No "code" displayed in wrappers' documentation #187
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I found the solution in the PR. |
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Co-authored-by: tdayris <[email protected]>
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* [fix] (template): Missing code in wrappers' doc. Error #187 * [dev] (Picard): Memory Co-authored-by: tdayris <[email protected]>
This was referenced Oct 19, 2020
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* [fix] (template): Missing code in wrappers' doc. Error #187 * [dev] (Picard): Memory * [dev] (applybqsr): Automatic Xmx fill * [dev] (baserecal): Automatic Xmx fill * [dev] (baserecalspark): Automatic Xmx fill * [dev] (combinegvcf): Automatic Xmx fill * [dev] (genotypegvcfs): Automatic Xmx fill * [dev] (haplotypecaller): Automatic Xmx fill * [dev] (selectvariants): Automatic Xmx fill * [dev] (splitncigarreads): Automatic Xmx fill * [dev] (variantfiltration): Automatic Xmx fill * [dev] (variantrecalibrator): Automatic Xmx fill * [dev] (snpsift_annotate): Automatix Xmx fill * [dev] (snpsift_dbnsfp): Automatic Xmx fill * [dev] (snpsift): genesets, gwascat and varType: automatic Xmx fill * [dev] (trinity): Aotumatix Xmx fill * [dev] (Mutect2): Java options added, with automatic Xmx fill * [fix] (Picard): Test if -Xmx was not set before * [dev] (SnpEff): Automatic Xmx fill * [dev] (SnpEff): Automatic Xmx fill in download wrapper * [dev] (Jannovar): Automatic Xmx fill * [dev] (Varscan): Automatic Xmx fill * [dev] (trimmomatic): Automatic Xmx fill * [dev] (gatk4): Update with comments from @dlaehnemann and java_tmp * [dev] (jannovar): Update with comments from @dlaehnemann and java temp * [dev] (picard): AddOrReplaceGroups updated, missing test added. * [dev] (picard): Update with comments from @dlaehnemann and java temp * [dev] (collecttargetedpcametrics): Updated and missing test added * [dev] (snpeff): Update with comments from @dlaehnemann and java temp * [dev] (snpsift): Update with comments from @dlaehnemann and java temp * e[dev] (trimmomatic): Updatr with comments from @dlaehnemann, javatemp * [dev] (trinity): Update with comments from @dlaehnemann * [dev] (varscan): Update with comments from @dlaehnemann and java temp * [fix] (black): Files now blacked * [doc] (varscan): Snakefiles updated * [fix] (varscan): Test for varscan somatic had a wrong name * [doc] (trimmomatic): Snakefiles updates * [fix] (Trinity): Missing whitespace * [fix] (Trinity): Missing whitespace * [doc] (Snpsift): Snakefiles updated * [doc] (Snpeff): Snakefiles updated * [fix] (snpeff-download): Useless extra parameters removed * [doc] (picard): Snakefiles updated * [doc] (GATK): Snakefiles updated * [dev] (GATK4): Update with snakemake-wrappers-utils * [dev] (GATK3): Update with snakemake-wrappers-utils * [dev] (Jannovar): Update with snakemake-wrappers-utils * [dev] (Picard): Update with snakemake-wrappers-utils * [dev] (SnpEff): Update with snakemake-wrappers-utils * [dev] (SnpSift): Update with snakemake-wrappers-utils * [dev] (Trimmomatic): Update with snakemake-wrappers-utils * [dev] (Varscan): Update with snakemake-wrappers-utils * [fix] (NameError): snakemake-wrapper-utils updated * [doc] (Documentations): Links to todumentation added * [fix] (Black): Formatting error fixed * [fix] (SyntaxError): trailing quote removed * fix] (SyntaxError): Starting quote removed * [fix] (KeyError): missing extra definition * add mem_gb spec explanation comment in bio/jannovar/test/Snakefile * [dev] (gatk3): Snakefile resources specifications * [fix] (gatk3): Removing trailing comma Co-authored-by: tdayris <[email protected]> Co-authored-by: David Laehnemann <[email protected]>
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* [fix] (template): Missing code in wrappers' doc. Error #187 * [dev] (bwa): Automatic prefix detection (#228) * [dev] (bwa): Automatix prefix detection (#228) * [doc] (bwa): Snakefiles updated * [dev] (bwa): Aln was forgotten at first * [dev] (black): Reformatting * Update Snakefile_samtools * minimal formatting commit to trigger tests test logs are not available any more * revert test trigger change * feat!: remove tmp dir parameter in bwa mem wrapper as this is now handled automatically by snakemake * fix: fixed index adressing * fmt * fixes * fixes * fixed failing lint, fixed syntax * add missing logfile Co-authored-by: tdayris <[email protected]> Co-authored-by: Johannes Köster <[email protected]> Co-authored-by: David Laehnemann <[email protected]> Co-authored-by: Johannes Köster <[email protected]>
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May 13, 2022
