From b4e40280a46ba3b5464e05fb8031dfbce2fa834a Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
Date: Fri, 19 Jul 2024 16:35:22 +0200
Subject: [PATCH] Release PR 0.2.0 (#94)
* Birth of a pipeline (#2)
* cleaned up the code and docs before starting
* cleaned up the github actions
* cleaned some more code
* removed unused pipeline code
* added an easily adjustable input checker
* removed some CI
* added the variant callers
* linting
* tests update
* ci update
* linting
* linting
* linting
* turned off actions
* added read counts + delly updates
* added scatter count to delly call
* added versions and multiqc
* updated the manta workflow
* updated the whamg workflow
* added versions to whamg
* added some additional test data
* updated the test data
* updated the test data
* updated the test data
* updated the test data
* overal updates and improvements
* small updates
* small updates
* metrics part 1
* metrics part 2
* Module evidence qc (#3)
* make bincov matrix part 1
* added ploidy and parts of calcmedcov
* added WGD
* removed delly and added a reheader to MANTA
* added all code to the module (some parts are still broken)
* small updates
* small ploidy matrix fix
* small updates to evidenceQC + re-added delly
* Module gather batch evidence (#4)
* added groundwork for the module
* added groundwork for the module
* more work done
* removed commented lines
* Continue module gather batch evidence (#19)
* printsvevidence update (not done yet)
* restructured the pipeline to match nf-core v2.6
* updated module paths
* some small "improvements"
* Template update for nf-core/tools version 2.6
* additional fixes to the template
* removed wrong file
* Added clarifying comments to GSE
* updated some of the modules to 4.3.0.0
* fixed some issues caused by gatk4.3.0.0
* latest additions
* Refactoring (#20)
* refactored gather sample evidence
* refactor the rest
* New series of fixes and features (#21)
* update whamg
* update local tests
* updated whamg officially
* updated whamg + fixed svtk standardize
* small work on scramble (still no correct data for this tool)
* updated schema
* improved whamg bed file integration
* added a merge vcfs subworkflow
* small fix
* update test config
* added the samplesheet validation and conversion script
* hotfix dev test (#22)
* Add smoove & tests (#23)
* Template update for nf-core/tools version 2.6
* hotfix dev test
* fixed a lot of issues
* added smoove
* updated the schema
* fix samplesheet and schema
* add better outdir folders
* add tests
* tests fix
* fix secrets
* fix typo
* add more tests
* add template yml
* Template update for nf-core/tools version 2.7.2
* fixes after template merge
* linting
* more linting
* even more linting
* black
* Refactor the pipeline to prepare for subworkflow export to nf-core (#24)
* refactored the pipeline
* remove unused modules
* removed unused workflows
* Add gridss (#25)
* refactored the pipeline
* remove unused modules
* removed unused workflows
* add gridss
* add stub to local modules
* fix stubs
* fully add gridss
* add tests
* copy fix?
* add gridss test to ci
* exclude gridss vcfs from metrics (not supported)
* update min nextflow version to fix caching issue
* update gridss
* remove TODOs [no ci]
* Add genotyping (#26)
* update scattering
* update delly
* bump commit
* add --output_callers parameter
* small fix to --output_callers
* fix schema and test config
* removed reheadering from manta
* update bcftools/sort
* update bcftools/sort
* update headers after jasmine merge
* small fix
* finished genotyping
* fix for paragraph/multigrmpy
* updated the samplesheet conversion
* removed some unused modules
* add merging of samples from the same family
* removed scattering from whamg
* Updated jasmine (added support for bgzip to the module)
* fix prettier
* fix tests
* fix tests again and remove black CI
* add linting ci to nf-core.yml
* Adopted SVINSSEQ as uniform ins sequence info key
* disabled whamg for now
* add missing format header
* add patch for delly
* fix header typo
* remove local test profile
* updated test profiles and added big tests
* add delly args
* add new args to schema and config
* Add annotation + viola + join checks + cleanup (#29)
* add join checks
* fix delly mismatches
* Added viola
* fix header issues in single caller runs
* header fix?
* appease eclint
* add stub to reverse_bed
* fix for gridss?
* appease eclint again!
* typo
* fix permissions
* fix shebang
* fix shebang again
* disable gridss
* fix tests
* remove old code from gatk-sv
* Add VEP to the pipeline
* add some QOL parameters
* update tests
* QOL changes (variables and joins)
* disable scattering for delly
* remove unused gatk modules
* update modules
* made BED files optional
* add metro map and update readme
* forgot to save svg
* fix linting
* fix vep test
* free up CI space?
* use another cache for vep
* edit PosCon3 samplesheet_big.csv (#30)
* Add bcftools sort (#31)
* add join checks
* fix delly mismatches
* Added viola
* fix header issues in single caller runs
* header fix?
* appease eclint
* add stub to reverse_bed
* fix for gridss?
* appease eclint again!
* typo
* fix permissions
* fix shebang
* fix shebang again
* disable gridss
* fix tests
* remove old code from gatk-sv
* Add VEP to the pipeline
* add some QOL parameters
* update tests
* QOL changes (variables and joins)
* disable scattering for delly
* remove unused gatk modules
* update modules
* made BED files optional
* add metro map and update readme
* forgot to save svg
* fix linting
* fix vep test
* free up CI space?
* use another cache for vep
* add bcftools sort
* fix smoove output (#33)
* fix smoove output
* update according to other modules
* Fully implement annotation (#35)
* Template update for nf-core/tools version 2.6
* Template update for nf-core/tools version 2.7.2
* first steps
* fully implement the annotation
* update test
* offer a lamb to the linting gods
* bug fix
* offer a virgin to the linting gods (hope this is enough)
* Add dynamic VCFanno config creation
* go on a pilgrimage to the mountain of the linting gods and make a blood sacrifice
* fix and update annotate test to stub
* update vep container on stub runs
* add postannotations support to the configs
* simplified the vcfanno config code and made it smarter
* added new fields from the annotsv vcf to the default configs
* added a param for the default annotsv file name
* fix small bug with param
* fix small bug with param
* Add all default configs
* sacrificing my firstborn child to the linting gods
* Moved the unused configs to a separate folder
* update configs
* update vep config
* add option to annotate on small variants with AnnotSV (real test files should still be added)
* Remove unused VEP parameters
* fix issues
* add tests for small variants vcfs
* add an option to also output the annotsv outputs
* Merge wrongly placed commits (#40)
* fixes for big tests
* metro map update
* Template update for nf-core/tools version 2.8
* black linting
* update modules
* update modules
* fix local modules
* bump
* eclint
* update genome in docs
* update vcfanno configs retina and rpe
* fix rpe bed file in config
* Cnv support (#50)
* Template update for nf-core/tools version 2.6
* Template update for nf-core/tools version 2.7.2
* first steps
* fully implement the annotation
* update test
* offer a lamb to the linting gods
* bug fix
* offer a virgin to the linting gods (hope this is enough)
* Add dynamic VCFanno config creation
* go on a pilgrimage to the mountain of the linting gods and make a blood sacrifice
* fix and update annotate test to stub
* update vep container on stub runs
* add postannotations support to the configs
* simplified the vcfanno config code and made it smarter
* added new fields from the annotsv vcf to the default configs
* added a param for the default annotsv file name
* fix small bug with param
* fix small bug with param
* Add all default configs
* sacrificing my firstborn child to the linting gods
* Moved the unused configs to a separate folder
* update configs
* update vep config
* add option to annotate on small variants with AnnotSV (real test files should still be added)
* Remove unused VEP parameters
* fix issues
* add tests for small variants vcfs
* add an option to also output the annotsv outputs
* Merge wrongly placed commits (#40)
* fixes for big tests
* metro map update
* Template update for nf-core/tools version 2.8
* black linting
* update modules
* update modules
* fix local modules
* bump
* eclint
* update genome in docs
* update vcfanno configs retina and rpe
* fix rpe bed file in config
* adjust test to new data
* remove unused data from workflows
* remove simple event annotation
* update modules config
* remove unused modules
* fix compile error
* another compile error
* remove comments in config
* guess what! another compile error
* small fixes to annotsv
* update viola
* circumvent a annotsv bug
* add gridss genotyping
* filter out variants with 0/0 genotype from gridss
* move ref variants filtering to before annotsv
* update tests
* fix linting and add meta to references
* black
* install expansionhunter
* fix merge conflict issues
* fix linting
* fix config
* fix stub
* add expansionhunter
* some concurrency debugging
* add nf-validation support
* revert to using linkedhashmap for now
* fix jasmine issue
* update tests
* fix typos
* fix linting
* there you go editorconfig
* let's make it pretty
* update nf-test config
* fix even more tests
* add concat output and fix tests
* fix schema
* now be nice please
* i'm pretty again
* update big test samplesheet [no ci]
* fix max_time pattern [no ci]
* add bcftools sort to single runs
* only apply viola on gridss VCFs and change prefixes
* remove unused comment [no ci]
* fix input pattern
* improve the efficiency of viola
* black
* added a sort step to gridss
* updated the gridss label
* patch gridss module
* remove estimate_read_length
* remove unused code
* small typo
* add -ends to vcfanno
* add full test config
* fix full test description
* update samplesheet
* add exists tags to the samplesheet schema
* specify advised resources for gridss
* possible fix for gridss OOM?
