* 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>
* fasta_fai_dict tuple is now split into separate input channels
* fix: lint errors
* fix: pytest errors
* Update modules/gatk4/splitncigarreads/meta.yml
* Update modules/gatk4/splitncigarreads/main.nf
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>
* feat: update gatk4 from 4.2.0.0 to 4.2.3.0
* update md5checksum
* commit all files
* actually checksum was good, but I suspect something fishy with the tests
* 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>
* 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
* bug fixes, multicalling samples and gendb emissions now fixed
* Update pytest_modules.yml
* Update meta.yml
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>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* 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>
* Add CRAM support to allelecounter
* Update meta.yml
* Rename bam,bai to input,input_index
* Apply suggestions from code review
* Fix reference to renamed variable
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* 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>
* files created for createsompon, script written, meta written, still needs tests
* updated to 2.0.0 method input, however this requires a genomicsDB input now
* script finished, meta yaml updated. Tests working locally, test yaml made, needs genomicsdb example on nf-core to run repository tests
* versions updated, issue with test data not able to download directory
* updated tests to include repo-side data
* Apply suggestions from code review
* Update modules/gatk4/createsomaticpanelofnormals/main.nf
* temp commit to allow checkout
* updated createsompon tests to use tarred gendb
* resolve conflict
* Update tests/modules/gatk4/createsomaticpanelofnormals/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.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>
* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* Added extension input for bedtools sort
* whitespace
* Updated docs
Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Svyatoslav Sidorov <svet.sidorov@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>
* Templates for new module
* pe only test passing
* only_pe and only_se passing
* only_pe, only_se, mixed passes
* Multiple pe + se tc passes
* Passing args works
* Add 'interleaved' to description
* Fixed linting message
* Update modules/khmer/normalizebymedian/main.nf
Good point.
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* Update meta.yml
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* Make samtools/merge cram compliant
* samtools/stats cram compliance
* update yml file
* samtools/view to deal with crams
* Update tests to make sure cram works
* also fix tmp dir and min mem in one go
* basequalityrecal test for cram + min mem + tmpdir
* update haplotypecaller for sarek
* update haplotype yml
* update markdup to allow multiple bams, take out params to be passed with options.args
* remove TODO statement
* Remove variable md5sum
* add emtpy input to stats module in subworkflows
* subworkflows seem to work now on my side
* Apply code review
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* replace bam with input to be more inclusive
* rename everywhere
* rename input
* remove variable checksum
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* new mitochondria mode added, tests updated to allow for temp fix for test data
* add cram test
* bam/bam_idx renamed to input and input_index
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
* added template for module
* update main
* added specific code
* wrong variable name in else script
* added tests for both split and nosplit
* docker test successful - updating yaml
* adding echo to version print
* add new assembly scan module
* add newline endings
* fix newline ending
* add newline at end
Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* First step into creating a seqtk/mergepe module to interleave fastQ input
* First rewrite of main.nf to make the module perform the desired (interleave/merge of pe reads) task
* Modifications to test the new seqtk/mergepe module.
* Improving the seqtk/mergepe module to output single end reads as well, and making sure tests work
* Modified so that gzip uses -n and that single read entries are symlinked with ln -s instead of copied, therefore updated test.yml as well.
* Fix trailing whitespaces
Co-authored-by: Daniel Lundin <daniel.lundin@lnu.se>
* Provide an exisiting bam file for optitype
* Update main.nf
Attempt at fixing this with new testing data
* Trying slightly different approach
* Mini fixes, not sure whats wrong here
* Add bam file with NM tags in all reads for optitype
Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
Co-authored-by: Alexander Peltzer <alexander.peltzer@boehringer-ingelheim.com>
* add module main porechop
* update porechop main
* add porechop functions
* update meta porechop
* add test main porechop
* add porechop pytest yml
* add porechop test.yml
* Update modules/porechop/meta.yml
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* re-add porechop avoid conflict
* Update modules/porechop/meta.yml
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* fix prefix suffix
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* add new module samtools_depth
* fixed main.nf for samtools/depth
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* added template for fastqtobam
* porting old code into new template
* update with missing getprocessname function
* test completed - updating all
* fixed linting issues
* improved reading
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 📦 NEW: Add galgal6 chr30 test data
* 📦 NEW: Add bamtools module
* 👌 IMPROVE: Ignore test data
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 📦 NEW: Add galgal6 chr30 test data
* 📦 NEW: Add bamtools module
* 👌 IMPROVE: Ignore test data
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Update with new versions.yml file
* 🐛 FIX: Update meta.yml + correct typos
* Update modules/bamtools/split/meta.yml
Add bam, split, chunk tags
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* 🐛 FIX: Correct meta.yml
* 🐛 FIX: Grab software name using ${getSoftwareName(task.process)}
* 🐛 FIX: Update test.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* files created for createsompon, script written, meta written, still needs tests
* updated to 2.0.0 method input, however this requires a genomicsDB input now
* script finished, meta yaml updated. Tests working locally, test yaml made, needs genomicsdb example on nf-core to run repository tests
* versions updated, issue with test data not able to download directory
* updated tests to include repo-side data
* Apply suggestions from code review
* Update modules/gatk4/createsomaticpanelofnormals/main.nf
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* add liftOver module
* add liftover module tests
* fix getProcessName
* fix tests
* fix out of date function
* version numbers should be numeric
* drop versions.yml from test.yml
* Update modules/ucsc/liftover/main.nf
Remove software name variable
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update tests/modules/ucsc/liftover/main.nf
Use test chain file
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* add genome_chain_gz to test data config
* update md5sum for new chain test data
* Fix indentation in file declaration
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* Updated seacr callpeak to include a control threshold
* Whitespace
Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com>
* Reduce number of required input files for damage profiler
* Remove rebugging
* Add optional species list file.
