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feat: gatk collectalleliccount wrapper #1316
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fgvieira
merged 4 commits into
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add-wrapper-gatk-collectreadcounts-collectAllelicCounts
May 3, 2023
Merged
feat: gatk collectalleliccount wrapper #1316
fgvieira
merged 4 commits into
master
from
add-wrapper-gatk-collectreadcounts-collectAllelicCounts
May 3, 2023
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fgvieira
reviewed
Apr 29, 2023
fgvieira
reviewed
May 2, 2023
Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>
fgvieira
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May 3, 2023
fgvieira
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add-wrapper-gatk-collectreadcounts-collectAllelicCounts
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May 3, 2023 06:21
tgroth97
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May 3, 2023
### Description Add wrapper for gatk CollectAllelicCount ### QC <!-- Make sure that you can tick the boxes below. --> * [ ] I confirm that: For all wrappers added by this PR, * 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](https://en.wikipedia.org/wiki/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](https://stackoverflow.com/a/64594513/2352071), * 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 `Snakefile`s 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](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir); 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, * `Snakefile`s pass the linting (`snakemake --lint`), * `Snakefile`s are formatted with [snakefmt](https://github.com/snakemake/snakefmt), * Python wrapper scripts are formatted with [black](https://black.readthedocs.io). * Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays). --------- Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>
johanneskoester
pushed a commit
that referenced
this pull request
May 4, 2023
🤖 I have created a release \*beep\* \*boop\* --- ## [1.29.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.28.0...v1.29.0) (2023-05-04) ### Features * Add seqkit subseq ([#1318](https://www.github.com/snakemake/snakemake-wrappers/issues/1318)) ([262d9bb](https://www.github.com/snakemake/snakemake-wrappers/commit/262d9bb50cf8d03edca00916bc29fe5f1009209a)) * Deeptools Alignement seive ([#1320](https://www.github.com/snakemake/snakemake-wrappers/issues/1320)) ([b7cb7ab](https://www.github.com/snakemake/snakemake-wrappers/commit/b7cb7ab5b70c1eec3b89d02f0bc94a2294e6a9aa)) * fix threads and new IO options in Bowtie2 ([#1324](https://www.github.com/snakemake/snakemake-wrappers/issues/1324)) ([a9c7117](https://www.github.com/snakemake/snakemake-wrappers/commit/a9c711718533f18429db50fb052549c49aa6fcf7)) * gatk CallCopyRatioSegments ([#1323](https://www.github.com/snakemake/snakemake-wrappers/issues/1323)) ([528c91a](https://www.github.com/snakemake/snakemake-wrappers/commit/528c91a5b87ffe0d34964b01478a9b5d520ed80f)) * gatk collectalleliccount wrapper ([#1316](https://www.github.com/snakemake/snakemake-wrappers/issues/1316)) ([158c328](https://www.github.com/snakemake/snakemake-wrappers/commit/158c328d1b846fb45c90c946edbcf2a7a0da15de)) * gatk collectreadcount wrapper ([#1315](https://www.github.com/snakemake/snakemake-wrappers/issues/1315)) ([ee55de4](https://www.github.com/snakemake/snakemake-wrappers/commit/ee55de4cc2a850775ef94d5394f9a220844d8a7b)) * gatk DenoisedReadCounts wrapper ([#1319](https://www.github.com/snakemake/snakemake-wrappers/issues/1319)) ([0288ace](https://www.github.com/snakemake/snakemake-wrappers/commit/0288ace7e61fbf2adf79514eefa2ff8f3566041e)) * gatk modelsegments wrapper ([#1321](https://www.github.com/snakemake/snakemake-wrappers/issues/1321)) ([dfecc26](https://www.github.com/snakemake/snakemake-wrappers/commit/dfecc26de3c649c4661ac26203d846a54f7dd0b0)) * Pyroe make-spliced+unspliced ([#1290](https://www.github.com/snakemake/snakemake-wrappers/issues/1290)) ([96a2cbb](https://www.github.com/snakemake/snakemake-wrappers/commit/96a2cbbf667fb45676087c2002fa875a76982e6b)) ### Bug Fixes * Lofreq indelqual ([#1325](https://www.github.com/snakemake/snakemake-wrappers/issues/1325)) ([dabecf0](https://www.github.com/snakemake/snakemake-wrappers/commit/dabecf065975b7e53102221a63ec11b2c812cdee)) ### Performance Improvements * Updated version of datavzrd to 2.19.1 ([#1328](https://www.github.com/snakemake/snakemake-wrappers/issues/1328)) ([fd89645](https://www.github.com/snakemake/snakemake-wrappers/commit/fd89645aa28773f872a3b2f54192d66129852d83)) --- 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>
