* 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>
* 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>
* 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>
* feat: each output type has dedicated channel replace bgzip with gzip can only zip one at a time
* Add condition moving of unbinned files
* fix: solution for moving sometimes non-existant files
* fix: update meta.yml to add the new channels
* fix: remove most of the checksums due to variability
* fix: tweaking of output
* Update modules/metabat2/metabat2/main.nf
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
* Fix find commands
* Fix find commands
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
* added code for subworkflow fgbio call umi consensus
* ironing out a few typos etc
* fixing last things
* fixed md5sum - lets see if it changes
* removing file accidentally deleted
* tidy indents
* added bwamem2 alternative
* fixed entry for both tests
* changed name second test workflow entry
* fixed workflow entry names
* fixed md5sum for file generated with bwamem2
* added syntax new DSL2
* added new config location in test command line
* added new config location in test command line
* use of prefix instead of suffix because modules have been changed in this way
* explicit alias to bwa mem1 to avoid confusion
* removed param that should be an ext optional argument in fgbio groupreadsbyumi
* missing colon in config
* missing colon in module config too
* order list alphabetically
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* remove params from body
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* improving readability of input structure
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
* reverting to mandatory input
* fixed tests and workflow take values
* remove param
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* simplify tests params
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* formatting inputs for readability
* factoring in changes to bwamem2_mem and bwa_mem sort/view inputs
* updating test md5sum for grouped file following code update in bwamem
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
* feat: view is now in args2 so we can use sort
* forgot one split_cpus
* feat: update with new logic
* fix: add more info
* fix: remove split_cpus logic
* 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