* Working pending updated test-dataset update
* Add genome header to config
* 📦 NEW: Add isoseq3/cluster module
* 🐛FIX: Fix reports channel and add .pbi to it
* 🐛FIX: Fix report channel definition
* 👌IMPROVE: Move .pbi file into reports channel
* 👌IMPROVE: remove --use_qvs option from command line
* 👌 IMPROVE: Add in addParams removed options from command line
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 👌 IMPROVE: The module accept one channel (primers moved into the first channel)
* 📦 NEW: Add galgal6 chr30 test data
* 📦 NEW: Add bamtools module
* 👌 IMPROVE: Ignore test data
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: add singletons parameter and improve outputs
* 🐛 FIX: Update test with last module model
* 👌 IMPROVE: Add test tag
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Update test data config
* 👌 IMPROVE: Remove pbi from input files
* 👌 IMPROVE: Remove unused index
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Fill contains args
* 📦 NEW: Add isoseq3/cluster module
* 🐛FIX: Fix reports channel and add .pbi to it
* 🐛FIX: Fix report channel definition
* 👌IMPROVE: Move .pbi file into reports channel
* 👌IMPROVE: remove --use_qvs option from command line
* 👌 IMPROVE: Add in addParams removed options from command line
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 👌 IMPROVE: The module accept one channel (primers moved into the first channel)
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: add singletons parameter and improve outputs
* 🐛 FIX: Update test with last module model
* 👌 IMPROVE: Add test tag
* 👌 IMPROVE: Update test data config
* 👌 IMPROVE: Remove pbi from input files
* 👌 IMPROVE: Remove unused index
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Fill contains args
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 📦 NEW: Add galgal6 chr30 test data
* 📦 NEW: Add bamtools module
* 👌 IMPROVE: Ignore test data
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Update code to new versions capture + better output channels
* 👌 IMPROVE: Update with new versions.yml file
* 🐛 FIX: Update meta.yml + correct typos
* 👌 IMPROVE: Clean output file names + correct typo
* 🐛 FIX: Remove bamtools/split module from isoseq3/cluster
* 🐛 FIX: Update output filename pattern
input filename and output filename were the same
* 👌 IMPROVE: Update meta.yml
* added template for tiddit/cov
* test finished
* quick fix to meta info
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* applying suggestions
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* chore: use template to create fasterq module
* feat: add fasterq-dump process module
* docs: provide input and output descriptions
* docs: add comment on `--temp`
* fix: use correct variable
* tests: define test output
* refactor: address review comments
* refactor: remove vdb-config input
* chore: add new test data to config
* tests: define single-end and paired-end cases
* refactor: choose specific output
* tests: do not expect single FASTQ for paired-end
* feat: add compression
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* tests: revert the test data name
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 📦 NEW: Add galgal6 chr30 test data
* 📦 NEW: Add bamtools module
* 👌 IMPROVE: Ignore test data
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 📦 NEW: Add galgal6 chr30 test data
* 📦 NEW: Add bamtools module
* 👌 IMPROVE: Ignore test data
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Update with new versions.yml file
* 🐛 FIX: Update meta.yml + correct typos
* Update modules/bamtools/split/meta.yml
Add bam, split, chunk tags
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* 🐛 FIX: Correct meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* feat(subworkflows): Add align_bowtie2 subworkflow
For testing CI setup
* test(align_bowtie2): Add initial list of changes to test
* test(align_bowtie2): Add initial test
* refactor: Use tags to run subworkflows ci
For every underlying module used by workflow and allow the modules
pytest-modules definition be the source of truth.
* refactor: Use individual directories for subworkflows
* docs(align_bowtie2): Add initial meta.yml
Copied most of it from the bowtie2/align module.
* fix(align_bowtie2): Fix module include paths
* test(bam_sort_samtools): Add initial test
* ci(bam_sort_samtools): Add modules that trigger the tag
* test(bam_stats_samtools): Add initial test
* ci(bam_stats_samtools): Add keys to pick up changes
* docs(bam_samtools): Add initial meta.yml
* test(align_bowtie2): Fix path to subworkflow
* test(align_bowtie2): Update entry point
* fix(bam_sort_samtools): Update include paths
* test(bam_sort_samtools): Fix path
* style: Clean up addParams
* test(samtools_sort): Add suffix for test
* test(align_bowtie2): Add samtools_options for suffix
* test(bam_stats_samtools): Update path
* test(bam_stats_samtools): Use stats input
Otherwise it's just an example of how it's used in the bam_sort_samtools subworkflow
* ci(linting): Skip module linting of subworkflows
* ci(linting): Clean up startsWith statement
* test(bam_stats_samtools): Use single end test data for single end test
* test(bam_stats_samtools): Add expected files
* test(align_bowtie2): Add paired-end test
* test(align_bowtie2): Sort order of output
* test(align_bowtie2): Update hashes
* docs(align_bowtie2): Fix typo
* test(align_bowtie2): Update samtools output names
* test(align_bowtie2): Remove md5sums for bam/bai
* feat(subworkflows): Add nextflow.configs
These can be used for default settings in the future. They can then be
included in the conf/modules.config so that the params don't have to be
duplicated in the root nextflow.config.
