* 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* fix out of date function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>
* 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>
* 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>
* 👌 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>
* 📦 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>
* 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>
