* update to new cli args
* remove bam index from tuple, not needed by program
* bump picard version
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* 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>
* Changed tbi as optional output. HC cannot index a VCF from large chromosomes.
* Apply suggestions from code review
* Update modules/gatk4/haplotypecaller/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Add missing container folders as output channels
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tool name
* Update test output checksum
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Allow to pass arguments to the script itself
* Place args2 correctly
* Define args2 aaaaarrrrgggg
* Testing locally before commiting is a good practice
* Update modules/phantompeakqualtools/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.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>
* Rename process from STRINGTIE to STRINGTIE_STRINGTIE
* Bump Stringtie version to 2.2.1 and remove empty files in tests
* Fix tests for stringtie/merge
Co-authored-by: Júlia Mir Pedrol <mirp.julia@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>
* feat added index as input, to allow module to be used for subsampling
* fix test
* feat added index to meta.yml
* Update modules/samtools/view/meta.yml
feat corrected description of idea pattern file in meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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>
* updated kraken2 module to include optional classification of each input reads, and make fastq outputs optional
NB: this is a breaking change, because the output channels have been renamed as a consequence of changes
* updated yml
* pigz command made optional, in order to be executed only if fastq of classified/unclassified reads are saved
* updated test yaml file for kraken2
* fixed TODOs and renamed variables and outputs
* untar in conda cannot keep same md5sum of version, and therefore md5sum check removed
* improved description of the options
Co-authored-by: James A. Fellows Yates <jfy133@gmail.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>
* Add optional variant catalog input
* fix for no variant catalog test
Co-authored-by: ljmesi <37740329+ljmesi@users.noreply.github.com>
Co-authored-by: Lauri Mesilaakso <john.mesilaakso@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>
* Fix typo
* Add stub runs for testing input without matched normals
* Add missing -stub-run
* remove empty file checksum tests and change workflow names
* test controlfreec naming
* fix output file names
* fix output file names
* fix output file names
* fix conda and container path difference for R scripts
* update tar version to work with conda
* fix version number in docker
* try to fix path to script, pretty sure it won't work
* try new ways to set path with wildcard
* try which
* add which but with escape
* remove comment
* 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
* Make summary output optional as not generated if no sufficiently HQ bins found
* Make contig2bin optional as only generated if sufficient HQ bins found
* 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
* callcnvs stub and tests
* partition stub and test
* histogram stub and test
* importreaddepth stub and tests
* update module scripts
Co-authored-by: Sima Rahimi <sima.rahimi@gu.se>
* 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
* compressing and removing not reproducible md5sums
* follow symlinks while decompressing
* Update tests/modules/metabat2/metabat2/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tests/modules/metabat2/metabat2/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* split tests
* export env variable
* Update modules/metabat2/jgisummarizebamcontigdepths/main.nf
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>
* Update modules/metabat2/metabat2/main.nf
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>
* answer PR comments and switch to bgzip
* add bacillus fragilis alignments
* add meta to samtools/faidx
* move to bgzip
* update freebayes test results
* bump pydamage version to 0.70
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* fix(homer): Update tagdir to have a prefix
Otherwise they have a naming collision
* test(homer): Update paths
* style(homer): Align ,'s
* chore(homer): Update md5sums
* 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
* Use meta map and supply output file name via modules.config
* Remove all def declarations to make it work
* update tests & remove extra .
* fix ze tests
* update meta.yml with meta map info
* add tag line now that meta is available
* Mpileup also likes intervals
* Also update meta yml with inclusive input and intervals
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@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
* fix: remove left-over unnecessary code
* Adds support for meta lists for unzip and untar
* Fix test inputs
* Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple
* Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple
* Fix MALTEXTRACT/AMPS
* Fix further modules
* Fix cellranger
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fix: remove left-over unnecessary code
* Switch to more portable solution for singularity container issue by using bind paths
* Fix input collision of dummy files
* Repalce dummy with which bash
* Remove dummy usage from tests
* Apply suggestions from code review
* Fix singularity typo
* style: Add prettier config files
* build: Add prettier vscode extension
* ci: Replace markdownlint and yamllint with prettier
* style: Run prettier
* style: Use indent of 2 for markdown as well
https://github.com/nf-core/tools/pull/1470#issuecomment-1071028358
* style: Fix indent
* style: Let editorconfig take over tab widths
* style: yaml => yml
* ci: Run prettier once
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
* fix: remove left-over unnecessary code
* Adds --fakeroot option for singularity usage with DeepARG as workaround for broken conda dependency
* Update modules/deeparg/downloaddata/main.nf
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
* Update modules/deeparg/predict/main.nf
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
* Apply suggestions from code review
* Update main.nf
* Update main.nf
* Update main.nf
* Update main.nf
* Go back to original logic
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
* 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>
* fix: remove left-over unnecessary code
* Partial fix for AR module output declarations
* Remove `def` for prefix so useable in output block
* Fix tests
* Add adapterlist support
* Fix tests after addition of adapter list
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>
* Bump chromap version 0.2.0
* Temporary use the docker container until singularity container becomes available
* Temporary use the docker container until singularity container available
* Remove empty lines
* Update singularity container after became available
* 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>
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.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>
* update plink2/vcf to output zstandard compressed data automatically
* update meta
* set plink CPU and memory usage
Co-authored-by: Sateesh <33637490+sateeshperi@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>
* include intervals_index
In order to run the GATK `GenotypeGVCFs` tool with an interval file (such as a .bed file) you need to have the corresponding index file. Otherwise you get the following error message
```
A USER ERROR has occurred: An index is required but was not found for file genome.bed.gz: work/6c/541fce2dc670597f62a571c72288c6/genome.bed.gz. Support for unindexed block-compressed files has been temporarily disabled. Try running IndexFeatureFile on the input.
