* 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>
* backfilled modules with meta.yml that had no license identifier
* harmonized BSD license names
* whitespace linting at modules/unzip/meta.yml:12
* harmonized software from US NIH-NCBI/NIST to 'US-Government-Work'
* Update modules/bcftools/index/meta.yml
`bcftools` is dual-licensed, use associative array to allow for multiple licenses
Co-authored-by: Michael L Heuer <heuermh@acm.org>
Co-authored-by: Michael L Heuer <heuermh@acm.org>
* add liftOver module
* add liftover module tests
* fix getProcessName
* fix tests
* fix out of date function
* version numbers should be numeric
* drop versions.yml from test.yml
* Update modules/ucsc/liftover/main.nf
Remove software name variable
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update tests/modules/ucsc/liftover/main.nf
Use test chain file
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* add genome_chain_gz to test data config
* update md5sum for new chain test data
* Fix indentation in file declaration
Co-authored-by: Jose Espinosa-Carrasco <kadomu@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
* Updated seacr callpeak to include a control threshold
* Whitespace
Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com>
* Reduce number of required input files for damage profiler
* Remove rebugging
* Add optional species list file.
* Working pending updated test-dataset update
* Add genome header to config
* 📦 NEW: Add isoseq3/cluster module
* 🐛FIX: Fix reports channel and add .pbi to it
* 🐛FIX: Fix report channel definition
* 👌IMPROVE: Move .pbi file into reports channel
* 👌IMPROVE: remove --use_qvs option from command line
* 👌 IMPROVE: Add in addParams removed options from command line
* 👌 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 module accept one channel (primers moved into the first channel)
* 📦 NEW: Add galgal6 chr30 test data
* 📦 NEW: Add bamtools module
* 👌 IMPROVE: Ignore test data
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: add singletons parameter and improve outputs
* 🐛 FIX: Update test with last module model
* 👌 IMPROVE: Add test tag
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Update test data config
* 👌 IMPROVE: Remove pbi from input files
* 👌 IMPROVE: Remove unused index
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Fill contains args
* 📦 NEW: Add isoseq3/cluster module
* 🐛FIX: Fix reports channel and add .pbi to it
* 🐛FIX: Fix report channel definition
* 👌IMPROVE: Move .pbi file into reports channel
* 👌IMPROVE: remove --use_qvs option from command line
* 👌 IMPROVE: Add in addParams removed options from command line
* 👌 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 module accept one channel (primers moved into the first channel)
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: add singletons parameter and improve outputs
* 🐛 FIX: Update test with last module model
* 👌 IMPROVE: Add test tag
* 👌 IMPROVE: Update test data config
* 👌 IMPROVE: Remove pbi from input files
* 👌 IMPROVE: Remove unused index
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Fill contains args
* 👌 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 code to new versions capture + better output channels
* 👌 IMPROVE: Update with new versions.yml file
* 🐛 FIX: Update meta.yml + correct typos
* 👌 IMPROVE: Clean output file names + correct typo
* 🐛 FIX: Remove bamtools/split module from isoseq3/cluster
* 🐛 FIX: Update output filename pattern
input filename and output filename were the same
* 👌 IMPROVE: Update meta.yml
* added template for tiddit/cov
* test finished
* quick fix to meta info
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* applying suggestions
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* chore: use template to create fasterq module
* feat: add fasterq-dump process module
* docs: provide input and output descriptions
* docs: add comment on `--temp`
* fix: use correct variable
* tests: define test output
* refactor: address review comments
* refactor: remove vdb-config input
* chore: add new test data to config
* tests: define single-end and paired-end cases
* refactor: choose specific output
* tests: do not expect single FASTQ for paired-end
* feat: add compression
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* tests: revert the test data name
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* 👌 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
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* feat(subworkflows): Add align_bowtie2 subworkflow
For testing CI setup
* test(align_bowtie2): Add initial list of changes to test
* test(align_bowtie2): Add initial test
* refactor: Use tags to run subworkflows ci
For every underlying module used by workflow and allow the modules
pytest-modules definition be the source of truth.
* refactor: Use individual directories for subworkflows
* docs(align_bowtie2): Add initial meta.yml
Copied most of it from the bowtie2/align module.
* fix(align_bowtie2): Fix module include paths
* test(bam_sort_samtools): Add initial test
* ci(bam_sort_samtools): Add modules that trigger the tag
* test(bam_stats_samtools): Add initial test
* ci(bam_stats_samtools): Add keys to pick up changes
* docs(bam_samtools): Add initial meta.yml
* test(align_bowtie2): Fix path to subworkflow
* test(align_bowtie2): Update entry point
* fix(bam_sort_samtools): Update include paths
* test(bam_sort_samtools): Fix path
* style: Clean up addParams
* test(samtools_sort): Add suffix for test
* test(align_bowtie2): Add samtools_options for suffix
* test(bam_stats_samtools): Update path
* test(bam_stats_samtools): Use stats input
Otherwise it's just an example of how it's used in the bam_sort_samtools subworkflow
* ci(linting): Skip module linting of subworkflows
* ci(linting): Clean up startsWith statement
* test(bam_stats_samtools): Use single end test data for single end test
* test(bam_stats_samtools): Add expected files
* test(align_bowtie2): Add paired-end test
* test(align_bowtie2): Sort order of output
* test(align_bowtie2): Update hashes
* docs(align_bowtie2): Fix typo
* test(align_bowtie2): Update samtools output names
* test(align_bowtie2): Remove md5sums for bam/bai
* feat(subworkflows): Add nextflow.configs
These can be used for default settings in the future. They can then be
included in the conf/modules.config so that the params don't have to be
duplicated in the root nextflow.config.
* docs(subworkflows): Include modules instead of tools
* fix: Update to versions
* chore(align_bowtie2): Remove duplicate tag
* style: Format yamls
* test(subworkflows): Only check versions for modules
* chore: Update subworkflows to match rnaseq dev
* fix(subworkflows): Update paths
* fix(bam_sort_samtools): Fix sort parameters for testing
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* docs: Update TODOs with a message
* ci: Try using a matrix for strategy
* ci: Try passing an array
* Revert "ci: Try passing an array"
This reverts commit d3611fcd8332bbb9a8501e8dd299d0a623aaecaa.
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* files for learnreadorientationmodel initialised for first commit
* finished scripts and yml files. test working locally but needs an f1r2 test data on nf-core before it can be submitted
* updated test data location
* versions file updated, test data added
* updated versions file, edited test file
* small formatting update to main.nf
* Update main.nf
* Update test_data.config
* updated tests main.nf
* Update test_data.config
* Apply suggestions from code review
* Update modules/gatk4/learnreadorientationmodel/main.nf
* Update modules/gatk4/learnreadorientationmodel/meta.yml
* fixed tests failing
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
