* 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 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>
* 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>
* 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>
* 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>
* Fixing test.yml
* hmmbuild passing tests
* Output meta
* Linting problem
* Linting problem again
* Fix prettier
* Update modules/hmmer/hmmbuild/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Fix missing prefix
* Accept mxfile param
* Output gzipped hmm
* Moved input file for test to modules branch
* Update modules/hmmer/hmmbuild/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Describe mxfile
* Get LENG 80 check back
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Added fq/lint module
Additions:
- fq/lint module, which checks paired end FASTQ files and confirms they
are valid.
Relates to #1967
* fq/lint linting
* Correct Singularity image
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* added module files
* latest version
* latest version
* latest version
* latest version
* updated test, failing
* added comment on why to use tail -n+3
* same as latest test
* moved args to the end of script
* updated test
* double quotes for esearch input
* removed tail -n+3, stderr is redirected by nextflow
* changed single to double quotes
* Update modules/entrezdirect/esearch/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/entrezdirect/esearch/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update meta.yml
removed default from database parameter
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* 1882 FASTP now supports interleaved FASTQ files
Changes:
- single_end FASTP pipes the FASTQ file
- Using args, it can be configured for interleaved in `--interleaved_in`
- Out is automatically interleaved if input is paired end.
- Removed md5sum checks for FASTQ files as compression seemed to cause
differences
- Instead, we check inside the FASTQ files for content.
Relates to #1882
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
* add module hamronization/amrfinderplus
* deleted comments
* 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>
* create pear module
* add command and tests
* remove md5sum from known empty file
* add force -f to gzip and gunzip to avoid problems with symbolic links
* apply suggestions from review