```
including the index file fixes this problem
* Update meta.yml
* 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
* Update versions
* update checksums + remove variables as input for applyvqsr
* sneak in removal of values and provide them via modules.config
* update another checksum
* more checksums
* move vairable to config
* remove controlfreec, wrong branch
* add line break
* 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>
* 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
* updated to follow the new mergebam syntax, also made unaligned input sample specific
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* refactor: add bcl2fastq to cellranger dockerfile
bcl2fastq required for the cellranger mkfastq module and was therefore
added to the cellranger dockerfile. Further, cellranger was updated to
the latest version, 6.1.2., with naming and containers across
cellranger modules updated accordingly.
* chore: add bcl2fastq zip to .gitignore
* style: fix code linting error
* test(cellranger): Add tiles to mkfastq
* additional dockerfile for mkfastq
* update readme and dockerfiles
* update readme
* fix: update container for mkfastq
* docs: correct typos in readme
* test: update md5sum following cellranger update
* test: update md5sum following cellranger update
* fix: new line for external args in mkfastq
* test: update mkfastq tiles argument
* test: comment out mkfastq tests until smaller test data found
* test: stub-run mkfastq test until smaller test data found
* test: fix incorrect file path for mkfastq
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
* Bump version 0.1.5 to chromap/chromap
* Bump conda samtools version to 1.14
* Get read of inconsistent md5sum in conda
* Bump version in conda and retry md5 checks
* genome index md5 hash removed, conda failed
* 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>
* Add functionality to handle vbz compression
In order for nanopolish to be able handle the default compression for Mk1C Minions (vbz) it must be aware of where to find the plugin. Exporting the HDF5_PLUGIN_PATH found in the conda install (also used to make the biocontainer image) is the solution
* Make the HDF5_PLUGIN_PATH more configurable
Allow the HDF5_PLUGIN_PATH to be changed via a section in a config file e.g
```
params {
modules {
.....
'nanopore_artic_minion' {
.....
hd5_plugin_path = '/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin'
}
......
}
}
```
* Update modules/artic/minion/main.nf
* Export HDF5_PLUGIN_PATH
The HDF5_PLUGIN_PATH variable should be exported for `artic minion` to use it
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Add functionality to handle vbz compression
In order for nanopolish to be able handle the default compression for Mk1C Minions (vbz) it must be aware of where to find the plugin. Exporting the HDF5_PLUGIN_PATH found in the conda install (also used to make the biocontainer image) is the solution
* Make the HDF5_PLUGIN_PATH more configurable
Allow the HDF5_PLUGIN_PATH to be changed via a section in a config file e.g
```
params {
modules {
.....
'nanopore_artic_minion' {
.....
hd5_plugin_path = '/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin'
}
......
}
}
```
* Update modules/artic/minion/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Bump software versions for viralrecon modules
* Remove custom params.save_unaligned from bowtie2_align
* Unify samtools modules and error if input and output names are the same
* Fix ALL the tests
* Removed if-statement to only run on more than 1 file, now it will run on single files as well.
* Added a test for running the cat_cat module on a single file.
* Created a new test.yml with nf-core modules create-test-yml -t cat/cat
* Edited test.yml to not include paths and md5sums for versions.yml, and also removed sometimes variable md5sums
* 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
* Change intervals to be part of sample specific input
* Fix some tests
* Update checksum
* Update intervals
* Update intervals
* Try out gavins idea for adding the file
* update test line
* update test line
* update test line
* revert contains line
* 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>
