* add base code from samblaster
* added test yml
* fixing versions files, should this be the cause of online lint failures
* removed tmp files that shouldn't be there
* fixing output file name - 1
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fixing output file name - 2
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fixing output file name - 3
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fixing output file name - 4
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fixing output file name - 5
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fixing output file name - 6
* fixed indent
* fixed input name and updated test.yml file with new name
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
* feat: add megahit module, currently decompressed output
* Update main.nf
* Update tests/modules/megahit/test.yml
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* feat: compress all outputs, remove md5sums due to gz stochasicity
* fix: wrong conda channel for pigz
* fix: broken singleend tests and update meta.yml
* Missed one
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fix: pigz formatting
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Apply suggestions from code review
* Add GUNC download_db and run commands
* Bump with version without zgrep
* Apply suggestions from code review
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* Harshil formatting
* 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>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* Add CRAM support to allelecounter
* Update meta.yml
* Rename bam,bai to input,input_index
* Apply suggestions from code review
* Fix reference to renamed variable
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* readcounter module for hmmcopy
* Changed version number
* Fix indentation
* Update main.nf
* Update modules/hmmcopy/readcounter/main.nf
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
* hmmcopy gccounter working
* Update modules/hmmcopy/gccounter/main.nf
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
* Update main.nf
Changed version to 0.1.1 as the container says
Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
* 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
* temp commit to allow checkout
* updated createsompon tests to use tarred gendb
* resolve conflict
* Update tests/modules/gatk4/createsomaticpanelofnormals/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* saving changes to checkout
* saving to sort out other branch
* removed yml tracking of files that cant be tracked due to directory name changing between runs
* test data added, ready for pr
* fix eol linting error
* Update modules/gatk4/genomicsdbimport/main.nf
Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
* merging with master
* update push to show progress
* tests now working untar able to pass data to genomicsdbimport
* commit to checkout
* tests updated, module reworked to simplify and emit updated gendb
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* update meta.yml
Priority of input options changed, updated to reflect this
* Update test.yml
name prefix changed in main script, test.yml updated to reflect this
* fix tests due to review changes
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* add new module samtools_depth
* fixed main.nf for samtools/depth
* add new module mtnucratio
* fix main.nf
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* layout in main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* Added extension input for bedtools sort
* whitespace
* Updated docs
Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com>
* adding template for module groupreadsbyumi
* update modules with code
* strategy is required argument so moving it to input rather than options.args
* tests successful committing yml
* added meta to output
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* Templates for new module
* pe only test passing
* only_pe and only_se passing
* only_pe, only_se, mixed passes
* Multiple pe + se tc passes
* Passing args works
* Add 'interleaved' to description
* Fixed linting message
* Update modules/khmer/normalizebymedian/main.nf
Good point.
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* Update meta.yml
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* Make samtools/merge cram compliant
* samtools/stats cram compliance
* update yml file
* samtools/view to deal with crams
* Update tests to make sure cram works
* also fix tmp dir and min mem in one go
* basequalityrecal test for cram + min mem + tmpdir
* update haplotypecaller for sarek
* update haplotype yml
* update markdup to allow multiple bams, take out params to be passed with options.args
* remove TODO statement
* Remove variable md5sum
* add emtpy input to stats module in subworkflows
* subworkflows seem to work now on my side
* Apply code review
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* replace bam with input to be more inclusive
* rename everywhere
* rename input
* remove variable checksum
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* new mitochondria mode added, tests updated to allow for temp fix for test data
* add cram test
* bam/bam_idx renamed to input and input_index
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
* added template for module
* update main
* added specific code
* wrong variable name in else script
* added tests for both split and nosplit
* docker test successful - updating yaml
* adding echo to version print
* add new assembly scan module
* add newline endings
* fix newline ending
* add newline at end
Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* First step into creating a seqtk/mergepe module to interleave fastQ input
* First rewrite of main.nf to make the module perform the desired (interleave/merge of pe reads) task
* Modifications to test the new seqtk/mergepe module.
* Improving the seqtk/mergepe module to output single end reads as well, and making sure tests work
* Modified so that gzip uses -n and that single read entries are symlinked with ln -s instead of copied, therefore updated test.yml as well.
* Fix trailing whitespaces
Co-authored-by: Daniel Lundin <daniel.lundin@lnu.se>
* Provide an exisiting bam file for optitype
* Update main.nf
Attempt at fixing this with new testing data
* Trying slightly different approach
* Mini fixes, not sure whats wrong here
* Add bam file with NM tags in all reads for optitype
Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
Co-authored-by: Alexander Peltzer <alexander.peltzer@boehringer-ingelheim.com>
* add module main porechop
* update porechop main
* add porechop functions
* update meta porechop
* add test main porechop
* add porechop pytest yml
* add porechop test.yml
* Update modules/porechop/meta.yml
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* re-add porechop avoid conflict
* Update modules/porechop/meta.yml
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* fix prefix suffix
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* add new module samtools_depth
* fixed main.nf for samtools/depth
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* added template for fastqtobam
* porting old code into new template
* update with missing getprocessname function
* test completed - updating all
* fixed linting issues
* improved reading
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* 👌 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
* 🐛 FIX: Grab software name using ${getSoftwareName(task.process)}
* 🐛 FIX: Update test.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* 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>
