* 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>
* first commit with imputeme as a module. Extensive re-write of imputeme-code, resulting in release v1.0.7 that is runnable in the next-flow framework.
Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Pontus Freyhult <pontus_github@soua.net>
* add base code from samblaster
* added test yml
* fixing versions files, should this be the cause of online lint failures
* removed tmp files that shouldn't be there
* fixing output file name - 1
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fixing output file name - 2
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fixing output file name - 3
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fixing output file name - 4
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fixing output file name - 5
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fixing output file name - 6
* fixed indent
* fixed input name and updated test.yml file with new name
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* feat: add megahit module, currently decompressed output
* Update main.nf
* Update tests/modules/megahit/test.yml
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* feat: compress all outputs, remove md5sums due to gz stochasicity
* fix: wrong conda channel for pigz
* fix: broken singleend tests and update meta.yml
* Missed one
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fix: pigz formatting
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Apply suggestions from code review
* Add GUNC download_db and run commands
* Bump with version without zgrep
* Apply suggestions from code review
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* Harshil formatting
* Apply suggestions from code review
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* readcounter module for hmmcopy
* Changed version number
* Fix indentation
* Update main.nf
* Update modules/hmmcopy/readcounter/main.nf
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
* hmmcopy gccounter working
* Update modules/hmmcopy/gccounter/main.nf
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
* Update main.nf
Changed version to 0.1.1 as the container says
Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
* saving changes to checkout
* saving to sort out other branch
* removed yml tracking of files that cant be tracked due to directory name changing between runs
* test data added, ready for pr
* fix eol linting error
* Update modules/gatk4/genomicsdbimport/main.nf
Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
* merging with master
* update push to show progress
* tests now working untar able to pass data to genomicsdbimport
* commit to checkout
* tests updated, module reworked to simplify and emit updated gendb
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* update meta.yml
Priority of input options changed, updated to reflect this
* Update test.yml
name prefix changed in main script, test.yml updated to reflect this
* fix tests due to review changes
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* add new module samtools_depth
* fixed main.nf for samtools/depth
* add new module mtnucratio
* fix main.nf
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* layout in main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* adding template for module groupreadsbyumi
* update modules with code
* strategy is required argument so moving it to input rather than options.args
* tests successful committing yml
* added meta to output
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
