New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
fix: Lofreq indelqual #1325
Merged
Merged
fix: Lofreq indelqual #1325
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
fgvieira
reviewed
May 4, 2023
fgvieira
approved these changes
May 4, 2023
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
this pull request
May 11, 2023
### Description Fixed an error within indelqual wrapper that kept indelqual from running properly. ### QC <!-- Make sure that you can tick the boxes below. --> * [ x] 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 Fixed an error within indelqual wrapper that kept indelqual from running properly. ### QC <!-- Make sure that you can tick the boxes below. --> * [ x] 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>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description
Fixed an error within indelqual wrapper that kept indelqual from running properly.
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,