* Bump checkM version and add support for pre-defined database
* Add markfile output to checkm/lineagewf and add checkm/qa
* Remove unnecessary BAM from tests
* Fix channels to ensure single meta
* Blah
* Use secondary name evwyhere
* Remove second incovcatiojn
* Don't run module directrly for join
* And for the other test
* Correct module name
* Fix name again
* Try and fix out_format 9 not being picked up
* Contains to matches to allow regex
* Fix tests (finally)
* Fix verisoning
* [automated] Fix linting with Prettier
* Update modules/checkm/qa/main.nf
Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
* [POC] Get subworkflows working again - bam_stats_samtools
* Comment out aliased anchors
* Add explicit anchor to pytest_modules.yml
* test(subworkflows): Remove anchors
There are two options to get the tests to trigger:
1. Add the module anchors to the subworkflows (less things to update and maintain because we only have to update the module triggers)
2. Add the tags to the pytest workflow spec.
This is option 2.
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
* added module endorspy and test
* added endorspy
* Fixed spaces and remove unnecessary lines from test
* added extra new line to test.yml
* added a prefix to to avoid name collision
* Update modules/endorspy/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/endorspy/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/endorspy/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/endorspy/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/endorspy/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/endorspy/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/endorspy/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/endorspy/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Apply suggestions from code review
* Update modules/endorspy/main.nf
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Adding new module gfaffix.
* add missing entry to pytest_modules.yml
* update to 0.1.4--hec16e2b_0
* fixup after prettier
* add when section
* update md5sum
* Change to process_single as discussed
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: Simon Heumos <simon.heumos@qbic.uni-tuebingen.de>
* Update main.nf
* Update meta.yml
* Re-add logos as not staged in a way that works with MultiQC config files
* Add ANGSD doCounts
* Prettier
* Update main.nf
* Apply suggestions from code review
* Apply suggestions from code review
* Apply suggestions from code review
* Try loosening test due to conda
* Remove md5 for binary file
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* Update seqwish to version 0.7.2
* seqwish can work with a comma-separated list of PAFs
* level with nf-core/modules master branch
* update seqwish/induce to v0.7.6
* add pangenome test data
* test seqwish/induce v0.7.6 with pangenomics test data
* we already have pointed to the pangenomics test data sets
* update paths to test data
* add path to bgzipped fa, gzi, fai
* remove one tab
* remove one tab
* actually execute the 2nd test
* try to fix versions.yml
* pangenomic tests can be run in their own subworkflow
* maybe the csv input is the problem
* remove space as suggested by Rike
* csv input was not the problem
* update test.yml
* typo
* enable pangenome tests
* add md5sum for pangenomic test
* Update tests/modules/seqwish/induce/test.yml
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
* PAF input is a list of files
* beautify comment
Co-authored-by: Michael L Heuer <heuermh@acm.org>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
* cherry pick the module files from sanger-tol branch and update the test data from official nf-core test datasets
* Update modules/blast/tblastn/main.nf, align the emit
Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
* 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>
* 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
