* create files with nf-core command
* update meta.yml files
* starting to work on index main.nf
* prelim test for index
* index test working; not finding all output files
* index passing tests
* index and align passing tests
* prototyping biscuitblaster and pileup
* update containers
* updates to pileup
* pileup passing tests
* template creation for more biscuit tools
* tests passing on blaster,bsconv,pupsom
* epiread passing tests, but need to update SNP bed file path
* vcf2bed working; change test file
* all biscuit commands passing tests
* biscuitblaster rename
* try to fix permissions
* more permission fixes
* trying a couple more permission changes
* hopefully last permission fixes
* really last permission changes
* few more permissions
* add when blocks
* Remove read group meta
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* remove read group meta
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* changes for first round of review
* update meta.yml with more specific links
* Update modules/biscuit/biscuitblaster/main.nf
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Apply new version reporting
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Update modules/biscuit/pileup/main.nf
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Update main.nf
* Update modules/biscuit/pileupsomatic/main.nf
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* update test file path
* Update modules/biscuit/align/main.nf
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Update modules/biscuit/align/main.nf
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* tests passing again
* Update modules/biscuit/align/main.nf
* Update modules/biscuit/bsconv/main.nf
* Update modules/biscuit/epiread/main.nf
* Update modules/biscuit/index/main.nf
* Update test.yml
* Update modules/biscuit/pileupsomatic/main.nf
* remove module-specific extension/prefix
* remove module-specific extension/prefix
* add missing args
* switch pileup strategy
* update test.yml
* remove debug
* whitespace cleanup
* add in newline escapes
* requested changes
* Update modules/biscuit/pileup/meta.yml
Co-authored-by: Spix <nathan.spix@submit.cm.cluster>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Spix <nathan.spix@node107.cm.cluster>
Co-authored-by: njspix <nathan.spix@vai.org>
NGSCheckMate ncm mode, working on bam files and vcf files to check that (human) samples match as expected
Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
* added module seqkit replace
* added when
* removed extra line
* Update modules/seqkit/replace/main.nf
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* Updated meta
* updated indents
Co-authored-by: Cipriano <rrn8@cdc.gov>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* implement plink2/score module
* fix test yml
* fix typo :(
* set cpu
* set mem
* fix input process input block
* fix tests
Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
* fix: remove left-over unnecessary code
* Add hamronizer/deeparg
* Add hamronisation/summarise
* Update test.yml
* Update modules/hamronization/summarize/meta.yml
Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
* line up outputs
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
* add drafty controlfreec
* get sofatware version
* use maps in map
* update paths to new and soon-to-be merged test files, add more input docu
* Stab at documenting args map
* Update syntax
* Bit more description
* Make the linter happy
* tests pass locally
* Add outputs & docu
* tests are failing locally now :/ but cpn file can also be added
* All tests passing, need to update test data again to add folder
* Clean up files
* Clean up files
* Clean up files
* Don't know how to get the test to run with the direcotry for now. they pass locally though
* Make linter happy
* Name process back
* Update to use tar folder
* fix the checksum
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* Initial commit of seqtk/seq module files
* pytest.yml
* updated module and tests code, need to finish modules/main.nf
* Initial commit of seqtk/seq module files
* pytest.yml
* updated module and tests code, need to finish modules/main.nf
* Adding code and configs for seqtk/seq module
* Re-tested module following minor code update
* removed trailing whitespace errors
* Changed variable name to following reviewer suggestions
Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
* add gatk4/combinegvcfs module
* update gatk4/combinegvcfs
* loop to create a string adding -V to each vcf file
* add contains for variable md5
* rm whitespace
* meta in output
* fix indentations
* fix indentations
* move tmpdir to args and update conda version
Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
* add picard-addorreplacereadgroups
* add picard_addorreplacereadgroups
* add new line to main.nf
* remove trailing whitespaces
* remove trailing whitespaces
* change to output in test yml
* add when directive
* picard 2.26.10 -> 2.26.9
* picard 2.26.10 -> 2.26.9 test yml
Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* add picard-cleansam
* add picard/cleansam
* update test yml with output
* picard 2.26.10 -> 2.26.9
* add output to test yml
Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* add picard/createsequencedictionary module
* add picard-CreateSequenceDictionary
* add picard/createsequencedictionary/
* add contains to test yml
* update test yml contains
* update test yml contains
Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* add picard-fixmateinformation
* add picard-fixmateinformation
* fix trailing whitespace
* fix trailing whitespace
Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* Add deeptools bamcoverage
* remove todo string
* Add in when
* fix c&p version format error
* Fix md5sums
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
* Added seqtk/rename module and tests code
* Updated files and testing code for seqtk rename
* Added meta map to seqtk/rename module def
* updated prefix parameter usage
* updated test.yml to remove local filepaths --> change to output
* Added empty line to main.nf
* First version of the biobambam/bammarkduplicates2 module
* Fixed the path of versions.yml
* Regenerated the checksums as the previous files were generated with a single core
* Added the `when:` block, as per #1261
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* hmmcopy/mapCounter
* update test
* Remove bam tag
* Remove /tmp/ path from test.yml
* Update modules/hmmcopy/mapcounter/meta.yml
Incorporate formatting changes
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/hmmcopy/mapcounter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tests/modules/hmmcopy/mapcounter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* ichorCNA run
* Add panel of normals code
* Try and fix tests
* Edit string detection in tests
* Fix linting issues
* Just failing END_VERSIONS
* Fixed versions.yml
* Added DOI
* Optional name for file
* Add when command
* Updated when
* Update modules/ichorcna/createpon/main.nf
Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* Add msisensorpro
* remove absolute paths
* fixing tests
* fix msisensorpro tests
* Update modules/msisensorpro/msi_somatic/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Update modules/msisensorpro/msi_somatic/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* add when back in
* add when back in
* Update modules/msisensorpro/msi_somatic/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* update description
* Update main.nf
* Update main.nf
* Update main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* add plink2_extract
* fix test yml path
* Update modules/plink2/extract/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/plink2/extract/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* compress output
* add DOI
* make outputs less ambiguous
* update test for compressed output
* brain is dumb
* Update modules/plink2/extract/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Remove old nextclade module
* Add nextclade/datasetget and nextclade/run modules
* Fix ECLint
* Add reference and tag as inputs to datasetget module
* Fix tests
* Adjust spacing
