* 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
* 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
* Change syntax from task.ext.suffix to tast.ext.prefix
* Change nextflow.config in all tests to use ext.prefix instead of ext.suffix
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>
* 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>
* Fix picard/markduplicates with new options syntax
* Delete md5sum for bam files and add contains for metrics.txt
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* Added vcf_index to vcf tuple; output to vcf.gz format.
* Fix: extra new line in meta.yml.
* addressed review feedback
* fix: editorconfig error
* fix: gatk memory flag
* fix: editorconfig error
* fix: Indentation
fix: Indentation
* Fix: lint editorconfig error
Removed one extra space
Co-authored-by: Robert A. Petit III <robbie.petit@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
* 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>