tdayris
pushed a commit
to tdayris/snakemake-wrappers
that referenced
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May 11, 2023
### Description Add wrapper for gatk CollectAllelicCount ### QC <!-- Make sure that you can tick the boxes below. --> * [ ] I confirm that: For all wrappers added by this PR, * 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](https://en.wikipedia.org/wiki/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](https://stackoverflow.com/a/64594513/2352071), * 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 `Snakefile`s 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](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir); 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, * `Snakefile`s pass the linting (`snakemake --lint`), * `Snakefile`s are formatted with [snakefmt](https://github.com/snakemake/snakefmt), * Python wrapper scripts are formatted with [black](https://black.readthedocs.io). * Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays). --------- Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>
tdayris
pushed a commit
to tdayris/snakemake-wrappers
that referenced
this pull request
May 11, 2023
🤖 I have created a release \*beep\* \*boop\* --- ## [1.29.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.28.0...v1.29.0) (2023-05-04) ### Features * Add seqkit subseq ([snakemake#1318](https://www.github.com/snakemake/snakemake-wrappers/issues/1318)) ([262d9bb](https://www.github.com/snakemake/snakemake-wrappers/commit/262d9bb50cf8d03edca00916bc29fe5f1009209a)) * Deeptools Alignement seive ([snakemake#1320](https://www.github.com/snakemake/snakemake-wrappers/issues/1320)) ([b7cb7ab](https://www.github.com/snakemake/snakemake-wrappers/commit/b7cb7ab5b70c1eec3b89d02f0bc94a2294e6a9aa)) * fix threads and new IO options in Bowtie2 ([snakemake#1324](https://www.github.com/snakemake/snakemake-wrappers/issues/1324)) ([a9c7117](https://www.github.com/snakemake/snakemake-wrappers/commit/a9c711718533f18429db50fb052549c49aa6fcf7)) * gatk CallCopyRatioSegments ([snakemake#1323](https://www.github.com/snakemake/snakemake-wrappers/issues/1323)) ([528c91a](https://www.github.com/snakemake/snakemake-wrappers/commit/528c91a5b87ffe0d34964b01478a9b5d520ed80f)) * gatk collectalleliccount wrapper ([snakemake#1316](https://www.github.com/snakemake/snakemake-wrappers/issues/1316)) ([158c328](https://www.github.com/snakemake/snakemake-wrappers/commit/158c328d1b846fb45c90c946edbcf2a7a0da15de)) * gatk collectreadcount wrapper ([snakemake#1315](https://www.github.com/snakemake/snakemake-wrappers/issues/1315)) ([ee55de4](https://www.github.com/snakemake/snakemake-wrappers/commit/ee55de4cc2a850775ef94d5394f9a220844d8a7b)) * gatk DenoisedReadCounts wrapper ([snakemake#1319](https://www.github.com/snakemake/snakemake-wrappers/issues/1319)) ([0288ace](https://www.github.com/snakemake/snakemake-wrappers/commit/0288ace7e61fbf2adf79514eefa2ff8f3566041e)) * gatk modelsegments wrapper ([snakemake#1321](https://www.github.com/snakemake/snakemake-wrappers/issues/1321)) ([dfecc26](https://www.github.com/snakemake/snakemake-wrappers/commit/dfecc26de3c649c4661ac26203d846a54f7dd0b0)) * Pyroe make-spliced+unspliced ([snakemake#1290](https://www.github.com/snakemake/snakemake-wrappers/issues/1290)) ([96a2cbb](https://www.github.com/snakemake/snakemake-wrappers/commit/96a2cbbf667fb45676087c2002fa875a76982e6b)) ### Bug Fixes * Lofreq indelqual ([snakemake#1325](https://www.github.com/snakemake/snakemake-wrappers/issues/1325)) ([dabecf0](https://www.github.com/snakemake/snakemake-wrappers/commit/dabecf065975b7e53102221a63ec11b2c812cdee)) ### Performance Improvements * Updated version of datavzrd to 2.19.1 ([snakemake#1328](https://www.github.com/snakemake/snakemake-wrappers/issues/1328)) ([fd89645](https://www.github.com/snakemake/snakemake-wrappers/commit/fd89645aa28773f872a3b2f54192d66129852d83)) --- 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>
tdayris
pushed a commit
to tdayris/snakemake-wrappers
that referenced
this pull request
Jul 5, 2023