* remove code duplication
* remove an unused parameter
* added a check for callers support being higher than the amount of sv callers
* update metro map
* increase gridss memory
* try to optimize gridss part 2
* try to optimize gridss part 3
* oops
* oops 2
* oops 3
* update to advised amounts
* increase viola time
* discourage the use of gridss for now
* typo
* linting fix
* rename SV subworkflow
* fix expansionhunter catalog and add qdnaseq ref
* add qdnaseq
* add a check for the qdnaseq reference
* fixed some issues with qdnaseq
* add cram merging and index creation
* update resources for qdnaseq
* update resources for qdnaseq
* update resources for qdnaseq
* fix resources qdnaseq
* add wisecondorx
* updated the metro map
* fix background of metro map
* update resolution
* update resolution
* remove old samplesheet conversion script
* moved available callers to a groovy script
* removed the manual check for file exists (now fully uses nf-validation)
* fix a bug with concat when a cnv caller has been supplied
* added some comments for the last fix
* update optional input handling
* fix small issue with annotsv annotations
* fix a no process matching selector warning
* revert last changes
* temp fix for warning
* improve vep cache handling + update modules
* typo
* fix container declaration
* fix for manta issue?
* undo last commit
* version bump expansionhunter
* added support for manta configs
* made qdnaseq references gender specific
* update manta resources
* add contig input to manta
* moved the contigs file creation to the manta subwf
* fix vep params in schema
* fix linting with no template update
* fix nf-test tests
* fix eclint
* fix eclint
* change gender to sex
* typo
* added the sex arg to expansionhunter
* fix nf-test config for v0.8.0
* revert nf-test to 0.7.3
* prettier
* set default sex to female instead of male
* fix tests samplesheet
* Fix vep container issue (#52)
* add dynamic container fetching for vep
* linting fix
* moved the function to the process itself
* fix conda issue
* eclint
* fix params schema
* fix linting
* fix for vep issue?
* fix for missing singularity container
* Add filtering on annotations + fix linting (#55)
* Add filtering on annotations
* fix linting
* begone trailing whitespace
* add annotation filter to test
* CNV VCFs (#58)
* add vcf creation to wisecondorx
* add qdnaseq vcfs
* update tests
* add a simple qdnaseq filter
* small fix in the wisecondorx config
* small naming fix
* add jasmine
* fix for config?
* fix tests
* prettier
* fix tests again
* fix output logic
* fix jasmine + add annotation
* eclint
* more output logic fixes
* eclint (again)
* more output logic fixes
* fix cnv outputs
* remove obsolete if statement
* fix issue with meta joining
* Family merging (#61)
* add vcf creation to wisecondorx
* add qdnaseq vcfs
* update tests
* add a simple qdnaseq filter
* small fix in the wisecondorx config
* small naming fix
* add jasmine
* fix for config?
* fix tests
* prettier
* fix tests again
* fix output logic
* fix jasmine + add annotation
* eclint
* more output logic fixes
* eclint (again)
* more output logic fixes
* fix cnv outputs
* remove obsolete if statement
* fix issue with meta joining
* add family name to the samplesheet and meta
* changes to jasmine subwf + add family merging subwf
* add correct reheadering
* add family merging (does not work rn)
* some more work
* fix repeat VCF error
* add z-score to VCF header
* small fixes to sex defining
* Add proper testing + fix some issues found (#64)
* add vcf creation to wisecondorx
* add qdnaseq vcfs
* update tests
* add a simple qdnaseq filter
* small fix in the wisecondorx config
* small naming fix
* add jasmine
* fix for config?
* fix tests
* prettier
* fix tests again
* fix output logic
* fix jasmine + add annotation
* eclint
* more output logic fixes
* eclint (again)
* more output logic fixes
* fix cnv outputs
* remove obsolete if statement
* fix issue with meta joining
* add family name to the samplesheet and meta
* changes to jasmine subwf + add family merging subwf
* add correct reheadering
* add family merging (does not work rn)
* some more work
* fix repeat VCF error
* first commit
* add z-score to VCF header
* small fixes to sex defining
* add test for bam_cnv_calling
* test bam_prepare_samtools
* test bam_repeat_estimation_expansionhunter
* test bam_sv_calling
* test bam_variant_calling_delly
* test bam_variant_calling_gridss
* test bam_variant_calling_manta
* test bam_variant_calling_qdnaseq
* test bam_variant_calling_smoove
* test bam_variant_calling_wisecondorx
* uniformize config
* test vcf_annotate_vep_annotsv_vcfanno
* test vcf_concat_bcftools
* test vcf_merge_callers_jasmine
* fix header
* update vep annotations
* oops
* add gnomad to vep
* revert vep container changes
* add sift
* fix merge crams with families
* fix join duplication for replicates
* fully test jasmine family merge
* uniformize tests
* fix duplication glitch
* add pipeline tests for callers
* add families tests
* add duplicates tests
* remove old tests and add new tests to ci
* fix linting
* use nf-core dev for linting
* update minimum nextflow version
* revert nf-core version to latest
* upload artifacts
* fix artifacts
* only upload nf-test folder
* fix artifact again?
* fix artifact again?
* fix artifact again?
* prettier
* only get artifacts on failure
* only get artifacts on failure
* only get artifacts on failure
* fix qdnaseq test
* set nf-test to v0.8.1
* try to fix permission errors
* update family jasmine tests
* small clarification in the header
* Fix annotsv TCL error (#69)
* add vcf creation to wisecondorx
* add qdnaseq vcfs
* update tests
* add a simple qdnaseq filter
* small fix in the wisecondorx config
* small naming fix
* add jasmine
* fix for config?
* fix tests
* prettier
* fix tests again
* fix output logic
* fix jasmine + add annotation
* eclint
* more output logic fixes
* eclint (again)
* more output logic fixes
* fix cnv outputs
* remove obsolete if statement
* fix issue with meta joining
* add family name to the samplesheet and meta
* changes to jasmine subwf + add family merging subwf
* add correct reheadering
* add family merging (does not work rn)
* some more work
* fix repeat VCF error
* first commit
* add z-score to VCF header
* small fixes to sex defining
* add test for bam_cnv_calling
* test bam_prepare_samtools
* test bam_repeat_estimation_expansionhunter
* test bam_sv_calling
* test bam_variant_calling_delly
* test bam_variant_calling_gridss
* test bam_variant_calling_manta
* test bam_variant_calling_qdnaseq
* test bam_variant_calling_smoove
* test bam_variant_calling_wisecondorx
* uniformize config
* test vcf_annotate_vep_annotsv_vcfanno
* test vcf_concat_bcftools
* test vcf_merge_callers_jasmine
* fix header
* update vep annotations
* oops
* add gnomad to vep
* revert vep container changes
* add sift
* fix merge crams with families
* fix join duplication for replicates
* fully test jasmine family merge
* uniformize tests
* fix duplication glitch
* add pipeline tests for callers
* add families tests
* add duplicates tests
* remove old tests and add new tests to ci
* fix linting
* use nf-core dev for linting
* update minimum nextflow version
* revert nf-core version to latest
* upload artifacts
* fix artifacts
* only upload nf-test folder
* fix artifact again?
* fix artifact again?
* fix artifact again?