* docs(subworkflows): Include modules instead of tools
* fix: Update to versions
* chore(align_bowtie2): Remove duplicate tag
* style: Format yamls
* test(subworkflows): Only check versions for modules
* chore: Update subworkflows to match rnaseq dev
* fix(subworkflows): Update paths
* fix(bam_sort_samtools): Fix sort parameters for testing
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* docs: Update TODOs with a message
* ci: Try using a matrix for strategy
* ci: Try passing an array
* Revert "ci: Try passing an array"
This reverts commit d3611fcd8332bbb9a8501e8dd299d0a623aaecaa.
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* files for learnreadorientationmodel initialised for first commit
* finished scripts and yml files. test working locally but needs an f1r2 test data on nf-core before it can be submitted
* updated test data location
* versions file updated, test data added
* updated versions file, edited test file
* small formatting update to main.nf
* Update main.nf
* Update test_data.config
* updated tests main.nf
* Update test_data.config
* Apply suggestions from code review
* Update modules/gatk4/learnreadorientationmodel/main.nf
* Update modules/gatk4/learnreadorientationmodel/meta.yml
* fixed tests failing
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* 📦 NEW: Add isoseq3/cluster module
* 🐛FIX: Fix reports channel and add .pbi to it
* 🐛FIX: Fix report channel definition
* 👌IMPROVE: Move .pbi file into reports channel
* 👌IMPROVE: remove --use_qvs option from command line
* 👌 IMPROVE: Add in addParams removed options from command line
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 👌 IMPROVE: The module accept one channel (primers moved into the first channel)
* 📦 NEW: Add galgal6 chr30 test data
* 📦 NEW: Add bamtools module
* 👌 IMPROVE: Ignore test data
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: add singletons parameter and improve outputs
* 🐛 FIX: Update test with last module model
* 👌 IMPROVE: Add test tag
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Update test data config
* 👌 IMPROVE: Remove pbi from input files
* 👌 IMPROVE: Remove unused index
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Fill contains args
* 📦 NEW: Add isoseq3/cluster module
* 🐛FIX: Fix reports channel and add .pbi to it
* 🐛FIX: Fix report channel definition
* 👌IMPROVE: Move .pbi file into reports channel
* 👌IMPROVE: remove --use_qvs option from command line
* 👌 IMPROVE: Add in addParams removed options from command line
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 👌 IMPROVE: The module accept one channel (primers moved into the first channel)
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: add singletons parameter and improve outputs
* 🐛 FIX: Update test with last module model
* 👌 IMPROVE: Add test tag
* 👌 IMPROVE: Update test data config
* 👌 IMPROVE: Remove pbi from input files
* 👌 IMPROVE: Remove unused index
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Fill contains args
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 📦 NEW: Add galgal6 chr30 test data
* 📦 NEW: Add bamtools module
* 👌 IMPROVE: Ignore test data
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Update code to new versions capture + better output channels
* 👌 IMPROVE: Update with new versions.yml file
* 🐛 FIX: Update meta.yml + correct typos
* 👌 IMPROVE: Clean output file names + correct typo
* 🐛 FIX: Remove bamtools/split module from isoseq3/cluster
* 📦 NEW: Add isoseq3/refine module
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add parallelization
* 🐛 FIX: Correct Typo
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 👌 IMPROVE: The module accept one channel (primers moved into the first channel)
* 👌 IMPROVE: Assign a value channel to primers input
Improve workflow code readability
* 👌 IMPROVE: Update to the version of templates
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Remove pbi from input files
* 👌 IMPROVE: Update test file
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Fill contains args
* 📦 NEW: Add isoseq3/refine module
* 👌 IMPROVE: Add parallelization
* 🐛 FIX: Correct Typo
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 👌 IMPROVE: The module accept one channel (primers moved into the first channel)
* 👌 IMPROVE: Assign a value channel to primers input
Improve workflow code readability
* 👌 IMPROVE: Update to the version of templates
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Remove pbi from input files
* 👌 IMPROVE: Update test file
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Fill contains args
* 👌 IMPROVE: Add one channel per output file
* 👌 IMPROVE: Minor updates
* 👌 IMPROVE: Minors Update
- Remove TODO from test.yml
- Remove useless piece of code
* 📦 NEW: Add isoseq3/refine module
* 👌 IMPROVE: Add parallelization
* 🐛 FIX: Correct Typo
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 👌 IMPROVE: The module accept one channel (primers moved into the first channel)
* 👌 IMPROVE: Assign a value channel to primers input
Improve workflow code readability
* 👌 IMPROVE: Update to the version of templates
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Remove pbi from input files
* 👌 IMPROVE: Update test file
* 👌 IMPROVE: Fill contains args
* 📦 NEW: Add isoseq3/refine module
* 👌 IMPROVE: Add parallelization
* 🐛 FIX: Correct Typo
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 👌 IMPROVE: The module accept one channel (primers moved into the first channel)
* 👌 IMPROVE: Assign a value channel to primers input
Improve workflow code readability
* 👌 IMPROVE: Update to the version of templates
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Remove pbi from input files
* 👌 IMPROVE: Update test file
* 👌 IMPROVE: Add one channel per output file
* 👌 IMPROVE: Minor updates
* 👌 IMPROVE: Minors Update
- Remove TODO from test.yml
- Remove useless piece of code
* 🐛 FIX: Remove unwanted files
* 🐛 FIX: Protect \
* 🐛 FIX: Remove test files
* Apply suggestions from code review
* Apply suggestions from code review
* Update tests/modules/isoseq3/refine/test.yml
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Correct parsing versions with trailing zeros
* Fix test
* Update modules/custom/dumpsoftwareversions/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Fix tests and go back to output versions.yml
* Update tests/test_versions_yml.py to use BaseLoader
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* 👌 IMPROVE: Add some pacbio test files
* 📦 NEW: Add pbbam/pbmerge module
* 🐛 FIX: Add optional arguments to command line
