* Working version of somalier relate
* few changes
* new changes
* corrected test.yml
* updated container paths and file paths
* changed container and inputFile paths
* changed left padding
* requested changes
* Update modules/somalier/relate/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/somalier/relate/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/somalier/relate/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/somalier/relate/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/somalier/relate/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/somalier/relate/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/somalier/relate/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* requested changes
* requested changes
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Set process label to `process_single` for modules with no `task.cpus` usage
* Fix tests of 'borked' modules
* prettier
* More modules are single-threaded and can use process_single
* Adding process_single to hmmer/esl* modules
* Fix failing tests
* Prettier
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
* Created gappa/examineassign from template
* Test passing
* Run only when taxonomy is set
* Revert adding taxonomy to when
* Add period after prefix
* Fix test
* Add some keywords
* Add one more keyword
* Added Somalier extract module
* changed somalier_dbg4 to somalier for versions.yml
* added and minor changes in meta.yml
* Apply suggestions from code review
* Update main.nf
* Typo in quay.io rl
* updated the input
* new updates
* linting
* linting
* changed the test.yml
* Update modules/somalier/extract/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/somalier/extract/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/somalier/extract/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/somalier/extract/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tests/modules/somalier/extract/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/somalier/extract/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tests/modules/somalier/extract/test.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* last changes
* Update modules/somalier/extract/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/somalier/extract/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/somalier/extract/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update eido/validate module
* Update modules/eido/validate/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update eido/validate module
* Update modules/eido/convert/meta.yml
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
* Update main.nf
* Remove now unnecessary input channel
* Remove unused channel from tests
* Update main.nf
* Update meta.yml
* Re-add logos as not staged in a way that works with MultiQC config files
* Add meta to mOTUs merge
* Put tests back to use downloaded db
* Apply suggestions from code review
* Fix test text string
* md5sum -> contains
* Update nextflow.config
* Update main.nf
* Update meta.yml
* Re-add logos as not staged in a way that works with MultiQC config files
* Add support for secondary custom configs
* 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
* 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>
* add deepbgc prodigal version to versions.yml
* 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>
* 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
* Updating MultiQC to released v1.13
Now using released MultiQC version: https://github.com/ewels/MultiQC/releases/tag/v1.13
* Update MultiQC conda environment to v1.13
Co-authored-by: Robert Syme <rob.syme@gmail.com>
* 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>
