* 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
* 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>
* 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
* added output channel for tbi files, tweaked method of adding blank inputs for gendb tests
* Update main.nf
* Update main.nf
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* greatly simplify syntax
* feat: add subworkflows to annotate (+ bgzip/tabix index) with ensemblvep and snpeff
* feat: get versions from all tools
* add commented infor for new annotation modules
* Add comment line for consistency
* Remove all functions.nf
* Remove include functions.nf and publishDir options
* Replace options.args3 with task.ext.args3 - 3 modules
* Replace options.args3 with task.ext.args3 - 17 modules
* Replace {task.cpus} with task.cpus
* Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with
* Add def args = task.ext.args line to all modules in script section
* Replace options.args with args and args_list
* Initialise args2 and args3 properly
* Replace container syntax
* Revert container changes for cellranger/mkref
* Replace getProcessName in all modules
* Replace getSoftwareName in all modules
* Unify modules using VERSION variable
* Replae options.suffix with task.ext.suffix
* Remove NF version restriction for CI
* Bump NF version in README
* Replace task.process.tokenize logic with task.process
* Minor tweaks to unify syntax in tests main.nf
* Add a separate nextflow.config for each module
* Transfer remaining module options to nextflow.config
* Remove addParams from tests main.nf
* Remove TODO statements
* Use -c to import module specific config
* Bump NF version to 21.10.3
* Fix tests for artic/minion
* Fix broken publishDir syntax
* Standardise and fix obvious failing module tests
* Remove kronatools to krona
* Comment out tags in subworkflow test.yml
* Fix failing module tests
* Add consistent indentation to nextflow.config
* Comment out subworklow definitions
* Fix kallistobustools/ref
* Fix rmarkdownnotebook
* Fix jupyternotebook
* Quote task.process
* Add plink2/vcf to pytest_modules.yml
* Remove NF_CORE_MODULES_TEST from pytest CI
* Fix more tests
* Move bacteroides_fragilis to prokaryotes folder
* Fix cooler merge tests
* Fix kallistobustools/count tests
* Fix kallistobustools/ref tests
* Update test_10x_1_fastq_gz file for kallistobustools/count tests
* Fix bcftools/query tests
* Fix delly/call tests
* Fix cooler/zoomify tests
* Fix csvtk/split tests
* Fix gatk4/intervallisttools tests
* Fix gatk4/variantfiltration
* Fix pydamage/filter tests
* Fix test data for unicycler
* Fix gstama/collapse module
* Fix leehom tests
* Fix metaphlan3 tests
* Fix pairtools/select tests
* Update nextflow.config
* Update nextflow.config
* feat: update syntax
* Fix arriba tests
* Fix more failing tests
* Update test syntax
* Remove comments from tests nextflow.config
* Apply suggestions from code review
* Fix kallistobustools/count module
* Update dumpsoftwareversions module
* Update custom/dumpsoftwareversions
* Add args2 to untar module
* Update leftover modules
* Remove last remaining addParams
Co-authored-by: JoseEspinosa <kadomu@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
* Make targets.bed optional when running in wgs mode
* added test for cram
* Update test_data_config with new reference.cnn
* Update main.nf to allow tumor-only running
Still need a unit-test for this. Almost ready, but needs this file as input https://github.com/nf-core/test-datasets/blob/modules/data/generic/cnn/reference.cnn
* re-writing previous changes, but now it wont crash the entire CI-setup
* fixing overlooked merge conflict
* last overlooked merge-conflict
* move all files to batch subfolder
* adding an optional input for a reference file (needed when running germline and tumoronly)
* minor typo
* update meta.yml
* aligning code, renaming cnvkit to cnvkit_batch, renaming tumorbam to tumor, normalbam to normal
* Update pytest_modules.yml
Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal>
Co-authored-by: Lasse Folkersen <lassefolkersen@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* 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
* tests should now work after the yml update
* Update pytest_modules.yml
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
* initial commit to set up new branch
* save changes to checkout
* workflow working, still needs test.yml and meta.yml, also fix versions file
* subworkflow finished
* Update pytest_subworkflows.yml
* Update pytest_subworkflows.yml
* Update pytest_subworkflows.yml
* fix config subworkflow name
* Update main.nf
* Update pytest_subworkflows.yml
* fixed md5sum issue likely caused by gatk version update
* tumour changed to tumor
* old dir deleted
* Comments added to explain use of placeholders '[]'
* updated index names, input channel renamed to input
* Apply suggestions from code review
* updated to perform new subworkflow testing
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* add new nucmer module
* Apply suggestions from code review
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* update tests with file produced by input
* Update main.nf
* Update meta.yml
Co-authored-by: Michael Cipriano <mcipriano@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* ci: Remove pytest_subworkflows
* ci(bam_sort_samtools): Depend on paths-filter instead of pytest-workflow
Co-authored-by: Harshil Patel <drpatelhh@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* ci: Revert back to one job branch
* ci(align_bowtie2): Run tests that depend on bam_sort_samtools
* ci: Fix anchor not being created yet
* ci: Update sra_fastq tags and pytest_modules
* fix(bam_sort_samtools): Update nextflow.config with params
* test(subworkflows): Update gatk_create_som_pon tags
* ci: Point to subworkflow_hacks branch of nf-core tools
Co-authored-by: Harshil Patel <drpatelhh@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* created and initialised krona module
* Added kronatools/ktimporttaxonomy module
* removing previous redundant work
* added contains info for html
* edited contains in test.yml
* Update get versions
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* remove old syntax
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* rewording module description
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* added detailed keywords
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* update syntax and tool version
* fixed meta.yml issues
* remove contains line from test.yml
* re-wrote module after nf-core/tools update - should work now
* removed md5
* Update modules/kronatools/ktimporttaxonomy/main.nf
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* update meta save
* removed typo
* double quotes to single quotes around html
* re-ran test, which updated md5
* removed md5
* 'classifier' removed to fix linting
* update version
* removed erroneous ktimporttaxonomy2
* Updated input to include meta and database
* fixed tab issues in yaml
* added `contains` to test.yml
* edited `contains` in test.yml
* trying another `contains`
* retrying `contains`
* contains with extra line
* removed classifier from tag
* Apply suggestions from code review
* Update meta.yml
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Add tests and yml file for macs2/callpeak
* add format option for macs2
* update macs2/callpeak to accept format argument
* update test.yml
* update the container version.
