* 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>
* bugfix: when there is a single input file, stageAs("?/*) returns the path directly, not in a list
* Added a test
* Added a test
* Added MD5 checksum
Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.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>
* When the `-i` option of bgzip is given, an index is created and needs to be considered an output
* It is not necessary to use a subfolder
* Updated meta.yml too
* Also check that an index name hasn't been requested
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* Multithreaded samtools commands
* Updated the checksums since the BAM files include the actual command line
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>
* 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
