* 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
* First commit
* putting correct links for singularity and docker containers (just had to search for bioconda+ascat to find them, and then put them in like the rest of the nf-core tools had it
* adding first try of relevant commands (not working yet, just took their basic pipeline example
* test commit
* remove test
* starting up work with module after 3.0.0 upgrade
* add ascat.prepareHTS statemet
* add location of docker for new mulled alleleCounter+ASCAT container
* first full run with ASCAT on HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
* add notes on dropbox download
* use a newer pytest_modules.yml
* add outpit
* trying to align with current Sarek output
* adding in FH comments
* busy clearing up arguments and testing. Still WIP
* first working run, in nextflow, with sarek-like output. Still needs more work on input arguments
* cleaning up before writing up findings
* testing with putting in arguments in args
* draft for solution 3 style for arguments
* one more test added
* adding FH map
* finished testing maps for args
* wrap-up cram/crai test successfully
* updates to address ability to put in ref.fasta argument for cram running
* adding remaining import-HTS commands in as args, and removing the chr21/chr22 only testing to test-nextflow.config
* first test with auto-downloading the s3-data (when not given as an argument)
* removing download-logic for supporting files, documenting in meta.yml, fixing ref_fasta bug
* adding mulled singularity container
* removing tests
* fix left padding lint issue
* lint failure in meta.yml
* more linting errors
* add when argument
* adding stub functionality
* add stub run
* correct md5sum for versions.yml
* more testing with -runstub
* stub code in pure bash - not mixed with R
* reformat version.yml
* get rid of absolute paths in test.yml
* correct wrong md5sum
* adding allelecount conda link
* rename normal_bam to input_bam etc
* let the pipeline dev worry about matching the right loci and allele files
* dont hardcode default genomebuild
* adding download instruction comment
* add doi
* fix conda addition bug
* add args documentation
* test new indent
* new test with meta.yml indentation
* retry with new meta.yml
* retry with new meta.yml - now with empty lines around
* retry with new meta.yml - remove trailing whitepsace
* trying to fix found quote character that cannot start any token error
* try with one empty line above triple-quote and no empty line below
* trying with pipe character
* checking if its the ending triple quote
* one more try with meta.yml
* test update bioconda versioning for linting failure
* test update bioconda versioning for linting failure 2
* testing allelecounter version error on conda
Co-authored-by: @lassefolkersen
Co-authored-by: @FriederikeHanssen
* Added cnvpytor/importreaddepth module
* Corrected process name in meta.yml file
* added -chrom argument
* space correction
* Added complementary info
* fixed typo
* md5sum added
* modified the module to work on cram files as well
* Added cnvpytor/histogram module and test files
* Added cnvpytor/partition module and test files
* added cnvpytor/callcnvs module and tests
* modified by new modules
* Added test file and fixed input path in modules
* added when block
* little fixes
* skip tracking test.yml
* removed changes to test if conflicts get resolved
* updated outfile name
* corrected the version.yml content
* 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
* bcf annotate ready2go
* edited output name
* fixed output
* updated bcftools ver
* changed contain output string
* removed contain key entirely
* fixed md5sum for test.yml
* using match instead of find
* bcftools/annotate refactored with complete test
* rm trailing white space
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
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>
* Match target bed to input files
* Intervals in getpileupsumamries
* more interval updates
* change targets in strelka
* remove leftover channel
* fix checksums
* add new test vcfs
* add new test vcfs
* Update modules/freebayes/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* 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
* Add stubs for deepvariant [ci skip]
* Update the stubs for deepvariant [ci skip]
* functional with google docker image
* cleanup
* consume docker container within singularity executor
* update the meta.yml file and ask for review
* tweak the input channel shape and test data
* tweak input data [ci skip]
* update for the new syntax
* remove the functions and rename meta vars
* Update the arguments mechanism
* update chr, region and checksum
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format
* fix ci failures
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
* Update seqwish to version 0.7.2
* seqwish can work with a comma-separated list of PAFs
* level with nf-core/modules master branch
* add pangenome test data keys
* the odgi test data lives in its own folder
Co-authored-by: Michael L Heuer <heuermh@acm.org>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* Added files for bcftools/sort
* Fixed output format and removed md5 checksum
* Change input to avoid identical in/output names
* Created rows for bcftools/sort in pytest_modules.yml
* 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>
Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* added new module snpsift/split
* added options.args
* added .vcf.gz to input
* removed test and updated to new NF DSL2 syntax
* Updated to new NF DSL2 syntax
* added option to join vcf files
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* committing to pull updated nf-core files
* saving changes to checout other branch
* committing progress so far, difficulty with test data
* uploading to be used as draft PR
* fix linting error in meta.yml
* attempt to group reference inputs together
* updated input format for resources
* meta.yml updated with new resource names
* added output channel for recal index
* module only takes single vcf file input now
* committing to checkout
* update to new syntax, remove indel test for now
* updated to use memory options and new test data
* Update modules/gatk4/variantrecalibrator/main.nf
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* Update main.nf
* Update modules/gatk4/variantrecalibrator/main.nf
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* remove duplicate test keys from test_data.config
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* initial commit to setup branch
* workflow finished
* Update nextflow.config
* tumour to tumor, getpileup passed as nomral and tumor
* paired_somatic renamed to tumor_normal_somatic
* Apply suggestions from code review
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* updated index names in meta.yml
* changed index file names in main script and test
* Apply suggestions from code review
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Apply suggestions from code review
* fixed bug from changes
* Apply suggestions from code review
* modified yml to allow new subworkflow testing
* Update test.yml
* Update test.yml
* add applyvqsr
* added memory options, new test data used
* Update main.nf
* Update main.nf
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Initial structure
* Working with local singularity image
* Working generateMap.pl script
* Remote not working bioconda
* Working generateMap with biocontainer
* Lint changes
* Updated hmmcopy container version to be consistent
* Fix failing test
* Remove path to perl
* No hardpath to script
* Update main.nf
Moved version outside of process, add support for zipped fasta file
* Revert to not allowing gzip via pipe, as perl script can't cope
Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