* prettier
* only get artifacts on failure
* only get artifacts on failure
* only get artifacts on failure
* fix qdnaseq test
* set nf-test to v0.8.1
* try to fix permission errors
* update family jasmine tests
* split annotsv input files by svtype and merge them back
* small clarification in the header
* fix bcftools concat issue
* fix linting
* don't lint .prettierignore
* Add Svync standardization + other fixes (#72)
* add vcf creation to wisecondorx
* add qdnaseq vcfs
* update tests
* add a simple qdnaseq filter
* small fix in the wisecondorx config
* small naming fix
* add jasmine
* fix for config?
* fix tests
* prettier
* fix tests again
* fix output logic
* fix jasmine + add annotation
* eclint
* more output logic fixes
* eclint (again)
* more output logic fixes
* fix cnv outputs
* remove obsolete if statement
* fix issue with meta joining
* add family name to the samplesheet and meta
* changes to jasmine subwf + add family merging subwf
* add correct reheadering
* add family merging (does not work rn)
* some more work
* fix repeat VCF error
* first commit
* add z-score to VCF header
* small fixes to sex defining
* add test for bam_cnv_calling
* test bam_prepare_samtools
* test bam_repeat_estimation_expansionhunter
* test bam_sv_calling
* test bam_variant_calling_delly
* test bam_variant_calling_gridss
* test bam_variant_calling_manta
* test bam_variant_calling_qdnaseq
* test bam_variant_calling_smoove
* test bam_variant_calling_wisecondorx
* uniformize config
* test vcf_annotate_vep_annotsv_vcfanno
* test vcf_concat_bcftools
* test vcf_merge_callers_jasmine
* fix header
* update vep annotations
* oops
* add gnomad to vep
* revert vep container changes
* add sift
* fix merge crams with families
* fix join duplication for replicates
* fully test jasmine family merge
* uniformize tests
* fix duplication glitch
* add pipeline tests for callers
* add families tests
* add duplicates tests
* remove old tests and add new tests to ci
* fix linting
* use nf-core dev for linting
* update minimum nextflow version
* revert nf-core version to latest
* upload artifacts
* fix artifacts
* only upload nf-test folder
* fix artifact again?
* fix artifact again?
* fix artifact again?
* prettier
* only get artifacts on failure
* only get artifacts on failure
* only get artifacts on failure
* fix qdnaseq test
* set nf-test to v0.8.1
* try to fix permission errors
* update family jasmine tests
* split annotsv input files by svtype and merge them back
* small clarification in the header
* fix bcftools concat issue
* fix linting
* don't lint .prettierignore
* deprecate gridss for now
* implement delly svync
* implement manta svync
* implement smoove svync
* add better headering to merge callers
* small fix to bcftools annotate
* fix headers for family merging
* remove unused assets
* fix some stability issues
* simplify expansionhunter handling
* reheader with bcftools/reheader again
* fix the headering once and for all
* add a quick view statement
* change view to dump
* rename dump tag
* extra dump
* fix join issue
* fix header issues with annotsv
* add missing header line for annotsv
* fix callers info field
* remove some views
* add views for hpc debugging
* a workaround for double variants in annotsv
* a workaround for double variants in annotsv try 2
* remove view statements
* fix join error?
* fix some linting issues
* don't test gridss
* drop pinned nf-test version
* disable gridss tests for real
* fix some tests
* update subwf tests
* update pipeline tests
* fix annotate tests?
* fix annotate tests again?
* add views to annotation test
* fix join error + fix test jasmine
* revert join error changes?
* another try to fix weird join error
* join error fix try 3
* join error fix try 4
* join error fix try 5
* join error fix try 6
* join error fix try 7
* Template v2.13.1 sync + update all modules (#73)
* Template update for nf-core/tools version 2.6
* Template update for nf-core/tools version 2.7.2
* update pipeline name
* update test-data repo name
* update test data config name
* update pipeline name
* update pipeline name
* update nf-core yaml
* Template update for nf-core/tools version 2.13.1
* Merge branch 'TEMPLATE' into template-v2.13.1-sync
* fix some linting issues
* update all modules
* fix subwf in modules json
* remove unused code
* remove unused code
* fix jasminesv
* fix eclint
* prettier
* have nf-test in the CI
* fix samtools convert stub
* prettier
* fix tabix outputs + tests
* update test snapshots
* remove views
* rearrange joins
* revert last commit
* another try :crossed_fingers:
* another try 2 :crossed_fingers:
* try adding by
* fix wrong versions yml
* patch bcftools concat
* fix bcftools concat versions
* fix delly svync config
* use midnighter's approach of joining channels
* fix linting
* fix test
* Create beautiful docs with mkdocs (#74)
* create beautiful docs
* some small fixes
* set dev version to beta version
* Docs 0.1.0dev (#75)
* update docs
* fix linting
* update description of pipeline
* docs-output (#76)
* docs
* parameters.md adapted
* relative links
* comments for docs-output PR
* parameters.md correction
* Last fixes before v0.1.0 release (#77)
* fix tests
* some esthetic fixes
* move the logo in the metro map
* made the metro map logo a bit smaller
* update parameter docs
* bump to version 0.1.0
* update to dev version
* update docs building
* try to fix the doc building action
* merge master into dev
* Add keyword shortcuts to the `--callers` parameter (#85)
* add more keywords + update docs
* update tests
* prettier
* fix tests
* bump wisecondorx to v1.2.6 (#87)
* bump wisecondorx to v1.2.6
* add missing arguments to wisecondorx predict
* add seed 0
* Fix a wisecondorx arg typo
* Fix smoove output when using `--output_callers` (#89)
* fix smoove output
* fix copy paste error
* fix smoove tests
* update changelog
* Make the workflow pluggable (#91)
* make main workflow pluggable
* update svync config handling
* update bedgovcf config handling
* pluggable annotation workflow
* update bam_cnv_calling test
* update all modules
* another wave of module updates
* let the pipeline run again
* fix last modules
* make editorconfig happy
* fix tests
* Update/fix annotsv + add HPO terms (#93)
* make main workflow pluggable
* update svync config handling
* update bedgovcf config handling
* pluggable annotation workflow
* update bam_cnv_calling test
* update all modules
* another wave of module updates
* let the pipeline run again
* fix last modules
* make editorconfig happy
* fix tests
* update annotsv
* add hpo terms
* re-add samples to samplesheet
* fix the annotsv tests
* update changelog
* bump version to 0.2.0
* fix wrongly merged conflict in modules.config
* fix another weird issue
* use latest vep version
---------
Co-authored-by: mvheetve <57952494+mvheetve@users.noreply.github.com>
---
.github/workflows/build-docs.yml | 10 +-
CHANGELOG.md | 24 +
assets/multiqc_config.yml | 4 +-
assets/schema_input.json | 5 +
assets/test.npz | 0
conf/modules.config | 117 ++---
conf/test.config | 2 +-
docs/parameters.md | 18 +-
main.nf | 60 ++-
modules.json | 48 +-
.../nf-core/annotsv/annotsv/environment.yml | 7 +
modules/nf-core/annotsv/annotsv/main.nf | 20 +-
