* add kimporttext module
* fix the Prettier error.
* fix the Prettier error.
* fix the test.yml
* fix the test.yml
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* update the test files;
simplify the main script of krona/ktimporttext.
* update the test file url for krona ktimporttext
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* initial version of gamma module
* remove trailing whitespace
* prettier fix
* hardcode version number
* Update modules/gamma/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/gamma/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/gamma/meta.yml
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* update meta and prettier
* add whitespaces
* add fasta output and tests
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* first commit
* syntax fix
* fix input
* output sam during test for md5sum
* replace md5sum with contains
* add new test data, add extra in/outputs
* cli fixes
* fix outputs
* Update modules/elprep/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/elprep/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/elprep/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* fix suggestions by @jfy133
* Bit more verbose explanation for bool vals
* define variables
* fix prettier
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* bclconvert: initial commit
* add most of tool
* attempt at adding testing stub
* add dockerfile + instructions
* add container to module
* update readme
* more attempts at making stubs work
* finish stub run
* fix ci issues
* more fixes to stub
* add read version check to stub
* fix some tests
* update readme
* fix version number
* syntax fix
* revert edit to output directory
* Update modules/bclconvert/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/bclconvert/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* update meta.yaml
* update thread usage
* Update modules/bclconvert/main.nf
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
* Escape env variable
* Update modules/bclconvert/Dockerfile
Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
* fix comments by @Emiller88
* fix task.cpus
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
* Create module antismashlitedownloaddatabases
* Corrected user-specification of database directory
* Updated test.yml
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Fix typo in test.yml
* Feed database files via docker/singularity mount)
* Add external db file mounts to the containers
* Fixed docker command in main.nf
* Apply prettier
* Apply prettier and add PWD
* Add more output to test.yml
* Add more output paths to test.yml
* Fixed test.yml
* Apply suggestions from code review
Add documentation of why we need to mount files to the containers.
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Fix code linting errors (remove trailing whitespaces)
* Fix code linting error (remove trailing whitespace)
* Fix errors from Prettier linting
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add module AMPlify
* Apply suggestions from code review
Thanks for the review!
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
* removed trailing whitespaces
* Apply suggestions from code review
Thanks again!
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
* Apply suggestions from code review
Thank you for the suggestions!
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Apply suggestions from code review
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* including review suggestions
* fix versions.yml
* add model_dir input
* add model_dir to meta.yml
* complete faa pattern in meta.yml
* add fa.gz to pattern
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* first commit
* edit main.nf
* edit tests
* run prettier
* fix test
* indent script
* Update modules/snapaligner/paired/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/snapaligner/paired/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* fix version nr
* update meta
* fix versions
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* first commit
* first commit
* update test.yml
* update test.yml
* Update modules/picard/crosscheckfingerprints/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update modules/picard/crosscheckfingerprints/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* add support for vcf haplotype maps
* update test
* update test data config, use test data
* fix exit code
* Update modules/picard/crosscheckfingerprints/main.nf
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Update modules/picard/crosscheckfingerprints/main.nf
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* remove unused stub
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Building Picard liftovervcf module
* Building Picard liftovervcf module_test
* Building Picard liftovervcf pytest
* Module for picard liftover vcf created
* Fixed files after linting test
* Fixed trailing whitespace
* Checked files with prettier
* further formatting with prettier
* Fixed test.yml
* Fixed input variable names
* Changed contain test.liftef.vcf
* Changed contain in test.yml test.liftef.vcf
* Run prittier
* Going back to previous version of test.yml
* downgrading picard to 2.26.10 from 2.26.11
* Update modules/picard/liftovervcf/main.nf
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Update modules/picard/liftovervcf/main.nf
Print available memory
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Output from .vcf to .vcf.gz
* Added spaces to align emit
* Update modules/picard/liftovervcf/meta.yml
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Update modules/picard/liftovervcf/meta.yml
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Update modules/picard/liftovervcf/meta.yml
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Removing md5sum test
Co-authored-by: jemten <jemten@users.noreply.github.com>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
* add bamsormadup
* fix yaml
* add test.yml
* Update tests/modules/biobambam/bamsormadup/test.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* test meta.yaml: remove md5sums
* Tool bamsormadup:
- add (optional) reference input
- add bam index ouput
- add cram output option
- make metrics output: more general
* fix input and output formats
* update input file description
* drop sam output, goes against nf-core regs; add input check for cram files
* fix typo
* Update modules/biobambam/bamsormadup/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* improve ref fasta name
* fix if else shorthand
* fix syntax error
* kind of fix tests
* set fixed suffix for metrics file to keep it in line with picard and bammarkduplicates2
* fix command line
* update test.yml
* add support for multiple input bams
* Update modules/biobambam/bamsormadup/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/biobambam/bamsormadup/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tests/modules/biobambam/bamsormadup/test.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* fix: remove left-over unnecessary code
* Add prinseq++
* Remove last todo
* Fix tests due to variability of output FASTQs (reads can be ordered differently between runs)
* Apply suggestions from code review
* controlfreec significance
* move freec files to own subfolder
* Fix meta.yml naming
* Fix meta.yml naming
* Fix linting
* Forgot to refactor
* forgot more refactoring
* Too much refactoring on output paths
* Too little refactoring here
* update checksum
* NGSCheckMate v1
* Add some tests for UMItools
* Added tests for dedup
* Include pytest
* Delete main.nf
* Delete meta.yml
* Delete main.nf
* Delete nextflow.config
* Delete test.yml
* add prettier
* Add direct test on bam
* Update tests/modules/umitools/dedup/main.nf
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
* Update tests/modules/umitools/dedup/main.nf
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
* Update tests/config/pytest_modules.yml
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
* Not ignore-umi
Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
* fix(homer): Update expected file path to improve caching
* docs(homer): Update findpeaks
* test(homer): Add maketagdirectory dependency
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* feat(bbmap): Initialize pileup module
* test(bbmap): Update outputs
* test(bbmap): Add pileup tags
* style(bbmap): Add in when
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* feat: add template for Bracken
* chore: update version
* refactor: change command build
* refactor: rename report variable, change quotes
* docs: remove refactored input parameter
* fix: correctly assign arguments to options
* tests: set up single and paired end tests
* style: apply prettier
* chore: change data sources to official ones
* refactor: rename test workflows
* tests: use correct input to the new UNTAR module
* chore: update md5sums