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Update test data config and test script
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Add some pacbio test files
* 📦 NEW: Add pbbam/pbmerge module
* 🐛 FIX: Add optional arguments to command line
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Update test data config and test script
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Update and clean code
* 🐛 FIX: Update module path in test
* 🐛 FIX: Add missing () + correct module path in test
* 👌 IMPROVE: Update pbmerge from version 1.6.0 to 1.7.0
* 👌 IMPROVE: Change output filename suffix for something more generic
* 🐛 Update test.yml
* Apply suggestions from code review
* Update tests/modules/pbbam/pbmerge/test.yml
* Update tests/modules/pbbam/pbmerge/main.nf
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* initiated files for calculate contamination
* pushing local repo to remote
* created script, filled in meta yml, created tests and test yml. local checks passing, needs repo side test data
* added option and tests for outputting optional segmentation file
* saving for test push
* versions updated, test data added
* Update main.nf
* fixed versions info, should report correctly now
* small update to main.nf outputs formatting
* Apply suggestions from code review
* Update test_data.config
* Apply suggestions from code review
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* new module pirate
* remove md5 check for non reproducible binary files
* get those to-dos out
* Update main.nf
* Update meta.yml
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* initial commit [ci skip]
* reuse the modules code from nf-core/mag [ci skip]
* add contextual information for the module [ci skip]
* add stubs to avoid downloading db [ci skip]
* trigger test
* iterate on tests [ci skip]
* itereate tests [ci skip]
* add bins [ci skip]
* fix stubs [ci skip]
* interation on tests with stubs [ci skip]
* use the existing pattern and fasta for input
* accomodate the new version file format
* use variable for the stub [ci skip]
* update the versions file in meta.yml
* Accomodate code review regarding publishDir function [ci skip]
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* remove extra newline
* use bioconda channel
* update the description for filtered file
* Apply suggestions from code review
* Update main.nf
* Update main.nf
* Update modules/gtdbtk/classifywf/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* added classic mlst module
* removed nf-core TODO comments
* included drpatelh suggestions
* adjust version capture identation
* update main to pass lint
* follow output expected by test.yml
* suggested prefix change from rpetit3
* Apply suggestions from code review
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
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
* Start work, continue once on non-mobile internet
* finished and working on conda
* Update modules/amps/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Apply suggestions from code review
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Better error message for FileNotFoundErrors
* Update tests/test_versions_yml.py
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update test_versions_yml.py
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* Fix IQ tree
* Fix picard markdup and merge sam
* Fix plink/vcf version
* Fix plink version output
* Fix prokka version command
* Fix pydamage
* Try fixing markduplicates
* Fix snpEff
* Fix vcftools version
* Fix pydamage and filtersamreads test run
* Fix MarkDuplicates tests
* Add missing unsorted checks
* Remove MD5 sym due to stochasicity in BAM file
* 📦 NEW: Add module lima
* 👌 IMPROVE: Move .pbi output to reports channel
* 🐛 FIX: Fix report channel definition
* 👌IMPROVE; Remove options from command line
update test script with removed options
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 🐛 FIX: Add pbi input
* 👌 IMPROVE: Add parallelization to lima
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 👌 IMPROVE: The accept one channel (primers move into the first channel)
* 👌 IMPROVE: Assign a value channel for pimers
Improve code workflow readability
* 👌 IMPROVE: Update .gitignore
* 👌 IMPROVE: Update module to last template version
* 🐛 FIX: Correct Singularity and Docker URL
* 👌 IMPROVE: Update to the last version of modules template
* 👌 IMPROVE: Update test_data.config
* 👌 IMPROVE: Remove pbi from input files
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 🐛 FIX: Fill contains args
* 📦 NEW: Add module lima
* 👌 IMPROVE: Move .pbi output to reports channel
* 🐛 FIX: Fix report channel definition
* 👌IMPROVE; Remove options from command line
update test script with removed options
* 🐛 FIX: Add pbi input
* 👌 IMPROVE: Add parallelization to lima
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 👌 IMPROVE: The accept one channel (primers move into the first channel)
* 👌 IMPROVE: Assign a value channel for pimers
Improve code workflow readability
* 👌 IMPROVE: Update .gitignore
* 👌 IMPROVE: Update module to last template version
* 🐛 FIX: Correct Singularity and Docker URL
* 👌 IMPROVE: Update to the last version of modules template
* 👌 IMPROVE: Update test_data.config
* 👌 IMPROVE: Remove pbi from input files
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 🐛 FIX: Fill contains args
* 👌 IMPROVE: Add channel for each output
* 👌 IMPROVE: Remove comments
* 📦 NEW: Add module lima
* 👌 IMPROVE: Move .pbi output to reports channel
* 🐛 FIX: Fix report channel definition
* 👌IMPROVE; Remove options from command line
update test script with removed options
* 🐛 FIX: Add pbi input
* 👌 IMPROVE: Add parallelization to lima
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 👌 IMPROVE: The accept one channel (primers move into the first channel)
* 👌 IMPROVE: Assign a value channel for pimers
Improve code workflow readability
* 👌 IMPROVE: Update module to last template version
* 🐛 FIX: Correct Singularity and Docker URL
* 👌 IMPROVE: Update to the last version of modules template
* 👌 IMPROVE: Update test_data.config
* 👌 IMPROVE: Remove pbi from input files
* 🐛 FIX: Fill contains args
* 📦 NEW: Add module lima
* 👌 IMPROVE: Move .pbi output to reports channel
* 🐛 FIX: Fix report channel definition
* 👌IMPROVE; Remove options from command line
update test script with removed options
* 🐛 FIX: Add pbi input
* 👌 IMPROVE: Add parallelization to lima
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 👌 IMPROVE: The accept one channel (primers move into the first channel)