modules/nf-core/annotsv/annotsv/meta.yml | 8 +-
.../annotsv/annotsv/tests/main.nf.test | 52 +++
.../annotsv/annotsv/tests/main.nf.test.snap | 63 +++
.../annotsv/annotsv/tests/nextflow.config | 5 +
.../nf-core/annotsv/annotsv/tests/tags.yml | 2 +
.../installannotations/environment.yml | 2 +-
.../annotsv/installannotations/main.nf | 5 +-
.../annotsv/installannotations/meta.yml | 2 +-
.../installannotations/tests/main.nf.test | 25 +
.../tests/main.nf.test.snap | 29 ++
.../annotsv/installannotations/tests/tags.yml | 2 +
modules/nf-core/bcftools/annotate/main.nf | 4 +-
.../bcftools/annotate/tests/bcf.config | 6 +
.../bcftools/annotate/tests/main.nf.test | 108 +++++
.../bcftools/annotate/tests/main.nf.test.snap | 79 ++++
.../nf-core/bcftools/annotate/tests/tags.yml | 2 +
.../bcftools/annotate/tests/vcf.config | 6 +
modules/nf-core/bcftools/concat/main.nf | 14 +-
modules/nf-core/bcftools/concat/meta.yml | 8 +-
.../bcftools/concat/tests/main.nf.test | 99 ++++
.../bcftools/concat/tests/main.nf.test.snap | 101 ++++
.../bcftools/concat/tests/nextflow.config | 3 +
.../nf-core/bcftools/concat/tests/tags.yml | 2 +
modules/nf-core/bcftools/filter/main.nf | 4 +-
modules/nf-core/bcftools/filter/meta.yml | 4 +-
.../bcftools/filter/tests/main.nf.test | 82 ++++
.../bcftools/filter/tests/main.nf.test.snap | 101 ++++
.../bcftools/filter/tests/nextflow.config | 3 +
.../nf-core/bcftools/filter/tests/tags.yml | 2 +
modules/nf-core/bcftools/sort/main.nf | 4 +-
.../nf-core/bcftools/sort/tests/main.nf.test | 54 +++
.../bcftools/sort/tests/main.nf.test.snap | 68 +++
modules/nf-core/bcftools/sort/tests/tags.yml | 2 +
modules/nf-core/bedgovcf/environment.yml | 2 +-
modules/nf-core/bedgovcf/main.nf | 6 +-
.../nf-core/bedgovcf/tests/main.nf.test.snap | 20 +-
modules/nf-core/delly/call/environment.yml | 2 +-
modules/nf-core/delly/call/main.nf | 10 +-
modules/nf-core/delly/call/meta.yml | 10 +
modules/nf-core/delly/call/tests/main.nf.test | 187 ++++++++
.../delly/call/tests/main.nf.test.snap | 247 ++++++++++
modules/nf-core/delly/call/tests/tags.yml | 2 +
modules/nf-core/delly/call/tests/vcf.config | 5 +
.../ensemblvep/download/environment.yml | 2 +-
modules/nf-core/ensemblvep/download/main.nf | 14 +-
.../ensemblvep/download/tests/main.nf.test | 60 +++
.../download/tests/main.nf.test.snap | 322 +++++++++++++
.../ensemblvep/download/tests/nextflow.config | 12 +
.../ensemblvep/download/tests/tags.yml | 2 +
.../nf-core/ensemblvep/vep/environment.yml | 2 +-
modules/nf-core/ensemblvep/vep/main.nf | 10 +-
.../nf-core/ensemblvep/vep/tests/main.nf.test | 40 +-
.../ensemblvep/vep/tests/main.nf.test.snap | 26 ++
.../ensemblvep/vep/tests/nextflow.config | 11 +-
.../nf-core/expansionhunter/environment.yml | 2 +
modules/nf-core/expansionhunter/main.nf | 8 +-
.../expansionhunter/tests/main.nf.test | 35 +-
.../expansionhunter/tests/main.nf.test.snap | 133 +++++-
modules/nf-core/gawk/main.nf | 5 +-
modules/nf-core/gawk/tests/main.nf.test | 56 +++
modules/nf-core/gawk/tests/main.nf.test.snap | 68 +++
modules/nf-core/gawk/tests/nextflow.config | 6 +
.../tests/nextflow_with_program_file.config | 5 +
modules/nf-core/gawk/tests/tags.yml | 2 +
modules/nf-core/gridss/gridss/environment.yml | 7 +
modules/nf-core/gridss/gridss/main.nf | 7 +-
modules/nf-core/gridss/gridss/meta.yml | 6 +-
modules/nf-core/jasminesv/environment.yml | 1 +
modules/nf-core/jasminesv/main.nf | 6 +-
modules/nf-core/jasminesv/meta.yml | 16 +-
modules/nf-core/jasminesv/tests/iris.config | 6 +
modules/nf-core/jasminesv/tests/main.nf.test | 185 ++++++++
.../nf-core/jasminesv/tests/main.nf.test.snap | 167 +++++++
.../nf-core/jasminesv/tests/normalize.config | 5 +
modules/nf-core/jasminesv/tests/tags.yml | 2 +
.../manta/convertinversion/environment.yml | 2 +-
.../nf-core/manta/convertinversion/main.nf | 13 +
.../nf-core/manta/convertinversion/meta.yml | 9 +
.../manta/convertinversion/tests/main.nf.test | 92 ++++
.../convertinversion/tests/main.nf.test.snap | 85 ++++
.../manta/convertinversion/tests/tags.yml | 2 +
modules/nf-core/manta/germline/main.nf | 6 +-
.../nf-core/manta/germline/tests/main.nf.test | 162 +++++++
.../manta/germline/tests/main.nf.test.snap | 139 ++++++
.../manta/germline/tests/nextflow.config | 5 +
modules/nf-core/manta/germline/tests/tags.yml | 2 +
modules/nf-core/ngsbits/samplegender/meta.yml | 2 +-
.../ngsbits/samplegender/tests/main.nf.test | 47 ++
.../samplegender/tests/main.nf.test.snap | 35 ++
.../ngsbits/samplegender/tests/tags.yml | 2 +
.../samtools/convert/samtools-convert.diff | 2 +-
.../samtools/convert/tests/main.nf.test | 32 ++
.../samtools/convert/tests/main.nf.test.snap | 65 +++
.../nf-core/samtools/faidx/environment.yml | 3 +-
modules/nf-core/samtools/faidx/meta.yml | 4 +
.../nf-core/samtools/faidx/tests/main.nf.test | 122 +++++
.../samtools/faidx/tests/main.nf.test.snap | 249 ++++++++++
.../samtools/faidx/tests/nextflow.config | 7 +
.../samtools/faidx/tests/nextflow2.config | 6 +
modules/nf-core/samtools/faidx/tests/tags.yml | 2 +
modules/nf-core/wisecondorx/convert/main.nf | 8 +-
modules/nf-core/wisecondorx/convert/meta.yml | 2 +-
.../wisecondorx/convert/tests/main.nf.test | 97 ++++
.../convert/tests/main.nf.test.snap | 107 +++++
.../wisecondorx/convert/tests/tags.yml | 2 +
modules/nf-core/wisecondorx/predict/main.nf | 8 +-
modules/nf-core/wisecondorx/predict/meta.yml | 4 +-
.../wisecondorx/predict/tests/main.nf.test | 65 +++
.../predict/tests/main.nf.test.snap | 65 +++
.../wisecondorx/predict/tests/tags.yml | 2 +
nextflow.config | 8 +-
nextflow_schema.json | 62 +--
subworkflows/local/bam_cnv_calling/main.nf | 10 +-
subworkflows/local/bam_sv_calling/main.nf | 20 +-
.../local/bam_variant_calling_delly/main.nf | 22 +-
.../local/bam_variant_calling_manta/main.nf | 12 +-
.../local/bam_variant_calling_qdnaseq/main.nf | 12 +-
.../local/bam_variant_calling_smoove/main.nf | 34 +-
.../bam_variant_calling_wisecondorx/main.nf | 22 +-
.../vcf_annotate_vep_annotsv_vcfanno/main.nf | 39 +-
.../local/vcf_merge_callers_jasmine/main.nf | 4 +-
.../local/vcf_merge_family_jasmine/main.nf | 4 +-
tests/nextflow.config | 4 +
tests/pipeline/all_types/all.nf.test | 65 ++-
tests/pipeline/all_types/all.nf.test.snap | 442 +++++++++++-------
tests/pipeline/cnv/cnv.nf.test | 2 +-
tests/pipeline/families/families.nf.test | 8 +-
tests/pipeline/sv/sv.nf.test | 2 +-
.../local/bam_cnv_calling/main.nf.test | 31 +-
.../local/bam_prepare_samtools/main.nf.test | 26 +-
.../bam_prepare_samtools/main.nf.test.snap | 28 +-
.../main.nf.test.snap | 14 +-
.../local/bam_sv_calling/main.nf.test | 63 +--
.../local/bam_sv_calling/main.nf.test.snap | 4 +-
.../bam_variant_calling_delly/main.nf.test | 1 +
.../main.nf.test.snap | 12 +-
.../bam_variant_calling_manta/main.nf.test | 1 +
.../bam_variant_calling_qdnaseq/main.nf.test | 1 +
.../bam_variant_calling_smoove/main.nf.test | 1 +
.../main.nf.test.snap | 4 +-
.../main.nf.test | 1 +
.../main.nf.test.snap | 12 +-
.../main.nf.test | 41 +-
.../main.nf.test.snap | 78 +++-
.../nextflow.config | 6 +-
workflows/structural.nf | 265 ++++++-----
158 files changed, 5032 insertions(+), 770 deletions(-)
create mode 100644 assets/test.npz
create mode 100644 modules/nf-core/annotsv/annotsv/environment.yml
