of the example rules in the Snakefiles and their entries are explained via comments (input:/output:/params: etc.),
  • stderr and/or stdout are logged correctly (log:), depending on the wrapped tool,
  • temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to (see here; this also means that using any Python tempfile default behavior works),
  • the meta.yaml contains a link to the documentation of the respective tool or command,
  • Snakefiles pass the linting (snakemake --lint),
  • Snakefiles are formatted with snakefmt,
  • Python wrapper scripts are formatted with black.

fgvieira
fgvieira reviewed Jul 18, 2022
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bio/gatk/mutect/meta.yaml Outdated Show resolved Hide resolved
tdayris and others added 9 commits December 5, 2022 15:32
@tdayris @fgvieira
Update bio/gatk/mutect/wrapper.py
a76065b 
Co-authored-by: Filipe G. Vieira <fgarrettvieira@gmail.com>
@tdayris @fgvieira
Update bio/gatk/mutect/wrapper.py
717829a 
Co-authored-by: Filipe G. Vieira <fgarrettvieira@gmail.com>
@tdayris @fgvieira
Update bio/gatk/mutect/wrapper.py
4c143f2 
Co-authored-by: Filipe G. Vieira <fgarrettvieira@gmail.com>
@tdayris @fgvieira
Update bio/gatk/mutect/wrapper.py
e329ef1 
Co-authored-by: Filipe G. Vieira <fgarrettvieira@gmail.com>
@tdayris @fgvieira
Update bio/gatk/mutect/wrapper.py
5baf02b 
Co-authored-by: Filipe G. Vieira <fgarrettvieira@gmail.com>
define omp if variable not exists
ee48705
@tdayris
Merge branch 'master' into mutect2-additional-parameters
ff886b4
add parallelgc parameters for multithreading
ca5fe4d
fix syntax error
0bcf587
@fgvieira fgvieira merged commit f2b70ca into snakemake:master Mar 22, 2023
6 checks passed
johanneskoester pushed a commit that referenced this pull request Mar 23, 2023
@github-actions
chore: release 1.25.0 (#1153)
ff4eda9 
🤖 I have created a release \*beep\* \*boop\*
---
##
[1.25.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.24.0...v1.25.0)
(2023-03-23)


### Features

* added several Seqkit wrappers
([#1128](https://www.github.com/snakemake/snakemake-wrappers/issues/1128))
([9c4e667](https://www.github.com/snakemake/snakemake-wrappers/commit/9c4e66705de7f0db6c4cedae8b06359bacc9169a))
* added wrapper for loglog
([#1154](https://www.github.com/snakemake/snakemake-wrappers/issues/1154))
([08917f9](https://www.github.com/snakemake/snakemake-wrappers/commit/08917f991e60b19cac03b9b9cec82fdaf10891b9))
* added wrapper for tadpole
([#1152](https://www.github.com/snakemake/snakemake-wrappers/issues/1152))
([cb1372b](https://www.github.com/snakemake/snakemake-wrappers/commit/cb1372ba61ea3f92050b974e0dfa61e42b496806))
* Merqury
([#540](https://www.github.com/snakemake/snakemake-wrappers/issues/540))
([f7914c4](https://www.github.com/snakemake/snakemake-wrappers/commit/f7914c4025fcbcea124765732b4241cfe233f379))
* Mutect2 additional parameters
([#516](https://www.github.com/snakemake/snakemake-wrappers/issues/516))
([f2b70ca](https://www.github.com/snakemake/snakemake-wrappers/commit/f2b70ca7371d2bb7c031930d047d1e18f9f0610f))


### Bug Fixes

* use new java memory overhead utils
([#1150](https://www.github.com/snakemake/snakemake-wrappers/issues/1150))
([d15d5f5](https://www.github.com/snakemake/snakemake-wrappers/commit/d15d5f5dda23a60aa6c570c9b5da4d5a855cadf5))


