* 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>
* updated the delly/call module
* Update modules/delly/call/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@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>
* update tests
* update
* update
* make the manta inputs consistant for germline/somatic/tumoronly
* match chromosomes to cram file (chr21)
* undo genotypegvfs
* undo genotypegvfs
* include intervals
* update md5 with interval
Co-authored-by: Smith Nicholas <smith@in.tum.de>
* Added java options to vardict java
* updated test.yml
* correctly added java options
* Added automatic version numbers for vardictjava
* possible fix for version number in conda
* removed the cram tests
* linting
* Update modules/vardictjava/main.nf
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
* Update modules/vardictjava/main.nf
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
* removed the version line
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
* Use report insted of results for kreport
* Update modules/centrifuge/kreport/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Added support for meta in bwamem2/index
* Added missing description of the input meta map (fasta file)
* Made bwamem2/mem aware of the meta map the index carries
* The output meta map needs to be same as the input bam file
Don't merge it with the index's
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* 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>
* update for bcftools merge
* Update modules/bcftools/merge/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Update modules/bcftools/merge/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* updated test.yml
* added the bed file to the main input tuple
* merged all output into one output channel
* added a test for bcf.gz output
* Update modules/bcftools/merge/main.nf
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
* updated the tests
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
* Started (again) to work on bgzipping SVDB_MERGE output
* Updated test yml
* SVDB_MERGE now bgzips output
* Fixed singularity, renamed tests in test.yml
Co-authored-by: Cloud User <centos@oskar-instance.novalocal>
* 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>
* not yet working: add db version to versions.yml
* next try: db version number not in versions.yml
* Fix amrfinderplus versioning
* Update main.nf
* Apply suggestions from code review
* Update main.nf
* Dump version for syncrony with run
* Update test.yml
* Apply suggestions from code review
Co-authored-by: James Fellows Yates <jfy133@gmail.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>