create mode 100644 modules/nf-core/annotsv/annotsv/tests/main.nf.test
create mode 100644 modules/nf-core/annotsv/annotsv/tests/main.nf.test.snap
create mode 100644 modules/nf-core/annotsv/annotsv/tests/nextflow.config
create mode 100644 modules/nf-core/annotsv/annotsv/tests/tags.yml
create mode 100644 modules/nf-core/annotsv/installannotations/tests/main.nf.test
create mode 100644 modules/nf-core/annotsv/installannotations/tests/main.nf.test.snap
create mode 100644 modules/nf-core/annotsv/installannotations/tests/tags.yml
create mode 100644 modules/nf-core/bcftools/annotate/tests/bcf.config
create mode 100644 modules/nf-core/bcftools/annotate/tests/main.nf.test
create mode 100644 modules/nf-core/bcftools/annotate/tests/main.nf.test.snap
create mode 100644 modules/nf-core/bcftools/annotate/tests/tags.yml
create mode 100644 modules/nf-core/bcftools/annotate/tests/vcf.config
create mode 100644 modules/nf-core/bcftools/concat/tests/main.nf.test
create mode 100644 modules/nf-core/bcftools/concat/tests/main.nf.test.snap
create mode 100644 modules/nf-core/bcftools/concat/tests/nextflow.config
create mode 100644 modules/nf-core/bcftools/concat/tests/tags.yml
create mode 100644 modules/nf-core/bcftools/filter/tests/main.nf.test
create mode 100644 modules/nf-core/bcftools/filter/tests/main.nf.test.snap
create mode 100644 modules/nf-core/bcftools/filter/tests/nextflow.config
create mode 100644 modules/nf-core/bcftools/filter/tests/tags.yml
create mode 100644 modules/nf-core/bcftools/sort/tests/main.nf.test
create mode 100644 modules/nf-core/bcftools/sort/tests/main.nf.test.snap
create mode 100644 modules/nf-core/bcftools/sort/tests/tags.yml
create mode 100644 modules/nf-core/delly/call/tests/main.nf.test
create mode 100644 modules/nf-core/delly/call/tests/main.nf.test.snap
create mode 100644 modules/nf-core/delly/call/tests/tags.yml
create mode 100644 modules/nf-core/delly/call/tests/vcf.config
create mode 100644 modules/nf-core/ensemblvep/download/tests/main.nf.test
create mode 100644 modules/nf-core/ensemblvep/download/tests/main.nf.test.snap
create mode 100644 modules/nf-core/ensemblvep/download/tests/nextflow.config
create mode 100644 modules/nf-core/ensemblvep/download/tests/tags.yml
create mode 100644 modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap
create mode 100644 modules/nf-core/gawk/tests/main.nf.test
create mode 100644 modules/nf-core/gawk/tests/main.nf.test.snap
create mode 100644 modules/nf-core/gawk/tests/nextflow.config
create mode 100644 modules/nf-core/gawk/tests/nextflow_with_program_file.config
create mode 100644 modules/nf-core/gawk/tests/tags.yml
create mode 100644 modules/nf-core/gridss/gridss/environment.yml
create mode 100644 modules/nf-core/jasminesv/tests/iris.config
create mode 100644 modules/nf-core/jasminesv/tests/main.nf.test
create mode 100644 modules/nf-core/jasminesv/tests/main.nf.test.snap
create mode 100644 modules/nf-core/jasminesv/tests/normalize.config
create mode 100644 modules/nf-core/jasminesv/tests/tags.yml
create mode 100644 modules/nf-core/manta/convertinversion/tests/main.nf.test
create mode 100644 modules/nf-core/manta/convertinversion/tests/main.nf.test.snap
create mode 100644 modules/nf-core/manta/convertinversion/tests/tags.yml
create mode 100644 modules/nf-core/manta/germline/tests/main.nf.test
create mode 100644 modules/nf-core/manta/germline/tests/main.nf.test.snap
create mode 100644 modules/nf-core/manta/germline/tests/nextflow.config
create mode 100644 modules/nf-core/manta/germline/tests/tags.yml
create mode 100644 modules/nf-core/ngsbits/samplegender/tests/main.nf.test
create mode 100644 modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap
create mode 100644 modules/nf-core/ngsbits/samplegender/tests/tags.yml
create mode 100644 modules/nf-core/samtools/faidx/tests/main.nf.test
create mode 100644 modules/nf-core/samtools/faidx/tests/main.nf.test.snap
create mode 100644 modules/nf-core/samtools/faidx/tests/nextflow.config
create mode 100644 modules/nf-core/samtools/faidx/tests/nextflow2.config
create mode 100644 modules/nf-core/samtools/faidx/tests/tags.yml
create mode 100644 modules/nf-core/wisecondorx/convert/tests/main.nf.test
create mode 100644 modules/nf-core/wisecondorx/convert/tests/main.nf.test.snap
create mode 100644 modules/nf-core/wisecondorx/convert/tests/tags.yml
create mode 100644 modules/nf-core/wisecondorx/predict/tests/main.nf.test
create mode 100644 modules/nf-core/wisecondorx/predict/tests/main.nf.test.snap
create mode 100644 modules/nf-core/wisecondorx/predict/tests/tags.yml
diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
index ac17c97c..a7eded4d 100644
--- a/.github/workflows/build-docs.yml
+++ b/.github/workflows/build-docs.yml
@@ -18,8 +18,11 @@ jobs:
with:
python-version: 3.x
- run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
- - name: Obtain version from MANIFEST.MF
- run: echo "pipeline_version=$(grep "version" nextflow.config | tail -1 | sed -e s'/[^=]*= //' | cut -d "'" -f 2)" >> $GITHUB_ENV
+ - name: Obtain version from nextflow config
+ run: |
+ version=$(grep "version" nextflow.config | tail -1 | sed -e s'/[^=]*= //' | cut -d "'" -f 2)
+ [[ $version == *"dev"* ]] && pipeline_version="dev" || pipeline_version=$version
+ echo "pipeline_version=$pipeline_version" >> $GITHUB_ENV
- name: Setup git user
run: |
git config --global user.name "${{github.actor}}"
@@ -33,6 +36,7 @@ jobs:
- name: Install dependencies
run: pip install mkdocs-material pymdown-extensions pillow cairosvg mike
- name: Build docs
- run: mike deploy --push --update-aliases ${{ env.pipeline_version }} latest
+ run: |
+ [[ ${{ env.pipeline_version }} == "dev" ]] && mike deploy --push ${{ env.pipeline_version }} || mike deploy --push --update-aliases ${{ env.pipeline_version }} latest
- name: Set default docs
run: mike set-default --push latest
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9d604104..e40e5264 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,10 +1,34 @@
# nf-cmgg/structural: Changelog
+# nf-cmgg/structural: Changelog
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## v0.2.0 - [19 July 2024] - Mighty Manneken Pis
+
+### `Added`
+
+1. Added keyword shortcuts to the `--callers` parameter (these can also be used as comma-separated entries to the parameter):
+ - `all`: Use all callers available in the pipeline
+ - `sv`: Use all SV callers available in the pipeline
+ - `cnv`: Use all CNV callers available in the pipeline
+ - `rre`: Use all repeat region expansion callers available in the pipeline
+2. Added the possibilty to annotate on HPO terms. Add the right HPO terms to the samplesheet in the `hpo` field
+
+### `Changes`
+
+1. Updated all WisecondorX modules to version 1.2.6 and added the `--seed` argument to `WisecondorX predict`
+2. Removed support for the `phenotypes` VEP plugin. Common VEP plugin support will be added later
+3. Made the main workflow pluggable, making it possible to use this pipeline in a meta pipeline
+4. Updated all modules to their latest version
+
+### `Fixed`
+
+1. The smoove outputs are now correct when using `--output_callers`
+
## v0.1.0 - [3 April 2024] - Amazing Atomium
+Initial release of nf-cmgg/structural, created with the [nf-core](https://nf-co.re/) template.
