* 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>
* raxml-ng is compute intensive - upgrade process label to high
* ensure raxmlng uses --all when bootstrapping
* remove block that should be taken of by the options passed in
* update tests
* Bump version and format references to use raw params.test_data
* Apply suggestions from code review
Co-authored-by: Kevin Menden <kevin.menden@live.com>
* Updated tags
Missed on in last commit.
Co-authored-by: Kevin Menden <kevin.menden@live.com>
* Update HISAT2 build module
* Bump preseq version
* Fix tests
* Add meta.yml for preseq to fix linting
* Auto-detect --genomeSAindexNbases for smaller genomes
* Add placeholder to use human data for the tests
* Add CSI output option to samtools/index
* Fix samtools/index tests
* 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>
* output constant sites as a val as well as a file so it can be passed into iqtree
* Using an env variable because that's far safer!
* Update software/snpsites/main.nf
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
* 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>
* Update test paths in bwa mappers
* Fix indentation
* indices pass lcoally now
* no idea how they could ever pass before, Tests pass locally no
* Update samtools and bwamem2 versions
* Correct mulled containers + md5
* update test data paths
* Update test md5sums
* gatk test fixes & update variantfiltration main
* few extra fixes after review
* fix suspected format error
* Update software/gatk4/variantfiltration/main.nf
* Update software/gatk4/variantfiltration/main.nf
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* 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
* nf-core template created
* boilerplate and sarek_dsl2 code merged
* adding an option to give it args
* bai got away
* seperating vcf files and vcf index files into seperate streams
* some minor spacefixes
* adding standard information about the module
* removing typos
* some basic tests based on tiddit tests
* removed the bed parameter, should be provided via options.args instead
* removing typos
* adding indexed bam file instead
* Adding changing out fasta with reference to deal with empty fasta input
* adding the correct fasta
* removing the empty test
* adding the correct data to the testoutput and removing the md5sum since
it constantly changes
* adding target_bed to input
* adding info on target bed
* adding target bed to test
* adding more files to the test
* adding meta for target bed test
* adding a test for target_bed
* typo
* fixing pytest with master
* Add default output dir for modules that create indices
* Change path for index module test output
* Fix bowtie2/align tests
* Fixing bowtie/align tests
* Fix genomegenerate test
* Fixing README linting
* Adding in optitype prototype (To be worked on these days)
* I've tried my best 😆
* No idea
* Add in YML stuff
* Fix paths
* Ok, lets try this
* Adding proper options
* Replacec configbuilder thing
* Fix seq_type
* Adding human bam - sarscov doesnt work
* Fix a bunch of things
* -def
* Make this test run
* Fancy as fuck
* Update tests/software/optitype/test.yml
* Add proper tag
* Remove md5sums
Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
* Inital nf-core create
* remove TODO comments, input and output files defined
* add get version in script
* added flow control for single/paired end data
* added script main commands
* removed completed TODO messages
* removed completed TODO messages
* added software info
* added input reads description
* added output description
* added description and keywords
* added single end test
* added paired end test
* fixed sample name flag
* fixed reverse read variable
* added test yaml
* update for pytest_software
* order in pytest_software was different
* replaced functions.nf with copy from another module
* simplify read command line
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* add bismark/align module
* bismark/align: add tests
* bismark/align: update meta.yml
* bismark/align: skip checksum for alignment logs
they contain timestamps
* bismark/align: restore correct checksum
caused some mixup in the last commit
* bismark/align: add genome_preparation to filters
* Fix conda version pin
* change options to be a global var
* remove params from meta.yml
* add bismark/summary
* remove md5sum check for bismark_summary_report.html
it contains a timestamp
* fix tests
* update meta.yml
* remove mysterious index files
* add bismark/align module
* bismark/align: add tests
* bismark/align: update meta.yml
* bismark/align: skip checksum for alignment logs
they contain timestamps
* bismark/align: restore correct checksum
caused some mixup in the last commit
* bismark/align: add genome_preparation to filters
* Fix conda version pin
* change options to be a global var
* remove params from meta.yml
* add bismark/report
* fix test filepaths
* remove mysterious index files
* add bismark/methylation_extractor
* add tests for bismark/methylation_extractor
* bismark/methylation_extractor: add genome_preparation to filters
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* remove params from meta.yml
* pytest: remove md5sum checks for gzipped output
gzip stores timestamps in the file header, so the checksum will be different each time
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Remove def from module options definition in main
* Fix bismark_deduplicate tests
* Fix bwameth_align tests
* Fixing gatk4 conda tests ("=" instead of ':' in build id)
* Same as previous commit (Fix gatk4 test)
* Fix qualimap bamqc test (no md5 check for pngs)
* Fix seqkit split2 tests. Changed to new test data
* Fix samtools tests. Some were missing initOptions include
* Removing TOOL SUBTOOL template module since now it is included on tools repo