* 👌 IMPROVE: Assign a value channel for pimers
Improve code workflow readability
* 👌 IMPROVE: Update module to last template version
* 🐛 FIX: Correct Singularity and Docker URL
* 👌 IMPROVE: Update to the last version of modules template
* 👌 IMPROVE: Update test_data.config
* 👌 IMPROVE: Remove pbi from input files
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 🐛 FIX: Fill contains args
* 👌 IMPROVE: Add channel for each output
* 👌 IMPROVE: Remove comments
* 🐛 FIX: Clean test_data.config
* Update modules/lima/main.nf
Add meta to each output
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update modules/lima/main.nf
Remove useless parenthesis
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* 🐛 FIX: Keep version number only
* 🐛 FIX: Reintegrate prefix variable and use it to define output file name
* 👌 IMPROVE: add suffix arg to check output files names
* 👌 IMPROVE: Use prefix for output filename
* 🐛 FIX: Set optional output
Allow usage of different input formats
* 👌 IMPROVE: Update meta file
* 👌 IMPROVE: Update test
One test for each input file type
* 👌 IMPROVE: add fasta, fastq.gz, fastq, fastq.gz test files
* 👌 IMPROVE: Update with last templates / Follow new version.yaml rule
* 🐛 FIX: Fix typos and include getProcessName function
* 👌 IMPROVE: Update .gitignore
* 👌 IMPROVE: Using suffix to manage output was not a my best idea
Add a bash code to detect extension and update output file name
* 👌 IMPROVE: clean code
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
* Update fastqc to produce multi-version versions.yml
* Update readme and pull request template
* Fix markdownlint
* remove variable
* Change publish dir to lowercase
* Re-add getSoftwareName
* Add custom pytest-workflow test to ensure versions.yml is valid
* Add docstring
* Remove __init__.py as it is not needed
* Remove changes to README, since this part went to nf-co.re
* Add NF_CORE_TEST env var
* Fix editorconfig
* Add additional consistency checks for versions.yml
* Update multiqc module
* Fix output channel
* initial commit [ci skip]
* remove todo from the module files [ci skip]
* add a sample test case [ci skip]
* push the latest work [ci skip]
* bump kleborate build
* test passing with the new build for kleborate [ci skip]
* ready for review
* 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>
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* Start maltextract module
* start tests
* Get tests working now we have test data
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Changes after review
* Update tests/modules/maltextract/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update tests/modules/maltextract/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update tests/modules/maltextract/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* bbmap/align done
* Tests for single end and prebuilt index
* Write bam file directly
* Forgot to use all cpus for bbmap
* Test md5sums
* Added pigz support
* Update modules/bbmap/align/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* process_medium and fastq
* cat/cat module
* Remove filter from CAT_CAT
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* added output channel for stats file, updated meta yml with description and test yml with check for stats file
* Update modules/gatk4/mutect2/main.nf
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Fix bug in gffread that would cause it to fail if the input has .gtf as extension
* Update test.yml
* Update meta file
* Update main.nf
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* adding plink module using nf-core tool [ci skip]
* Restructures the project for plink/vcf (#1)
* Add version string for plink
* Create a plink/vcf module
* small tweaks on main.nf and started to test [ci skip]
* small changes on test args, local test with docker passed!
* Update plink/vcf module listing
* Update tag
* fix tags as per linting guidelines
* revert to the original state of tags
* adding --threads to `main.nf` and `meta.yml` information
Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com>
* mutect2 files added, first draft of module code entered
* removing comment from main.nf
* removing comment from main.nf
* test added, commit made before editing yaml
* tests added, still needs final check and info/comments added
* gatk4 version changed to gatk4=4.2.0.0
* multiple sample support added, information added to module yaml file
* Update meta.yml
fixed linting error
* add keywords to meta.yml
* Corrections made to meta.yml
* removed whitespace from meta.yml
Co-authored-by: Gavin.Mackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
* first commit, added template files for new module
* created getpileupsummaries script, tests and both yml files
* fixed typo in meta.yml
* Update modules/gatk4/getpileupsummaries/meta.yml
changed gz_tbi to gz.tbi as suggested
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* feat(homer): Add initial makeTagDirectory
* feat(homer): Add initial findPeaks module
* feat(homer): Update with new options
See 1d30e2c21a
* fix(homer): Correct findpeaks process name
* fix(homer): Takes a bam file instead of bed
* feat(homer): Add initial makeTagDirectory test
* fix(homer): Hardcode genome and configureHomer
I'd like to modularize configureHomer, but I need to figure out how
exactly the genomes work.
* fix(homer): bam => bed
Bam requires samtools to be present, which it's not in this docker image
* feat(homer): Add initial configureHomer script
* ci(homer): Add initial test
* test(homer): Reproducible configuration workaround
- I can't run both tests(one file and two files) at the same time because it breaks
- I can't copy the genome stuff from the configurehomer module because it's read only
- So I can't make the makeTagDirectory module depend on configureHomer
* test(homer): Add placeholder annotatepeaks
The required inputs are necessarily required for all workflows from what
I've used, but I'll need to look at the actual docs
* test(homer): Add missing B.bed
* test(homer): Rename two => groseq
Then all of the various workflows that homer provides can be e2e tested
* feat(homer): Add initial makeUCSCfile module
* test(homer): Add start to makeUCSCfile testing
* chore(homer): Add various cleanups
* test(homer): Rewrite annotatepeaks
Not passing yet
* test(homer): Rewrite configurehomer
* test(homer): Rewrite findpeaks
Still failing
* test(homer): Rewrite makeucscfile
Not passing yet
* test(homer): Rewrite maketagdirectory
All homer modules now follow the new structure. Time to make them pass.