Initial release of nf-cmgg/structural, created with the [nf-core](https://nf-co.re/) template.
### `Added`
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index fa0a9adc..dc167595 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,6 +1,6 @@
report_comment: >
- This report has been generated by the nf-core/structural analysis pipeline. For information about how to interpret these results, please see the documentation.
+ This report has been generated by the nf-core/structural analysis pipeline. For information about how to interpret these results, please see the documentation.
report_section_order:
"nf-cmgg-structural-methods-description":
order: -1000
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 358cd2d1..62dec9ff 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -41,6 +41,11 @@
"type": "string",
"meta": ["sex"],
"enum": ["male", "female"]
+ },
+ "hpo": {
+ "type": "string",
+ "meta": ["hpo"],
+ "description": "HPO terms to be used for annotation with AnnotSV. Should be space or semicolon separated."
}
},
"required": ["sample", "cram"]
diff --git a/assets/test.npz b/assets/test.npz
new file mode 100644
index 00000000..e69de29b
diff --git a/conf/modules.config b/conf/modules.config
index 4180ec0f..f6c31019 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -10,16 +10,24 @@
----------------------------------------------------------------------------------------
*/
-def output_callers = params.output_callers
-def callers = params.callers.tokenize(",")
-def count_types = 0
-
-// When making changes here, make sure to also update the following files: lib/GlobalVariables.groovy
+// When making changes here, make sure to also update the following files: workflows/structural.nf
def svCallers = ["delly", "manta", "smoove"] //, "gridss"
def cnvCallers = ["qdnaseq", "wisecondorx"]
def repeatsCallers = ["expansionhunter"]
def annotationCallers = svCallers + cnvCallers
+def allCallers = svCallers + cnvCallers + repeatsCallers
+
+def output_callers = params.output_callers
+def lower_cased_callers = params.callers.toLowerCase()
+def callers = lower_cased_callers.tokenize(",").collect {
+ if(it == "all") {return allCallers}
+ if(it == "sv") {return svCallers}
+ if(it == "cnv") {return cnvCallers}
+ if(it == "rre") {return repeatsCallers}
+ return it
+}.flatten()
+def count_types = 0
def foundSvCallers = callers.intersect(svCallers)
def foundCnvCallers = callers.intersect(cnvCallers)
@@ -74,7 +82,7 @@ process {
//
if("delly" in callers){
- withName: "^.*:BAM_VARIANT_CALLING_DELLY:DELLY_CALL\$" {
+ withName: "^.*BAM_VARIANT_CALLING_DELLY:DELLY_CALL\$" {
ext.args = {"--svtype ${params.delly_sv_types} --map-qual ${params.delly_map_qual} --min-clique-size ${params.delly_min_clique_size}"}
ext.suffix = "vcf"
ext.prefix = { "${meta.id}.delly" }
@@ -99,7 +107,7 @@ process {
//
// if("whamg" in callers){
- // withName: "^.*:BAM_VARIANT_CALLING_WHAMG:WHAMG\$" {
+ // withName: "^.*BAM_VARIANT_CALLING_WHAMG:WHAMG\$" {
// ext.prefix = { "${meta.id}.whamg" }
// ext.args = {[
// meta.region ? "-r ${meta.region}" : "" ,
@@ -121,22 +129,22 @@ process {
if("manta" in callers){
- withName: "^.*:BAM_VARIANT_CALLING_MANTA:GAWK\$" {
+ withName: "^.*BAM_VARIANT_CALLING_MANTA:GAWK\$" {
ext.suffix = "bed"
ext.prefix = "contigs"
ext.args2 = '\'BEGIN {FS="\t"}; \$1 ~ /^chr[1-9XY][1-9]?\$/ {print \$1 FS "0" FS \$2 }\''
}
- withName: "^.*:MANTA_.*\$" {
+ withName: "^.*MANTA_.*\$" {
container = "quay.io/cmgg/manta:1.6.0"
}
- withName: "^.*:BAM_VARIANT_CALLING_MANTA:MANTA_GERMLINE\$" {
+ withName: "^.*BAM_VARIANT_CALLING_MANTA:MANTA_GERMLINE\$" {
label = "process_high"
cpus = { check_max( 20 * task.attempt, 'cpus' ) }
}
- withName: "^.*:BAM_VARIANT_CALLING_MANTA:MANTA_CONVERTINVERSION\$" {
+ withName: "^.*BAM_VARIANT_CALLING_MANTA:MANTA_CONVERTINVERSION\$" {
ext.prefix = { "${meta.id}.manta" }
publishDir = [[
enabled: !params.annotate && foundSvCallers.size() == 1 && (count_types == 1 || !params.concat_output),
@@ -159,7 +167,7 @@ process {
//
// if("scramble" in callers){
- // withName: "^.*:.*:BAM_VARIANT_CALLING_SCRAMBLE:SCRAMBLE_CLUSTERANALYSIS\$" {
+ // withName: "^.*.*:BAM_VARIANT_CALLING_SCRAMBLE:SCRAMBLE_CLUSTERANALYSIS\$" {
// ext.args = "--eval-meis"
// }
// }
@@ -169,7 +177,7 @@ process {
//
if("smoove" in callers){
- withName: "^.*:BAM_VARIANT_CALLING_SMOOVE:BCFTOOLS_SORT\$" {
+ withName: "^.*BAM_VARIANT_CALLING_SMOOVE:BCFTOOLS_SORT\$" {
ext.prefix = { "${meta.id}.smoove" }
publishDir = [[
enabled: !params.annotate && foundSvCallers.size() == 1 && (count_types == 1 || !params.concat_output),
@@ -186,7 +194,8 @@ process {
]]
}
- withName: "^.*:BAM_VARIANT_CALLING_SMOOVE:TABIX_TABIX\$" {
+ withName: "^.*BAM_VARIANT_CALLING_SMOOVE:TABIX_CALLER\$" {
+ ext.when = output_callers || (!params.annotate && foundSvCallers.size() == 1 && (count_types == 1 || !params.concat_output))
publishDir = [[
enabled: !params.annotate && foundSvCallers.size() == 1 && (count_types == 1 || !params.concat_output),
overwrite: true,
@@ -208,7 +217,7 @@ process {
//
if("gridss" in callers){
- withName: "^.*:BAM_VARIANT_CALLING_GRIDSS:GRIDSS_GRIDSS\$" {
+ withName: "^.*BAM_VARIANT_CALLING_GRIDSS:GRIDSS_GRIDSS\$" {
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
ext.prefix = { "${meta.id}.gridss" }
@@ -226,7 +235,7 @@ process {
]
}
- withName: "^.*:BAM_VARIANT_CALLING_GRIDSS:TABIX_TABIX\$" {
+ withName: "^.*BAM_VARIANT_CALLING_GRIDSS:TABIX_TABIX\$" {
publishDir = [
enabled: output_callers,
overwrite: true,
@@ -236,13 +245,13 @@ process {
]
}
- withName: "^.*:BAM_VARIANT_CALLING_GRIDSS:VIOLA\$" {
+ withName: "^.*BAM_VARIANT_CALLING_GRIDSS:VIOLA\$" {
time = { check_max( 20.h * task.attempt, 'time') }
ext.prefix = { "${meta.id}.viola" }
ext.args = { meta.read_length ? "--read_length ${meta.read_length}" : ""}
}
- withName: "^.*:BAM_VARIANT_CALLING_GRIDSS:BCFTOOLS_SORT\$" {
+ withName: "^.*BAM_VARIANT_CALLING_GRIDSS:BCFTOOLS_SORT\$" {
ext.prefix = { "${meta.id}.gridss" }
publishDir = [
enabled: !params.annotate && foundSvCallers.size() == 1 && (count_types == 1 || !params.concat_output),
@@ -253,7 +262,7 @@ process {
]
}
- withName: "^.*:BAM_VARIANT_CALLING_GRIDSS:TABIX_TABIX\$" {
+ withName: "^.*BAM_VARIANT_CALLING_GRIDSS:TABIX_TABIX\$" {
publishDir = [
enabled: !params.annotate && foundSvCallers.size() == 1 && (count_types == 1 || !params.concat_output),
overwrite: true,
@@ -274,7 +283,7 @@ process {
