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2 commits
| Author | SHA1 | Message | Date | |
|---|---|---|---|---|
Harshil Patel
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20d8250d9f
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Update all modules to new NF DSL2 syntax (#1099)
* Add comment line for consistency
* Remove all functions.nf
* Remove include functions.nf and publishDir options
* Replace options.args3 with task.ext.args3 - 3 modules
* Replace options.args3 with task.ext.args3 - 17 modules
* Replace {task.cpus} with task.cpus
* Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with
* Add def args = task.ext.args line to all modules in script section
* Replace options.args with args and args_list
* Initialise args2 and args3 properly
* Replace container syntax
* Revert container changes for cellranger/mkref
* Replace getProcessName in all modules
* Replace getSoftwareName in all modules
* Unify modules using VERSION variable
* Replae options.suffix with task.ext.suffix
* Remove NF version restriction for CI
* Bump NF version in README
* Replace task.process.tokenize logic with task.process
* Minor tweaks to unify syntax in tests main.nf
* Add a separate nextflow.config for each module
* Transfer remaining module options to nextflow.config
* Remove addParams from tests main.nf
* Remove TODO statements
* Use -c to import module specific config
* Bump NF version to 21.10.3
* Fix tests for artic/minion
* Fix broken publishDir syntax
* Standardise and fix obvious failing module tests
* Remove kronatools to krona
* Comment out tags in subworkflow test.yml
* Fix failing module tests
* Add consistent indentation to nextflow.config
* Comment out subworklow definitions
* Fix kallistobustools/ref
* Fix rmarkdownnotebook
* Fix jupyternotebook
* Quote task.process
* Add plink2/vcf to pytest_modules.yml
* Remove NF_CORE_MODULES_TEST from pytest CI
* Fix more tests
* Move bacteroides_fragilis to prokaryotes folder
* Fix cooler merge tests
* Fix kallistobustools/count tests
* Fix kallistobustools/ref tests
* Update test_10x_1_fastq_gz file for kallistobustools/count tests
* Fix bcftools/query tests
* Fix delly/call tests
* Fix cooler/zoomify tests
* Fix csvtk/split tests
* Fix gatk4/intervallisttools tests
* Fix gatk4/variantfiltration
* Fix pydamage/filter tests
* Fix test data for unicycler
* Fix gstama/collapse module
* Fix leehom tests
* Fix metaphlan3 tests
* Fix pairtools/select tests
* Update nextflow.config
* Update nextflow.config
* feat: update syntax
* Fix arriba tests
* Fix more failing tests
* Update test syntax
* Remove comments from tests nextflow.config
* Apply suggestions from code review
* Fix kallistobustools/count module
* Update dumpsoftwareversions module
* Update custom/dumpsoftwareversions
* Add args2 to untar module
* Update leftover modules
* Remove last remaining addParams
Co-authored-by: JoseEspinosa <kadomu@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
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Mahesh Binzer-Panchal
|
58134cb929
|
Chromap Module (#659)
* Initialise chromap module * Revert "Initialise chromap module" This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b. * Remake chromap base files with new layout * Copy chromap * Copy index * Add compression * Update padding * Update container * Update chromap input test data * Add chromap chromap tests * Add padding * Update comment * update yaml file * Remove TODOs * Add fasta input to yaml * Update YAML * Remove comment, update container * Remove comments * Import Chromap index * Update test.yml * Fix read input * Update test.yml * Add bcftools/concat module. (#641) * draft for bcftools modules [ci skip] * initial test for bcftools concat * Update the params for testing * fix tests * Accomodate code review [ci skip] Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update the meta file and open PR for review * Update the keyword * Update the tags for module [ci skip[ * add threads Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add module for dragonflye (#633) * add module for dragonflye * fix tests for dragonflye * Update test.yml * Update meta.yml * Update main.nf * Update main.nf * Update modules/dragonflye/meta.yml Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * update typos. change quote from ' to ". (#652) * Add bcftools/norm module (#655) * Initial draft [ci skip] * trigger first test * update output file path * Tests passing * finishing touches for meta.yml and update checksum * tweak checksum * add threads to the module * skip version info for matching test md5sum [ci skip] * Add ref fasta and finalize the module Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * Expansionhunter (#666) Please enter the commit message for your changes. Lines starting * adds expansionhunter module Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Update test.yml (#668) * Specify in guidelines one should split CPUs when module has n > 1 tool (#660) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Describe CPU splitting * Update README.md Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * More CPU examples Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * Add dsh-bio export-segments module (#631) Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * update: `BWA/ALN` (#653) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Remove reads from output channel following module guidelines. Should do a .join() based on $meta, to reassociate. Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * Update seqwish reported version to match bioconda version. (#678) * Bbmap index (#683) BBMap index module * Initialise chromap module * Revert "Initialise chromap module" This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b. * Remove unnecessary files * Remove unnecessary files * Update modules/chromap/index/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/chromap/index/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/chromap/chromap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/chromap/chromap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/chromap/chromap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/chromap/chromap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/chromap/index/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Remove pytest_software.yml * Apply suggestions from code review Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: JIANHONG OU <jianhong@users.noreply.github.com> Co-authored-by: Anders Jemt <jemten@users.noreply.github.com> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Michael L Heuer <heuermh@acm.org> Co-authored-by: Daniel Lundin <daniel.lundin@lnu.se> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> |