* test(homer): Fix typo for workflow name
* fix(homer): Use correct container
* fix(homer): Accept fasta in maketagdirectory
Apparently all of the homer stuff can just take any old fasta and you
don't need to configure the genome ahead of time with configureHomer
* test(homer): makeTagDirectory passes now
* fix(homer): Update containers in makeucscfile
* test(homer): Rewrite makeucscfile
Takes input from maketagdirectory which is how the module should be used
* fix(homer): Update makeUCSCFile bedgraph path
* test(homer): Update makeucscfile expected output
* fix(homer): Update containers in findpeaks
* fix(homer): Change findpeaks args
The user is just going to have to know what they're doing for now
* test(homer): findPeaks rewrite with tagDir input
* test(homer): Update expected files for findPeaks
And bump filters
* style: Appease editorconfig
* ci: Remove old workflow
* tests(homer): Add md5sums
* test(homer): Add meta test
* style(homer): Capitalize HOMER
* docs(homer): Add maketagdirectory meta.yml
* docs(homer): Add makeucscfile meta.yml
* docs(homer): Add findpeaks meta.yml
* test(homer): Update to new test data standards
* chore: Remove stuff that got revived in the rebase
* chore: software => modules
* test(homer): Update tags
* test(homer): Update annotatepeaks
* ci: Fix uploading of artifacts
GitHub actions doesn't like the / in the tags
* test(homer): Remove annotate md5sum
This is failing and breaking new tests
* test(homer): Use bams instead of beds
* test(homer): Fix meta maketagdirectory
* test(homer): Fix input in all tests
* test(homer): Move back to bed files
Forgot samtools isn't present
* chore(homer): Add TODOs for tests
* test(homer): Add bed format arg
* test(homer): Update md5sums
* test(homer): Fix tags tsvs
* style(homer): Appease nf-core linting
* docs(homer): Be in line with what is in the main.nf file
Co-authored-by: Kevin Menden <kevin.menden@live.com>
Co-authored-by: Kevin Menden <kevin.menden@live.com>
Please enter the commit message for your changes. Lines starting
* adds expansionhunter module
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Initial draft [ci skip]
* trigger first test
* update output file path
* Tests passing
* finishing touches for meta.yml and update checksum
* tweak checksum
* add threads to the module
* skip version info for matching test md5sum [ci skip]
* Add ref fasta and finalize the module
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* draft for bcftools modules [ci skip]
* initial test for bcftools concat
* Update the params for testing
* fix tests
* Accomodate code review [ci skip]
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update the meta file and open PR for review
* Update the keyword
* Update the tags for module [ci skip[
* add threads
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* Add MALT with incomplete tests
* Parameter typo fix
* Clean up test yaml
* Finish MALT module prior UNZIP and MALT_BUILD modiules
* Add required modules for tests
* Sync test out with malt-build
* Fix input parameters in tests based on final build module
* Update modules/malt/run/meta.yml
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* Add bwa/aln module
* Also output reads as required with SAI
* Add sampe
* Fix container paths
* Update based on code review from @grst
* Update input docs
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* Add bwa/aln module
* Also output reads as required with SAI
* Add bwa samse
* Fix container paths
* remove TODO comment
* Updated based on code from from @grst on bwa/sampe
* Clarify output docs
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* Add unzip module
* Remove missing TODOs update mtea
* Apply changes after code-review from @grst
* Account for user trying to supply two input archives
* Remove debugging test
* Update modules/unzip/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Correct output path
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Add blacklist of modules that shouldn't be updated to .nf-core.yml
* nf-core modules bump-versions for all modules
* Remove TODO statements identified by linting
* Fix md5sums for failing tests
* Fix more tests
* Updated the version of STAR in align and genomegenerate modules
* Changes in test.yml
* Changes in test.yml
* Added module arriba
* Changes in test configs
* Added module Arriba for fusion detection
* Fixed review comments
* Added an output option for discarded fusions
* Resolved some conflits
* conflicts
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Add option -p to set the # of cpus on stringtie
* Bump version 2.1.7 to stringtie modules
* Output stringtie/merge version
* Fix padding
* Apply suggestions from code review
* Defining software variable
* Fix test, gff can't be md5 check, contains instead
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Add picard/sortsam module
* Fix container links
* Changes after code review
* Input meta in the right place
* Correct output file suffix
* Define only `bam` in output tuple
* Updated the version of STAR in align and genomegenerate modules
* Changes in test.yml
* Changes in test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update README
* Rename pytest_software.yml to pytest_modules.yml
* Rename main software directory to modules
* Remove deprecated modules
* Rename tests software to modules
* Replace paths for tests in pytest_modules.yml
* Replace software with modules in Github Actions
* Replace software with modules in main.nf tests
* Rename software to modules in test.yml
* testing works but need to fix paths and add exclude list
* edited meta file and removed TODOs
* left over TODOs
* test passed, final push
* resolving initial comments
* Update software/delly/call/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* created templates
* updated functions.nf to the one on dev
* Created test main
* Fasta added and docker, conda, singularity passing
* Fixed output version lint
The `last/lastal` submodule takes query sequences to align to a target
index, and optionally takes one set of alignment parameters (including a
score matrix) computed by the `last/train` module for each of the
sequences.