if(foundCnvCallers){
if("qdnaseq" in callers) {
- withName: "^.*:BAM_VARIANT_CALLING_QDNASEQ:QDNASEQ.*\$" {
+ withName: "^.*BAM_VARIANT_CALLING_QDNASEQ:QDNASEQ.*\$" {
cpus = 1
memory = { check_max(50.GB * task.attempt, 'memory') }
ext.prefix = { "${meta.id}.qdnaseq" }
@@ -293,7 +302,7 @@ process {
]]
}
- withName: "^.*:BAM_VARIANT_CALLING_QDNASEQ:GAWK\$" {
+ withName: "^.*BAM_VARIANT_CALLING_QDNASEQ:GAWK\$" {
ext.prefix = { "${meta.id}.qdnaseq.abberations" }
ext.suffix = "bed"
ext.args = "-F '\\t'"
@@ -316,7 +325,8 @@ process {
}
if("wisecondorx" in callers) {
- withName: "^.*:BAM_VARIANT_CALLING_WISECONDORX:WISECONDORX_PREDICT\$" {
+ withName: "^.*BAM_VARIANT_CALLING_WISECONDORX:WISECONDORX_PREDICT\$" {
+ ext.args = "--seed 0 --bed --plot"
memory = { check_max(50.GB * task.attempt, 'memory') }
ext.prefix = { "${meta.id}.wisecondorx" }
publishDir = [[
@@ -335,7 +345,7 @@ process {
}
}
- withName: "^.*:BAM_CNV_CALLING:[^:]*:BEDGOVCF\$" {
+ withName: "^.*BAM_CNV_CALLING:[^:]*:BEDGOVCF\$" {
ext.prefix = { "${meta.id}.${meta.caller}" }
ext.args = { meta.caller == "qdnaseq" ? "--skip 1" : "--header" }
publishDir = [[
@@ -353,7 +363,7 @@ process {
]]
}
- withName: "^.*:BAM_CNV_CALLING:[^:]*:TABIX_TABIX\$" {
+ withName: "^.*BAM_CNV_CALLING:[^:]*:TABIX_TABIX\$" {
publishDir = [[
enabled: !params.annotate && foundCnvCallers.size() == 1 && (count_types == 1 || !params.concat_output),
overwrite: true,
@@ -378,7 +388,7 @@ process {
*/
if(foundCnvCallers.size() > 1 || foundSvCallers.size() > 1) {
- withName: "^.*:VCF_MERGE_CALLERS_JASMINE:JASMINESV\$" {
+ withName: "^.*VCF_MERGE_CALLERS_JASMINE:JASMINESV\$" {
ext.args = {[
meta.variant_type == "sv" ? "min_support=${params.sv_callers_support}" : "",
meta.variant_type == "cnv" ? "min_support=${params.cnv_callers_support}" : "",
@@ -386,15 +396,15 @@ process {
].join(' ').trim()}
}
- withName: "^.*:VCF_MERGE_CALLERS_JASMINE:FIX_CALLERS\$" {
+ withName: "^.*VCF_MERGE_CALLERS_JASMINE:FIX_CALLERS\$" {
ext.prefix = { "${meta.id}.callers-corrected" }
}
- withName: "^.*:VCF_MERGE_CALLERS_JASMINE:BCFTOOLS_CONSENSUS_REHEADER\$" {
+ withName: "^.*VCF_MERGE_CALLERS_JASMINE:BCFTOOLS_CONSENSUS_REHEADER\$" {
ext.prefix = { "${meta.id}.reheadered" }
}
- withName: "^.*:VCF_MERGE_CALLERS_JASMINE:BCFTOOLS_SORT\$" {
+ withName: "^.*VCF_MERGE_CALLERS_JASMINE:BCFTOOLS_SORT\$" {
ext.prefix = { "${meta.id}.${meta.variant_type}" }
publishDir = [
enabled: !params.annotate && (count_types == 1 || !params.concat_output),
@@ -405,7 +415,7 @@ process {
]
}
- withName: "^.*:VCF_MERGE_CALLERS_JASMINE:TABIX_TABIX\$" {
+ withName: "^.*VCF_MERGE_CALLERS_JASMINE:TABIX_TABIX\$" {
publishDir = [
enabled: !params.annotate && (count_types == 1 || !params.concat_output),
overwrite: true,
@@ -432,22 +442,26 @@ process {
if(params.annotate){
- withName: "^.*:VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:BCFTOOLS_FILTER\$" {
+ withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:BCFTOOLS_FILTER\$" {
ext.prefix = {"${meta.id}.filter"}
ext.args = "-e 'GT=\"ref\"' --output-type z"
}
- withName: "^.*:VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:ANNOTSV_ANNOTSV\$" {
- ext.args = "-SVminSize 20"
+ withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:ANNOTSV_ANNOTSV\$" {
+ ext.args = {[
+ "-SVminSize 20",
+ "-vcf 1",
+ meta.hpo ? "-hpo ${meta.hpo}" : ""
+ ].join(" ")}
ext.prefix = {"${meta.id}.annot"}
}
- withName: "^.*:VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:BCFTOOLS_CONCAT\$" {
- ext.prefix = params.annotsv_file_name
+ withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:BCFTOOLS_CONCAT\$" {
+ ext.prefix = "annotsv_annotated"
ext.args = "--output-type z --naive-force"
}
- withName: "^.*:VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:ENSEMBLVEP_VEP\$" {
+ withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:ENSEMBLVEP_VEP\$" {
ext.prefix = {"${meta.id}.vep"}
ext.args = {[
// specify we use VCF files
@@ -467,18 +481,16 @@ process {
// create stats file
"--stats_file ${prefix}.summary.html",
// proteins
- '--domains --biotype --canonical --mane --ccds --protein --polyphen s --sift s',
- // plugins
- (params.vep_phenotypes) ? "--plugin Phenotypes,file=${params.phenotypes.split('/')[-1]}": ""
+ '--domains --biotype --canonical --mane --ccds --protein --polyphen s --sift s'
].join(' ').trim()}
}
- withName: "^.*:VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:VCFANNO\$" {
+ withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:VCFANNO\$" {
ext.args = "-permissive-overlap -ends"
}
if(!params.annotations_filter) {
- withName: "^.*:VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:TABIX_ANNOTATED\$" {
+ withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:TABIX_ANNOTATED\$" {
ext.prefix = { "${meta.id}.${meta.variant_type}.annotated" }
publishDir = [
enabled: (count_types == 1 || !params.concat_output),
@@ -491,7 +503,7 @@ process {
}
if(params.annotations_filter) {
- withName: "^.*:VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:BCFTOOLS_FILTER_COMMON\$" {
+ withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:BCFTOOLS_FILTER_COMMON\$" {
ext.prefix = {"${meta.id}.${meta.variant_type}.annotated"}
ext.args = "${params.annotations_filter} --output-type z"
publishDir = [
@@ -504,7 +516,7 @@ process {
}
- withName: "^.*:VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:TABIX_FILTER\$" {
+ withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:TABIX_FILTER\$" {
publishDir = [
enabled: (count_types == 1 || !params.concat_output),
overwrite: true,
@@ -525,11 +537,11 @@ process {
if(foundRepeatsCallers){
- withName: "^.*:BAM_REPEAT_ESTIMATION_EXPANSIONHUNTER:EXPANSIONHUNTER\$" {
+ withName: "^.*BAM_REPEAT_ESTIMATION_EXPANSIONHUNTER:EXPANSIONHUNTER\$" {
ext.args = {"--sex ${meta.sex}"}
}
- withName: "^.*:BAM_REPEAT_ESTIMATION_EXPANSIONHUNTER:BCFTOOLS_ANNOTATE\$" {
+ withName: "^.*BAM_REPEAT_ESTIMATION_EXPANSIONHUNTER:BCFTOOLS_ANNOTATE\$" {
ext.args = "-c INFO/REPREF:=INFO/REF --output-type z"
ext.prefix = { "${meta.id}.expansionhunter" }
ext.tabix = true
@@ -548,7 +560,7 @@ process {
]]
}
- withName: "^.*:BAM_REPEAT_ESTIMATION_EXPANSIONHUNTER:TABIX_TABIX\$" {
+ withName: "^.*BAM_REPEAT_ESTIMATION_EXPANSIONHUNTER:TABIX_TABIX\$" {
publishDir = [[
enabled: (count_types == 1 || !params.concat_output),
overwrite: true,
@@ -573,7 +585,7 @@ process {
if(count_types > 1 && params.concat_output){
