* 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>
The previous one raises the warning
> WARNING: Skipping mount /path/to/singularity-v3.9.0/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* 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>
* Make gene and cluster TSVs optional output in case no hits found
* update indicating optional output
* Apply suggestions from code review
Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
* 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 multiqc version in CUSTOM_DUMPSOFTWAREVERSIONS
* update stelka version in STRELKA_GERMLINE
Co-authored-by: Alexander Peltzer <apeltzer@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
* Added samtools version
Co-authored-by: Cloud User <centos@oskar-instance.novalocal>
* 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
* add tool and db version to output
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update meta.yml
Co-authored-by: James 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
* 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
* Bump version of kallistobustools/count
* Trying to update the entire call of kbtools for scrnaseq
* Improved tests for kallistobustools/count
* Add memory, remove workflow as this is passed as args now
* Update modules/kallistobustools/count/main.nf
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* adding missing value
* workflow properly chained together
* changing --workflow to ext.args
* fix intron channel
* fixed checking whether filename is empty or not
* bump indentation
* fixed if else
* Fix linting
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Felipe Marques de Almeida <almeidafmarques@gmail.com>
* 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
* Support non-GFF input
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Fix linting error
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* 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>