* try to fix the issue in conda container.
* Update conda and containers
* Going back to previous container versions
Co-authored-by: JoseEspinosa <kadomu@gmail.com>
* add software/cooler
* fix the wrong files uploaded.
* create a branch for cooler/zoomify
* Apply suggestions from code review
* update functions.nf to new version.
* update the test file to test-datasets.
* update the test method of zoomify
* update dump test file.
* update version.txt to version.yml
* Update modules/cooler/dump/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fix the output bug of versions update to pytest_modules.yml
* update the test file path and fix the output versions.
* Update modules/cooler/dump/main.nf
* indent
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* New modules added: issues #200 and #310
* Update main.nf
* Update meta.yml
* Update tests/modules/gatk4/genotypegvcfs/main.nf
* Apply suggestions from code review
* Update main.nf
* Updating tests for GenomicsDB input and adding the path for this test resource to test_data.config
* Some minor changes on one of the test files I forgot to include
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com>
* add software/cooler
* fix the wrong files uploaded.
* create a branch for cooler/merge
* remove the bin_size from metadata.
* update the test_data to test-datasets
* update pytest_modules.yml
* update the test file from single input file to two input file.
update the output file from hdf5 to bedpe.
* update the version.txt to version.yml and functions.nf
* change version.yml to versions
* update the test file path and fix the output versions.
* Update meta.yml
Correct "version" to "versions"
* Update main.nf
Fix typo
* Update main.nf
Remove some spaces
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
* commit but won't be used because pmdtools should have a submodule
* added submodule pmdtools/filter
* removed pmdtools module created before deciding to design two submodules
* oops forgot to remove a TODO
* removed white space meta.yml, removed v in version and manually added submodule /filter to test
* Update pytest_modules.yml
* Update main.nf
added split_cpus for multi-tools module resources
* Update test.yml
added .pmd extension to match modules/ main.nf
* Update test.yml
update md5sum
* Update singularity and docker build in main.nf
From build 4 to 5 in order to match the conda one
* Update modules/pmdtools/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update main.nf adding samtools version
we need both pmdtools and samtools versions
* Update main.nf remove .pmd extension
* Update test.yml md5sum
Because file extension changed
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* added template
* integrated module
* added fasta index info
* test works, have placeholder data for baits until test-data PR is merged
* added new files to config
* updated test files
* fixing fails ✨
* okay final fix here on the md5sum :face_palm:
* md5sum variable
* update meta.yml to reflect consistency to main.nf
* reverted version so conda works
* Apply suggestions from code review
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
* md5sum can't be generated consistently for output
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
* add pydamage module
* remove TODOs
* split module by subcommands
* update version parsing
* remove forgotten TODOs
* update module names
* remove old holistic module
* Update modules/pydamage/analyze/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add keywords
* update resource requirement
* Update modules/pydamage/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pydamage/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* merge from upstream
* update pydamage from upstream
* add freebayes
* update pydamage test from upstream
* fix meta.yml
* update functions.nf
* update test.yml
* update version parsing
* update version parsing
* fix indentation
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add optional inputs
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add bed test
* add metabat2 module
* only freebayes
* remove metabat2
* update md5sum because of vcf including date of the day
* add keyword
* rescue conflicted files
* attempt to fix ECLint
* add pytest workflow for metabat
* remove -
* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/metabat2/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/metabat2/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add optional inputs/outpus
* remove trailing whitespace
* first cmseq commit
* compressing and removing not reproducible md5sums
* save intermediate work
* follow symlinks while decompressing
* add cmseq/polymut
* add polymut
* add extra test with optional input file
* remove metabat2
* Update modules/cmseq/polymut/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/cmseq/polymut/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/cmseq/polymut/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* fix file extension
* Update modules/cmseq/polymut/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add test without bam index
* split tests in workflows
* answer PR review
* report version from variable
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Implement PLINK_EXTRACT module
* fix plink version number
* Update main.nf
* Update test_data.config
* Update modules/plink/extract/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* just use one channel
* fix test with new channel input
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* commiting changes to switch branch
* commit to setup remote branch
* first draft of the sompon workflow
* keep branch in line with gendb bugfixing
* Update test.yml
* tidy up main.nf
* fixed md5sum
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
