* 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>
The new version of agrvate fixes an issue where sample names with a `.` (dot) in there names caused the name to be truncated
https://github.com/VishnuRaghuram94/AgrVATE/releases/tag/v1.0.1
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>