### Performance Improvements

* autobump bio/bcftools/filter
([#646](https://www.github.com/snakemake/snakemake-wrappers/issues/646))
([b7b98fd](https://www.github.com/snakemake/snakemake-wrappers/commit/b7b98fd9cd9ae819e116aa81c6d082585a77b41d))
* autobump bio/bismark/deduplicate_bismark
([#1141](https://www.github.com/snakemake/snakemake-wrappers/issues/1141))
([45cd1a6](https://www.github.com/snakemake/snakemake-wrappers/commit/45cd1a635a00d48dbbfbf591059364e0d6d09864))
* autobump bio/cooltools/dots
([#702](https://www.github.com/snakemake/snakemake-wrappers/issues/702))
([7ac6569](https://www.github.com/snakemake/snakemake-wrappers/commit/7ac656961dff08341e3d448932dda37c19f7d65d))
* autobump bio/fgbio/collectduplexseqmetrics
([#1100](https://www.github.com/snakemake/snakemake-wrappers/issues/1100))
([ae2a295](https://www.github.com/snakemake/snakemake-wrappers/commit/ae2a295303b987e9e1fb303a689bec6d0cbb4aa1))
* autobump bio/gatk/markduplicatesspark
([#1142](https://www.github.com/snakemake/snakemake-wrappers/issues/1142))
([190dd18](https://www.github.com/snakemake/snakemake-wrappers/commit/190dd18d6a29cdb1fefdfe98f7d25a5d9c4d00d1))
* autobump bio/gridss/preprocess
([#800](https://www.github.com/snakemake/snakemake-wrappers/issues/800))
([71463ad](https://www.github.com/snakemake/snakemake-wrappers/commit/71463adf79b2a12f3360e1f80f8452f3803c9315))
* autobump bio/gridss/setupreference
([#848](https://www.github.com/snakemake/snakemake-wrappers/issues/848))
([c2f9766](https://www.github.com/snakemake/snakemake-wrappers/commit/c2f976626319fde811e4a4043f9307f7fb7e6758))
* autobump bio/hisat2/align
([#1079](https://www.github.com/snakemake/snakemake-wrappers/issues/1079))
([dea181a](https://www.github.com/snakemake/snakemake-wrappers/commit/dea181a03196c4a6f8612651478ee07bbee16467))
* autobump bio/liftoff
([#953](https://www.github.com/snakemake/snakemake-wrappers/issues/953))
([0928808](https://www.github.com/snakemake/snakemake-wrappers/commit/0928808b812b2f4c24c3b747e4eee42cab534453))
* autobump bio/lofreq/call
([#1120](https://www.github.com/snakemake/snakemake-wrappers/issues/1120))
([a327d86](https://www.github.com/snakemake/snakemake-wrappers/commit/a327d860f3db5154007e3c527b584c5eadc9050f))
* autobump bio/muscle
([#612](https://www.github.com/snakemake/snakemake-wrappers/issues/612))
([659d106](https://www.github.com/snakemake/snakemake-wrappers/commit/659d10646b41c01b009a55b1f15503a7965bce6a))
* autobump bio/snpeff/annotate
([#1038](https://www.github.com/snakemake/snakemake-wrappers/issues/1038))
([5628ccd](https://www.github.com/snakemake/snakemake-wrappers/commit/5628ccdc4156f17ffa1b2a84bb255e81036b86ea))
* autobump bio/subread/featurecounts
([#1044](https://www.github.com/snakemake/snakemake-wrappers/issues/1044))
([b7d7ed4](https://www.github.com/snakemake/snakemake-wrappers/commit/b7d7ed4d6b7c58a774a8dd9c04d8a5880d3fc991))
* autobump bio/trinity
([#634](https://www.github.com/snakemake/snakemake-wrappers/issues/634))
([d084304](https://www.github.com/snakemake/snakemake-wrappers/commit/d084304a9afff1c460465d4db6bfa4898fa26e8e))
* autobump bio/vep/cache
([#1132](https://www.github.com/snakemake/snakemake-wrappers/issues/1132))
([d8c3faa](https://www.github.com/snakemake/snakemake-wrappers/commit/d8c3faac3f30b001534d104bf26f916c04787d71))
---


This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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@johanneskoester johanneskoester johanneskoester approved these changes

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@tdayris @fgvieira @johanneskoester