* [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>
* 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>
* Teach nf-core bot to lint
* Correct file
* Add empty line at end of file
* Ran prettier
Co-authored-by: SPearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@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>
Update main.nf
Add args in main command to allow for parsing of arguments from config file
Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
* [samtools] add optional csi output, when applicable
* Remove empty line
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
* 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>
