* Update main.nf
* Update meta.yml
* Re-add logos as not staged in a way that works with MultiQC config files
* Fix MeaPhlAn3 module name
* Fix metayaml
* Fix meta.yml
* Update main.nf
* Update meta.yml
* Re-add logos as not staged in a way that works with MultiQC config files
* Fix when only files or multiple directories
* Add test for only-files tar
* Fix bash check
* Add eido/convert module
* Run prettier
* Update modules/eido/convert/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/eido/convert/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update extension format
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Add eido/validate module
* Apply first batch of updates after code review
* Remove readlink, update sed, update paths
* Move sample table index parameter to config
* Update tests/modules/eido/validate/test.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tests/modules/eido/validate/test.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tests/modules/eido/validate/test.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tests/modules/eido/validate/test.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/eido/validate/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update main.nf
* Update meta.yml
* Re-add logos as not staged in a way that works with MultiQC config files
* Add meta to mergemetaphlan3 tables
* Actually combine the data together
* This process is single-threaded
* Added meta to match the other nf-core modules
* "custom" is not a great name
* Newer modules have a stub
* To match the other modules
* self promotion
* Output the gzi file too, if there is one
* More Fasta extensions
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update main.nf
* Update meta.yml
* Re-add logos as not staged in a way that works with MultiQC config files
* Removes duplicate input to single end FASTP
* Fix md5sums
* Separate interleaved from normal SE command to continue supporting `split_by_lines`
* Simplify save_trimmed_fail
* Update modules/fastp/meta.yml
* New module for fasta_windows
* Upgraded the code and the test to v2.4
* Standard list of Fasta file extensions
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Output file (and/or directory) names SHOULD just consist of only ${prefix}
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Separate MultiQC config from logo input channel
* Update meta.yml
* Update main.nf
* Add test for new check
* md5sum -> contains
* Remove logo input channel from MultiQC
* Created epang module from template
* Module seems to be working
* Namechange to epang_place
* Move model to meta map
* Fix linting problems
* Prettier
* Forgot --threads!
* Moved module to epang
* Move reference file params
* Directory output
* Make all args optional
* Added inputs for three other types of file arguments
* Update modules/epang/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Add directory to output doc, reorder the other
* Make model specification less hardcoded
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add snippy-core module
* Update modules/snippy/core/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tests/modules/snippy/core/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tests/modules/snippy/core/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/snippy/core/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update main.nf
* update test
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Move MetaPhlAn3 to a subcommand and add mergemetaphlantables
* Add mergemetaphlantables tests
* Add mergemetaphlantables to test config
* Apply suggestions from code review
* Revert now unnecessary input channel name change and now document
* Update modules/metaphlan3/mergemetaphlantables/main.nf
* Require database directory and more details in description
* not working yet (db not found)
* modify deeparg/download module to return db-path
* 🪄
* Prettier
* add test.yml
* much prettier
* test.yml delete md5 for pot. empty files
* adapt test.yml
* test.yml again
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Add combinebrackenoutputs
* Prettier and relax tests contains
* Apply suggestions from code review
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* Add krakentools_combinekreports
* Update test.yml
* Update main.nf
* Update tests/modules/krakentools/combinekreports/test.yml
* Prettier
* Update modules/krakentools/combinekreports/main.nf
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* deepbgc_download first version
* with test.yml
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Apply suggestions from code review
* delete trailing whitespace main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Created hmmer/eslalimask from template
* esl-alimask module with --rf-is-mask test case
* Add optional file output
* Add hmmer to test name
* Move from process_single to process_low
* Test for versions.yml, plus content
* Prettier
* Avoid gzipping input alignment
* hmmer/eslreformat from template
* Started on main.nf
* meta.id to prefix
* Continued work
* Fix version string so it's from *this* tool
* hmmer/eslreformat
* Prettier
* Get tests/config/pytest_modules.yml back
* Delete extra hmmer/eslalimask in pytest_modules.yml
* More prettier
* Fix path to versions.yml in test
* Remove 'format' param
* Fix problems with format param deletion
* Document format param
* Created hmmer/eslalimask from template
* esl-alimask module with --rf-is-mask test case
* Add optional file output
* Add hmmer to test name
* Move from process_single to process_low
* Test for versions.yml, plus content
* Prettier
* Avoid gzipping input alignment
* meta.id to prefix
* Fix version string so it's from *this* tool
* msisensor2: Add msisensor2 module
* msisensor2/scan module added
* msisensor2 tests added
Changes:
- tests added for msisensor2 from the msisensor2 github repo. No
available tests from NF-Core test repo.
Relates to #1976
* msisensor2 slight bump in stuff
* msisensor2: Replaced spelling of 'tumour' with 'tumor'
* msisensor2: fix linting, testing and containers
Relates to #1976
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
* updated the delly/call module
* Update modules/delly/call/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Creation of Glimpse Chunk
Add sub tools chunk with configuration and needed files for unitest.
* Code linting correction
* Prettier ran
Newline deleted in nextflow.config
* New final line and white spaces
* Change Pytest.yml to work as a subtool.
* Control for the parameters deleted.
Control for the size/count of the window and buffer not needed.
They have some defaults value.
* Changed the different recommended part by @nvnieuwk
Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
