* 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>
* 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>
* 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>
