* update for bcftools merge
* Update modules/bcftools/merge/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Update modules/bcftools/merge/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* updated test.yml
* added the bed file to the main input tuple
* merged all output into one output channel
* added a test for bcf.gz output
* Update modules/bcftools/merge/main.nf
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
* updated the tests
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
* style: Add prettier config files
* build: Add prettier vscode extension
* ci: Replace markdownlint and yamllint with prettier
* style: Run prettier
* style: Use indent of 2 for markdown as well
https://github.com/nf-core/tools/pull/1470#issuecomment-1071028358
* style: Fix indent
* style: Let editorconfig take over tab widths
* style: yaml => yml
* ci: Run prettier once
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
* bcf annotate ready2go
* edited output name
* fixed output
* updated bcftools ver
* changed contain output string
* removed contain key entirely
* fixed md5sum for test.yml
* using match instead of find
* bcftools/annotate refactored with complete test
* rm trailing white space
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* Bump software versions for viralrecon modules
* Remove custom params.save_unaligned from bowtie2_align
* Unify samtools modules and error if input and output names are the same
* Fix ALL the tests
* Added files for bcftools/sort
* Fixed output format and removed md5 checksum
* Change input to avoid identical in/output names
* Created rows for bcftools/sort in pytest_modules.yml
* 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
* Change syntax from task.ext.suffix to tast.ext.prefix
* Change nextflow.config in all tests to use ext.prefix instead of ext.suffix
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>
* 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>
* backfilled modules with meta.yml that had no license identifier
* harmonized BSD license names
* whitespace linting at modules/unzip/meta.yml:12
* harmonized software from US NIH-NCBI/NIST to 'US-Government-Work'
* Update modules/bcftools/index/meta.yml
`bcftools` is dual-licensed, use associative array to allow for multiple licenses
Co-authored-by: Michael L Heuer <heuermh@acm.org>
Co-authored-by: Michael L Heuer <heuermh@acm.org>
* 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>
* 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 blacklist of modules that shouldn't be updated to .nf-core.yml
* nf-core modules bump-versions for all modules
* Remove TODO statements identified by linting
* Fix md5sums for failing tests
* Fix more tests
* Update README
* Rename pytest_software.yml to pytest_modules.yml
* Rename main software directory to modules
* Remove deprecated modules
* Rename tests software to modules
* Replace paths for tests in pytest_modules.yml
* Replace software with modules in Github Actions
* Replace software with modules in main.nf tests
* Rename software to modules in test.yml