In the previous implementation the sequences and the alignment
parameters were provided in different channels, causing them to be
sometimes desynchronised.
In the patched implementation, `last/lastal` takes a 3-tuple as
input to ensure synchronicity. To produce this tuple in a pipeline,
one can use the `join` command as in the following example.
LAST_TRAIN ( query,
target )
LAST_LASTAL ( query.join(LAST_TRAIN.out.param_file),
target )
In case no parameter file is computed one can pass a dummy file
to the module as follows:
LAST_LASTAL ( query.map { row -> [ row[0], row[1], [] ] },
target )
* Created module template (#558)
* Created meta and implemented main (#558)
* Conda test and lint passing (#558)
* Updated functions.nf to the one on dev (#558)
* Update software/lofreq/filter/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* add software/pairtools
* create a branch for pairtools/select
* fix the different output of conda and docker.
* rmove the md5sum for gzip files.
* Update software/pairtools/select/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* update test file and documentation.
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update salmon/quant to provide '--libType A' option
* Modify lib_type description to be a string
* Update tests
* lyb_type can be explicitly overwrite
* Update main.nf
* Update main.nf
* Update main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update LAST to version 1238.
* Update functions.nf to the latest devel version.
* Update test MD5sums after updating software version.
* Make portable on MacOS
* Allow input alignments to be uncompressed.
While the strategy in this family of modules is to make all inputs and
outputs compressed, this change might be useful to some users.
As of LAST 2138, `last/split` does not allow its input to be compressed.
* Search for .des file, that is guaranteed to be unique.
Some LAST indexes have more than one .bck file and it makes the name
detection crash.
In this commit, I also standardise how the names are detected.
* Use value input channel and optional output channels to handle formats.
As discussed on Slack, it is preferred to use a value input channel
instead of sneaking options through `params.args2` or `params.format`
as we did.
Likewise, optional output channels with clearly labeled format are
preferred to 'catch-all' wildcards.
* Update test data names.
Closes: #459
Thanks: @FriederikeHanssen
(`samtools` tests are already fixed by another commit)
* Fix file names in tests.
The update of test data name required changes in the test yml files.
I also updated the `bismark/summary/main.nf` file to get its data
from the `params.test_data` map.
* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* Added seqtk/subseq and checking for seed in seqtk/sample
* Separate authors in software/seqtk/sample/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Align commans in output channesl software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Define prefix in software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Use prefix in output file name software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Define suffix in options in tests/software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Change output file name in tests/software/seqtk/subseq/test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Remove a to-do point from tests/software/seqtk/subseq/test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Added --no-name into gzip commands
* Update samtools from 1.10 to 1.12 (#530)
* feat: remove social preview image to use GitHub OpenGraph
* feat: update samtools from 1.10 to 1.12
* fix: CI tests
* fix: add meta.yml file for samtools/merge
* Update software/samtools/merge/meta.yml
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update software/samtools/merge/meta.yml
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* Added seqtk/subseq and checking for seed in seqtk/sample
* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* Separate authors in software/seqtk/sample/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Align commans in output channesl software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Define prefix in software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Use prefix in output file name software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Define suffix in options in tests/software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Change output file name in tests/software/seqtk/subseq/test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Remove a to-do point from tests/software/seqtk/subseq/test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Added --no-name into gzip commands
* Replaced functions.nf in seqtk/subseq
* Refreshed tests for sample and subseq
* Corrected paired-end test and YAML description for sample
Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* add software/pairtools
* create a branch for pairtools/restrict
* fix the different output of conda and docker
* remove customized code.
* add newline to Frag.bed file.
* change the folder of frag.bed.
* change \n to \r\n
* Remove work.frag.bed
Co-authored-by: JoseEspinosa <kadomu@gmail.com>
* New last/mafconvert module to convert MAF alignments.
The `maf-convert` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
reads alignmnts in [MAF](https://genome-asia.ucsc.edu/FAQ/FAQformat.html#format5)
format and converts them in another format (axt, blast, blasttab, chain,
gff, html, psl, sam, tab).
This new module is part of the work described in Issue #464. During this
development, we fix the versiob of LAST to 1219 to ensure consistency.
We will upgrade it later.
* Delete white space.
* Update the function.nf file to the dev version.
The `last-postmask` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
filters alignments in a MAF file to remove those with too many masked
(lower-case) positions compared with their score.
As other filter modules like `last/split`, its output file risks to
overwrite its input file as their names are constructed from the sample
ID when multiple filters are chained in the pipeline. I added a check
that gives a clearer error message in this case. Please let me know
what you think about; I can add this test to the existing LAST modules
as well.
This new module is part of the work discribed in Issue #464. During this
development, we fix the version of LAST to 1219 to ensure consistency.
We will upgrade it later.
* New last/dotplot module for pairwise similarity plots
The `last-dotplot` tool takes a pairwise alignment in
[MAF](http://genome.ucsc.edu/FAQ/FAQformat.html#format5) format,
possibly compressed with gzip, or in a tabular format produced by the
`maf-convert` tool, and produces a similarity dot-plot of the two
sequences in one of the graphical formats supported by the Python
Imaging Library.
A the tool guesses the output format by the file extension of the file,
which is constructed by the module at run time, I have used the `args2`
option to convey this information to the module.
This new module is part of the work described in Issue #464. During
this development, we fix the version of LAST to 1219 to ensure
consistency (hence please ignore lint's version warning).
