* 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>
* 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
* Updated container versions for fgbio groupreadsbyumi and callmolecularconsensusreads
* Corrected fgbio call container, trying to fix fgbio group tests
* Removed incorrect line
* diminish memory demand
Kallisto was being told to ask for the same amount of memory as it was said for nextflow to limit.
So, when kallisto tried to use it, nextflow was killing it. Thus, diminishing it per 1 GB solved the issue.
* fix prettier
* removing TODOs