### Description Add wrapper for gatk CollectAllelicCount ### QC <!-- Make sure that you can tick the boxes below. --> * [ ] I confirm that: For all wrappers added by this PR, * 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](https://en.wikipedia.org/wiki/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](https://stackoverflow.com/a/64594513/2352071), * 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 `Snakefile`s 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](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir); 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, * `Snakefile`s pass the linting (`snakemake --lint`), * `Snakefile`s are formatted with [snakefmt](https://github.com/snakemake/snakefmt), * Python wrapper scripts are formatted with [black](https://black.readthedocs.io). * Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays). --------- Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>
tdayris
pushed a commit
to tdayris/snakemake-wrappers
that referenced
this pull request
Jul 5, 2023
🤖 I have created a release \*beep\* \*boop\* --- ## [1.29.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.28.0...v1.29.0) (2023-05-04) ### Features * Add seqkit subseq ([snakemake#1318](https://www.github.com/snakemake/snakemake-wrappers/issues/1318)) ([262d9bb](https://www.github.com/snakemake/snakemake-wrappers/commit/262d9bb50cf8d03edca00916bc29fe5f1009209a)) * Deeptools Alignement seive ([snakemake#1320](https://www.github.com/snakemake/snakemake-wrappers/issues/1320)) ([b7cb7ab](https://www.github.com/snakemake/snakemake-wrappers/commit/b7cb7ab5b70c1eec3b89d02f0bc94a2294e6a9aa)) * fix threads and new IO options in Bowtie2 ([snakemake#1324](https://www.github.com/snakemake/snakemake-wrappers/issues/1324)) ([a9c7117](https://www.github.com/snakemake/snakemake-wrappers/commit/a9c711718533f18429db50fb052549c49aa6fcf7)) * gatk CallCopyRatioSegments ([snakemake#1323](https://www.github.com/snakemake/snakemake-wrappers/issues/1323)) ([528c91a](https://www.github.com/snakemake/snakemake-wrappers/commit/528c91a5b87ffe0d34964b01478a9b5d520ed80f)) * gatk collectalleliccount wrapper ([snakemake#1316](https://www.github.com/snakemake/snakemake-wrappers/issues/1316)) ([158c328](https://www.github.com/snakemake/snakemake-wrappers/commit/158c328d1b846fb45c90c946edbcf2a7a0da15de)) * gatk collectreadcount wrapper ([snakemake#1315](https://www.github.com/snakemake/snakemake-wrappers/issues/1315)) ([ee55de4](https://www.github.com/snakemake/snakemake-wrappers/commit/ee55de4cc2a850775ef94d5394f9a220844d8a7b)) * gatk DenoisedReadCounts wrapper ([snakemake#1319](https://www.github.com/snakemake/snakemake-wrappers/issues/1319)) ([0288ace](https://www.github.com/snakemake/snakemake-wrappers/commit/0288ace7e61fbf2adf79514eefa2ff8f3566041e)) * gatk modelsegments wrapper ([snakemake#1321](https://www.github.com/snakemake/snakemake-wrappers/issues/1321)) ([dfecc26](https://www.github.com/snakemake/snakemake-wrappers/commit/dfecc26de3c649c4661ac26203d846a54f7dd0b0)) * Pyroe make-spliced+unspliced ([snakemake#1290](https://www.github.com/snakemake/snakemake-wrappers/issues/1290)) ([96a2cbb](https://www.github.com/snakemake/snakemake-wrappers/commit/96a2cbbf667fb45676087c2002fa875a76982e6b)) ### Bug Fixes * Lofreq indelqual ([snakemake#1325](https://www.github.com/snakemake/snakemake-wrappers/issues/1325)) ([dabecf0](https://www.github.com/snakemake/snakemake-wrappers/commit/dabecf065975b7e53102221a63ec11b2c812cdee)) ### Performance Improvements * Updated version of datavzrd to 2.19.1 ([snakemake#1328](https://www.github.com/snakemake/snakemake-wrappers/issues/1328)) ([fd89645](https://www.github.com/snakemake/snakemake-wrappers/commit/fd89645aa28773f872a3b2f54192d66129852d83)) --- 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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Description
Add wrapper for gatk CollectAllelicCount
QC
For all wrappers added by this PR,
input:
andoutput:
file paths in the resulting rule can be changed arbitrarily,threads: x
statement withx
being a reasonable default,map_reads
for a step that maps reads),environment.yaml
specifications follow the respective best practices,input:
oroutput:
),Snakefile
s and their entries are explained via comments (input:
/output:
/params:
etc.),stderr
and/orstdout
are logged correctly (log:
), depending on the wrapped tool,tempfile.gettempdir()
points to (see here; this also means that using any Pythontempfile
default behavior works),meta.yaml
contains a link to the documentation of the respective tool or command,Snakefile
s pass the linting (snakemake --lint
),Snakefile
s are formatted with snakefmt,