* 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
vcf2maf module created
Additions:
- vcf2maf module created
- If VEP is present in PATH, it is added to command
- If VEP is missing, it is ignored (recommended to skip with --inhibit-vep)
- VEP version automatically added to versions.yml
- Uses VEP cache during testing which is added to test-datasets in https://github.com/nf-core/test-datasets/pull/563
- Default Docker image includes VEP and vcf2maf
- Test includes without VEP.
Relates to #490
* Trimmomatic main only first draft
* Add test files
* SE PE Adjustment
* Remove extra reads input
* chore: Remove TODOs
* Apply suggestions from code review
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
* fix(trimmomatic): Handle SE output correctly
Since there's never going to be unpaired reads for SE reads we can get
away with it for SE
* fix(trimmomatic): Use correct elvis operator to handle logic
* fix(trimmomatic): Add hack to work with SE and PE reads
* Update test.yml
* use the PE and SE trimming correctly
* Made user set adaptors
* Add documentation
* test(trimmomatic): Add files to pytest_modules
* test(trimmomatic): Update name of failing test
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
* update bclconvert module, as used in nf-core/demultiplex
* reconfigure test with new test data
* update test
* formatting
* update outputs, update meta
* update module and test
* update test config, test.yml
* fix linting
* emit logs and reports as dir
* fix typo, recreate test.yml
* fix linting
Co-authored-by: CMGG ICT Team <ict@cmgg.be>
* Add module definition for kreport2krona
* Add metadata for kreport2krona module
* Add tests for kreport2krona
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* Add atlas/splitmerge module
* Finish the tests for atlas/splitmerge
* Prettier
* Update modules/atlas/splitmerge/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Remove curly brackets from meta.yml parameters
For single-file outputs, as reviewed
* Lintung: Remove trailing white-space
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
