* 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
* Add motus/merge module, missing test yml
* Fix prefix
* Fix polymersase
* Update test meta.yml
* Try new version system
* Typo fix
* Clairfy docs for the version file
* Switch to directory auto detection
* Now with the change and not just meta
* Remove now unneeded input parameter from test
* Fix input type check
* Try adding db requirement to fix docker issue
* Update modules/motus/merge/main.nf
* Fix input
* Apply suggestions from code review
* Fix md5sums
* Replace debugging db location with actual
* Fix contains due to further varialbility
* Indenting
* Add MultiVCFAnalyzer
* Fix versions
* Fix tests due to md5sum var
* Apply suggestions from code review
* Linting
* 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 daa2info
* Add right flag in the config
* Fix config
* Apply suggestions from code review
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Add ultra/index and ultra/align modules
* Correct tag and prefix
* Fix typos
* Remove SAMTOOLS SORT from test
* Update: Convert sam to bam
* Add tag to docker image
* Fix typo
* Add args2 for samtools
* changing mv by gzip
* changing mv by gzip
* first module creation
* add test.yml
* add flye to pyestes_modules.yml
* update flye module
* delete functions.nf
* generate test.yml
* fix contains from test.yml
* test file assembly_info.txt with regex
* check that file contains at least contig_1
* fix typo in contains
* update version
* split fastq file for raw runs
* use asm-coverage to reduce memory usage
* fix module name error
* add genome-size
* decrease coverage
* change test data for raw runs
* add coverage and genome size
* Apply comments from code review
Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>
* after many trys, add a stub run
* remove md5sum for stub run
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* fix review comments
* Apply suggestions from code review
Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>
* no hardcoded version in stub run
* Update modules/flye/main.nf
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
* Added: gatk4/leftalignandtrimvariants
Additions:
- GATK4/LeftAlignAndTrimVariants module
- Use sars-ncov2 test data as this normalises a larger INDEL correctly.
Fixes#1801
* fixup: Added index to output spec
* fixup: Pattern of tbi output corrected to 'tbi'
* gatk4/leftalignandtrimvariants: Added intervals
Changes:
- gatk4/leftalignandtrimvariants now supports optional interval as BED
file
- Tests added with and without interval. Not test BED file excludes all
variants so no variants are actually normalised.
Fixes#1801
* fixup: leftalignandtrimvariants vcf->tbi fix
* fixup: gatk4/leftalignandtrimvariants Intervals added to meta.yml