* [fix] (template): Missing code in wrappers' doc. Error #187 * mashmap initial commit * refList parameters included in tests * fix fasta missing extension * passing tests * cleaning * comment about relist * formatting * miss-renaming files * miss-renaming files * cleaning * meta corrections : #485 (comment) * Gzipped fasta support + query list as text file * Gzipped support * Gzipped support * Documentation update #485 (comment) Co-authored-by: tdayris <[email protected]>
fgvieira
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May 23, 2022
* [fix] (template): Missing code in wrappers' doc. Error #187 * update salmon version, wrappers and documentation * update salmon index, since RepMap indexes are not accepted anymore * clean dev pipes * snakefmt changes * removed direct reference to resources for #482 (comment) * Use of f-strings and implicit string to bool conversion #482 (comment) * List all files through multiext #482 (comment) * snakefmt trailing comma addition * accept salmon index file list * salmon index wrapper now accepts either a list of files, or a single file * salmon quand now accepts either an index dir or a list of files * salmon quant now accepts gzipped files and raw fastq files automatically * bz2 support and threading error * formatting * adding bzip2 and gzip support in environment.yaml * Remove unnecessary line #482 (comment) * remove remaining dev print Co-authored-by: tdayris <[email protected]>
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Jun 14, 2022
* [fix] (template): Missing code in wrappers' doc. Error #187 * salmon decoy initial commit * string formatting * fix comment * fix comment * meta.yaml fixed * logging Co-authored-by: tdayris <[email protected]>
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Jun 14, 2022
* [fix] (template): Missing code in wrappers' doc. Error #187 * documentation update * fix wrong file edition Co-authored-by: tdayris <[email protected]>
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Aug 16, 2022
* [fix] (template): Missing code in wrappers' doc. Error #187 * Wrapper tested * test written * format * file extension set to tsv * Update bio/bustools/text/environment.yaml Co-authored-by: tdayris <[email protected]> Co-authored-by: tdayris <[email protected]> Co-authored-by: Johannes Köster <[email protected]>
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Aug 16, 2022
* [fix] (template): Missing code in wrappers' doc. Error #187 * New tested wrapper * Remove automatic addition from my IDE * Removed automatic IDE addition * Update bio/bustools/count/environment.yaml Co-authored-by: tdayris <[email protected]> Co-authored-by: tdayris <[email protected]> Co-authored-by: Johannes Köster <[email protected]>
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Aug 16, 2022
* [fix] (template): Missing code in wrappers' doc. Error #187 * bustools sort * memory and tempdir used * environment update * fix typo * Update bio/bustools/sort/environment.yaml * Update bio/bustools/sort/test/Snakefile Co-authored-by: tdayris <[email protected]> Co-authored-by: tdayris <[email protected]> Co-authored-by: Johannes Köster <[email protected]>
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Aug 16, 2022
* [fix] (template): Missing code in wrappers' doc. Error #187 * Wrapper update * Test datasets * Update test case Co-authored-by: tdayris <[email protected]> Co-authored-by: tdayris <[email protected]>
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Aug 16, 2022
* [fix] (template): Missing code in wrappers' doc. Error #187 * wrapper * test datasets * tests themselves * fix meta format * Update bio/gatk/getpileupsummaries/wrapper.py Co-authored-by: Filipe G. Vieira <[email protected]> * Update bio/gatk/getpileupsummaries/environment.yaml Co-authored-by: tdayris <[email protected]> Co-authored-by: tdayris <[email protected]> Co-authored-by: Johannes Köster <[email protected]> Co-authored-by: Filipe G. Vieira <[email protected]>
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* [fix] (template): Missing code in wrappers' doc. Error #187 * initial commit * correct wrapper name * wrapper tested * snakefmt * Update bio/gatk/learnreadorientationmodel/environment.yaml Co-authored-by: tdayris <[email protected]> Co-authored-by: tdayris <[email protected]> Co-authored-by: Johannes Köster <[email protected]>
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Snakemake-wrappers 0.66.0, snakemake 5.24.0
The disparition of the displayed code appeared after addition of meta wrappers. So, the latest version of snakemake-wrappers
Describe the bug
There is no code displayed anymore in any wrapper's documentation. The code is still displayed in meta-wrappers.
Minimal example
See missing documentation in:
https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/bedtools/slop.html#code
See available documentation in:
https://snakemake-wrappers.readthedocs.io/en/stable/meta-wrappers/star_arriba.html#code
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