* New last/lastdb module to index sequences before alignment.
The `lastdb` command creates a sequence index for the LAST aligner
(https://gitlab.com/mcfrith/last). Input can be in FASTA or FASTQ
format, and compression is handled automagically. DNA or protein
sequences can be indexed.
The sequence index is a collection of files sharing the same basename.
This module sets the basename to the sample identifier (`$meta.id`) and
creates the index in a directory always called `lastdb`. The module's
output channel then conveys a copy of the metadata and the path to the
`lastdb` directory.
Other modules will follow (see Issue #464). The LAST aligner can align
proteins to proteins, DNA to DNA and can translate DNA align to
proteins.
* Remove trailing whitespace.
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update as suggested in PR.
* Attempt to pass linting.
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Basic kb-python count functionality for scRNA-seq quantification working.
* Added tests and test data for workflow kite.
* Removed trailing whitespace
* Changed output channels to tuples with meta
Based on suggestions by @KevinMenden.
* Moved workflow and technology to input variables. Currently create test-yaml file script failes with cryptic message.
* Update software/kallistobustools/count/main.nf
@KevinMenden fixed wrong path definition
Co-authored-by: Kevin Menden <kevin.menden@live.com>
* Increased version of kb-python
* Updated tests with raw links.
* Fixed subtool referencing: kallistobustools/count
* Added newline
* Update software/kallistobustools/count/main.nf
Co-authored-by: Kevin Menden <kevin.menden@live.com>
* Add new human data and fix sarscov paths
* Fix filename typo
* Apply code review
* replace index with to match sarscov data
* lower case
* indent everythin
* Adapt sarscov keys to new naming convention
* Update test_data.config
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* new raxml module
* new raxml module
* pass in args for bootstrap and add test for support file
* remove unnecessary tag
* ensure tags meet guidleines
* Apply suggestions from code review
* Update to latest functions file
Co-authored-by: avantonder <avt@sanger.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Adding bigWig and deeptools computeMatrix files to config
* Adding meta.yml for deeptools modules
* Add test for deeptools modules
* Fixing and reordering tags
* Fixing conda test that worked in local...
* Apply suggestions from code review
* Changing bigwig file pattern to include bigwig extension
* Saving after last change is a good practice
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Resolve suggests after PR review
* add newline to functions
* need variable interpolation using double quotes; remove unnecessary tag
* add a more resilient link to raw github files
* remove trailing slash
* Update software/iqtree/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Add abacas module
* Add test for abacas module
* Add Harshil to authorship
* Updating test with the data uploaded to nf-core/datasets
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* initial 'modules create' of minia
* fixed tests
* finished meta.yml
* fixed filters.yml
* resolved issues in pytest_software.yml
* add newline
* Update software/minia/main.nf
* fixing a bunch of module tests
* remove vscode
* fixed minia
* move test data directory to nf-core/test-datasets
* bump multiqc version
* remove the test data
* updated test data link
* update README
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* new submodule mash/sketch
* fixed submodule naming
* OK, tag is diff to keyword
* OK another round 🤣
* removed TODO comments
* updated as per review comments 🙆♂️
* updated functions.nf 😁
* Update software/mash/sketch/main.nf
* Update main.nf
Removed blank line at the 12th
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* new module: rasusa
* Removed blank line in software/rasusa/main
* updated code as per reviewcomments
* removed blank line as failed for lint
* updated as per review comments
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Added kallistobustools/ref. Local tests all passing with Docker. Linting passed. Test data currently in /tests/data/delete_me
* Removed trailing whitespace line 29
* Moved workflow from meta to options.
* Update main.nf
* Forgot to remove previous testing input channel for workflow.
* Apply suggestions from code review
Applied changes suggested by @drpatelh
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Added gtf to meta.yml.
* Apply suggestions from code review
Adding @drpatelh suggested changes.
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Moved workflow to input value. Fixed tests.
* Update tests/software/kallistobustools/ref/test.yml
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* adding fasttree module
* correct trailing whitespace
* using sarscov2 as a test dir
* remove TODO
* update test data naming
* further test data naming updates
* remove options in favour of $options.args
* ensure non standard exit codes don't cause an issue
* update md5sum
* ci: Add modules lint step
Moved it ahead of the nextflow install so ideally it'll fail before we
bother doing any more setup
* ci: _ => /
* Update tests/config/pytest_software.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* inital commit
* added meta.yaml info
* add initial logic for featurecounts test
* add args and change SE/PE to strandedness for featurecounts test
* added tests to pytest
* added test.yml
* removed GTF flag in options
* corrected test meta params
* meta yaml corrected tool info
* update test.yml
* fix lint errors meta.yml
Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
* Added fgbio callmolecularconsensusreads and sortbam modules
* Fixed naming issue in meta.yml
* fix: test.yml and config lint
* Revert "fix: test.yml and config lint"
This reverts commit 0453bc3a8dc3dab6997442a4349ee2241adcc380, which caused the sortbam tests to fail.
* style: Fix test names
* style: Remove trailing whitespace
* fixed test.yml
* fix: test data in sortbam
* fix: data format
* fix: test data for callmolecularconsensusreads
* Corrected with updated test data
* Apply suggestions from code review
Applied changes from code review, mainly syntactical changes
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Sruthi Suresh <sps180004@ganymede.utdallas.edu>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* initial commit hisat2/build
* initial commit hisat2/build
* changed names for hisat2
* fixed directory structure and args
* added splice site test data
* added splice site inputs
* replaced list with individual args
* fixed removed commas
* added test yml file
* updated hisat2 conda version
* added meta.yml
* added meta.yml description
* added meta.yml inputs
* added meta.yml outputs
* update conda version for hisat2
* removed trailing whitespace meta.yml
* fixed version number for containers
* added test data to test config
* updated for new test logic
* fix pytest issue?
* fix pytest issue
* fixed wrong tool in meta.yaml
* updated tets.yaml name
* handle build bug for testing
* handle build bug for testing in yaml
* moved test folder to fix build bug
* use old hisat2 version to avoid conda giving inconsistent md5sum
* initial commit
* removed temp file
* added meta yaml
* add to pytest
* added tests
* added test yml
* add align meta yaml
* add hisat2 align to pytest
* remove need for splice data by calling process
* add hisat2 align se test
* add hisat2 align pe test
* update names hisat2 align
* update software pytest for using mutiple modules
* remove splice site test data since using module instead
* remove splice site from config since using module instead
* fixed extra brace
* added hisat2 align test.yml
* removed md5sum for bam files
* updated build md5sums
* Apply suggestions from code review
Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Adding tar.gz kraken2 db to test data
* Update test path files for untar module
* Update test path files for kraken2/run module
* Update test path files for cat/fastq module
* Initial work on yara module
* Adding in index basics
* Updated the index stuff
* Adding in proper tests
* Fix editorconfig
* Odd paths
* that should do it
* Fix tests
* Fix tests
* FFS
* Once more
* Mapping is not deterministic
* Re-organise all test data
* Fix ECLint
* Fix ECLint agaaainn
* Now is not the time EClint
* Initial commit for test data config
* Rename test data
* Include test config
* Update indents
* Update test for FastQC via config
* Remove quotes of bottom-level variables
* Use underscores in key names
* Get tests working for fastp
* Remove whitespace at beginning of file