* Update the functions.nf file to the dev branch.
https://raw.githubusercontent.com/nf-core/tools/dev/nf_core/module-template/software/functions.nf
* feat: remove social preview image to use GitHub OpenGraph
* feat: update samtools from 1.10 to 1.12
* fix: CI tests
* fix: add meta.yml file for samtools/merge
* Update software/samtools/merge/meta.yml
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update software/samtools/merge/meta.yml
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* add software/pairtools
* create a branch for pairtools/sort
* fix the different output of conda and docker.
* remove customized code.
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* add software/pairtools
* create a branch for pairtools/parse
* fix the issue of bioconda output is different from docker.
* remove customized code from test.
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* add software/pairtools
* create a branch for pairtools/flip
* fix the issue of PG line in output
* remove custom code from test.
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* New last/lastal to align query sequences on a target index
`lastal` is the main program of the [LAST](https://gitlab.com/mcfrith/last)
suite. It align query DNA sequences in FASTA or FASTQ format to a
target index of DNA or protein sequences. The index is produced by
the `lastdb` program (module `last/lastdb`). The score matrix for
evaluating the alignment can be chosen among preset ones or computed
iteratively by the `last-train` program (module `last/train`). For
this reason, the `last/lastal` module proposed here has one input
channel containing an optional file, that has to be dummy when not used.
The LAST aligner outputs MAF files that can be very large (up to
hundreds of gigabytes), therefore this module unconditionally compresses
its output with gzip.
This new module is part of the work described in Issue #464. During
this development, we fix the version of LAST to 1219 to ensure
consistency (hence ignore lint's version warning).
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Un-hardcode the path to the LAST index.
Among multiple alternatives I have chosen the following command to
detect the sample name of the index, because it fails in situations
where there is no index files in the index folder, and in situations
were there are two indexes files in the folder. Not failing would
result in feeding garbage information in the INDEX_NAME variable.
basename \$(ls $index/*.bck) .bck
In case of missing file, a clear error message is given by `ls`. In
case of more than one file, the error message of `basename` is more
cryptic, unfortunately. (`basename: extra operand ‘.bck’`)
Alternatives that do not fail if there is no .bck file:
basename $index/*bck .bck
find $index -name '*bck' | sed 's/.bck//'
Alternatives that do not fail if there are more than one .bck file:
basename -s .bck $index/*bck
ls $index/*.bck | xargs basename -s .bck
find $index -name '*bck' | sed 's/.bck//'
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* New last/split module to find split alignments.
The `last-split` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
finds split or spliced alignments in a MAF file that is produced with, for
example, LAST `lastal` command.
This new module is part of the work discribed in Issue #464. During this
development, we fix the versiob of LAST to 1219 to ensure consistency. We will
upgrade it later.
* Update software/last/split/main.nf
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* add additional ucsc tools
* Update software/ucsc/wigtobigwig/meta.yml
Co-authored-by: Kevin Menden <kevin.menden@live.com>
* Update the functions.nf and software name for ucsc/wigtobigwig and bigwigaverageoverbed.
Co-authored-by: Kevin Menden <kevin.menden@live.com>
* New module last/mafswap to reorder sequences in alignments
The `maf-swap` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
reorders sequences in alignment files in Multiple Alignment Format.
When run without command-line arguments, it will swap the target and the
query sequences. This is useful when turning a many-to-many alignment
into a many-to-one and then a one-to-one alignment in conjunction with
the `last-split` command (split, swap, split and swap again).
The LAST aligner outputs MAF files, but other tools also use this
format. As MAF files can be very large (up to hundreds of gigabytes),
the module expects its input to be compressed with gzip and will
compress its output.
This new module is part of the work described in Issue #464. During
this development, we fix the version of LAST to 1219 to ensure
consistency (hence ignore lint's version warning).
* Update MD5 sum.
Actually, 7029066c27ac6f5ef18d660d5741979a is the MD5 sum of
an empty file compressed with `gzip --no-name`… This happened
because I forgot to update the config file after correcting the
module… sorry !
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Change name as suggested in pull request.
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* New last/train module to train alignment parameters.
The last-train command creates a parameter file that
will be used by last/lastal module for sequence alignment.
It takes indexed sequences and query sequences as input
and we use the metadata of both to create an id of the
parameter output file.
Submission of the LAST modules is discussed in more
details in the issue #464. For consistancy, we use LAST
version 1219 for this whole development and will upgrade later.
* Corrected files according to the nf-core v1.14 standards.
* Fixed function.nf file for the last-train module.
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Find index name.
* Correct after the input channels were changed.
* Use double underscore as a name separator.
Single underscores can happen in ids, therefore, we would like to keep two underscores.
* Remove extra spaces.
* Fixed the passing of the "score matrix" line.
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/last/train/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* added intervallisttools module
* add intervallisttools module
* arguments are now supplied using options.args
* removed java heapsize settings
* changes in main.nf and it is tested
* comment added
* Update software/gatk4/intervallisttools/meta.yml
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Update tests/software/gatk4/intervallisttools/test.yml
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* review comment on tags in bedtointerval
* modified the test to get input from bedtointerval module
* Update software/gatk4/intervallisttools/meta.yml
* Apply suggestions from code review
Co-authored-by: Kevin Menden <kevin.menden@live.com>
* Apply suggestions from code review
* Update tests/config/pytest_software.yml
Co-authored-by: Kevin Menden <kevin.menden@live.com>
* Apply suggestions from code review
* Apply suggestions from code review
Co-authored-by: @praveenraj2018 <praveen.raj.somarajan@ki.se>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Kevin Menden <kevin.menden@live.com>