- withName: "^.*:VCF_CONCAT_BCFTOOLS:BCFTOOLS_CONCAT\$" {
+ withName: "^.*VCF_CONCAT_BCFTOOLS:BCFTOOLS_CONCAT\$" {
ext.args = "--output-type z --allow-overlaps"
publishDir = [
enabled: true,
@@ -584,7 +596,7 @@ process {
]
}
- withName: "^.*:VCF_CONCAT_BCFTOOLS:TABIX_TABIX\$" {
+ withName: "^.*VCF_CONCAT_BCFTOOLS:TABIX_TABIX\$" {
publishDir = [
enabled: true,
overwrite: true,
@@ -601,30 +613,29 @@ process {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
- withName: "^.*:VCF_MERGE_FAMILY_JASMINE:JASMINESV\$" {
+ withName: "^.*VCF_MERGE_FAMILY_JASMINE:JASMINESV\$" {
ext.args = "--output_genotypes"
}
- withName: "^.*:VCF_MERGE_FAMILY_JASMINE:FIX_CALLERS\$" {
+ withName: "^.*VCF_MERGE_FAMILY_JASMINE:FIX_CALLERS\$" {
ext.prefix = { "${meta.id}.callers-corrected" }
}
- withName: "^.*:VCF_MERGE_FAMILY_JASMINE:BCFTOOLS_CONSENSUS_REHEADER\$" {
+ withName: "^.*VCF_MERGE_FAMILY_JASMINE:BCFTOOLS_CONSENSUS_REHEADER\$" {
ext.prefix = { "${meta.id}.reheadered" }
}
- withName: "^.*:VCF_MERGE_FAMILY_JASMINE:BCFTOOLS_SORT\$" {
+ withName: "^.*VCF_MERGE_FAMILY_JASMINE:BCFTOOLS_SORT\$" {
ext.args = "--output-type z"
publishDir = [
enabled: true,
overwrite: true,
path: { "${params.outdir}/${meta.family}" },
- mode: params.publish_dir_mode,
saveAs: { filename -> filename != "versions.yml" ? filename : null }
]
}
- withName: "^.*:VCF_MERGE_FAMILY_JASMINE:TABIX_TABIX\$" {
+ withName: "^.*VCF_MERGE_FAMILY_JASMINE:TABIX_TABIX\$" {
publishDir = [
enabled: true,
overwrite: true,
diff --git a/conf/test.config b/conf/test.config
index 715a83b6..9c5666fd 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -27,7 +27,7 @@ params {
// Fasta references
fasta = "https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/genome/seq/SVcontrol/reference.fasta"
fai = "https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/genome/seq/SVcontrol/reference.fasta.fai"
- bwa = "https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/genome/seq/SVcontrol/bwa.tar.gz"
+ // bwa = "https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/genome/seq/SVcontrol/bwa.tar.gz"
expansionhunter_catalog = params.test_data["homo_sapiens"]["genome"]["expansionhunter"]
qdnaseq_male = params.test_data["homo_sapiens"]["genome"]["genome_qdnaseq"]
qdnaseq_female = params.test_data["homo_sapiens"]["genome"]["genome_qdnaseq"]
diff --git a/docs/parameters.md b/docs/parameters.md
index d3a14c85..5661031a 100644
--- a/docs/parameters.md
+++ b/docs/parameters.md
@@ -82,15 +82,15 @@ Less common options for the pipeline, typically set in a config file.
Options specific to the execution of this pipeline
-| Parameter | Description | Type | Default | Required | Hidden |
-| --------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------- | ------- | -------- | ----------------------------------------------------------------------------------------------------------------------------------- |
-| `callers` | A comma-seperated list of callers to use. Can be one or more these: smoove | delly | manta | gridss | expansionhunter. At the moment Gridss runs very slowly compared to all other tools so it's only advised to use it when it's needed. | `string` | manta,smoove,delly,expansionhunter,wisecondorx | | |
-| `output_callers` | Output the VCF files from different callers. Warning: This produces a lot of additional output and should only be used for testing purposes | `boolean` | | | |
-| `sv_callers_support` | The minimum amount of SV callers that should detect a variant. All variants that have a lower amount of callers supporting it, will be removed. (Only used when more than one caller is given) | `integer` | 1 | | |
-| `cnv_callers_support` | The minimum amount of CNV callers that should detect a variant. All variants that have a lower amount of callers supporting it, will be removed. (Only used when more than one caller is given) | `integer` | 1 | | |
-| `annotate` | Run the annotation with Ensembl VEP and AnnotSV (and optionally VCFanno). | `boolean` | | | |
-| `concat_output` | Also output a concatenated VCF with all variant types analysed included. | `boolean` | | | |
-| `annotations_filter` | The filter arguments to use after annotating. Help
A common use case for this is to filter out common variants. You can supply a VCF file with common variants to VCFanno and filter out the matching variants using this parameterHelp
Following keywords can also be used as shortcuts to certain callers:
- all: Use all callers
- sv: Use all SV callers
- cnv: Use all CNV callers
- rre: Use all RRE callersHelp
A common use case for this is to filter out common variants. You can supply a VCF file with common variants to VCFanno and filter out the matching variants using this parameter\t120\tLowQual\tCALLERS=delly;CIEND=-9,9;CIPOS=-9,9;END=1349692;SVLEN=-1262759;SVTYPE=DEL\tGT:PE:SR\t1/1:0,0:0,7",
- "chr16\t1077371\tdelly_INV_2\tT\t\t58\tLowQual\tCALLERS=delly;CIEND=-392,392;CIPOS=-392,392;END=1078502;SVLEN=1131;SVTYPE=INV\tGT:PE:SR\t0/0:19,2:0,0",
- "chr16\t1123476\tdelly_INV_3\tA\t\t180\tPASS\tCALLERS=delly;CIEND=-3,3;CIPOS=-3,3;END=1604486;SVLEN=481010;SVTYPE=INV\tGT:PE:SR\t1/1:0,0:0,12",
- "chr16\t1135261\tdelly_INS_4\tC\t\t299\tPASS\tCALLERS=delly;CIEND=-2,2;CIPOS=-2,2;END=1135262;SVLEN=27;SVTYPE=INS\tGT:PE:SR\t1/1:0,0:0,25"
+ "chr16\t86933\tdelly_DEL_1\tT\t\t120\tLowQual\tCALLERS=delly;CIEND=-9,9;CIPOS=-9,9;END=1349691;SVLEN=-1262758;SVTYPE=DEL\tGT:PE:SR\t1/1:0,0:0,7",
+ "chr16\t1077371\tdelly_INV_2\tT\t\t58\tLowQual\tCALLERS=delly;CIEND=-392,392;CIPOS=-392,392;END=1078501;SVLEN=1130;SVTYPE=INV\tGT:PE:SR\t0/0:19,2:0,0",
+ "chr16\t1123476\tdelly_INV_3\tA\t\t180\tPASS\tCALLERS=delly;CIEND=-3,3;CIPOS=-3,3;END=1604485;SVLEN=481009;SVTYPE=INV\tGT:PE:SR\t1/1:0,0:0,12",
+ "chr16\t1135261\tdelly_INS_4\tC\tCAAAAAGTGAATGGATAAACCAACTGTA\t299\tPASS\tCALLERS=delly;CIEND=-2,2;CIPOS=-2,2;END=1135261;SVLEN=27;SVTYPE=INS\tGT:PE:SR\t1/1:0,0:0,25"
],
"test.svync.delly.vcf.gz.tbi",
3,
@@ -13,8 +13,8 @@
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.02.0"
+ "nextflow": "24.03.0"
},
- "timestamp": "2024-03-11T14:11:38.043228427"
+ "timestamp": "2024-05-06T15:21:39.34016826"
}
}
\ No newline at end of file
diff --git a/tests/subworkflows/local/bam_variant_calling_manta/main.nf.test b/tests/subworkflows/local/bam_variant_calling_manta/main.nf.test
index a65ea097..5d0d9240 100644
--- a/tests/subworkflows/local/bam_variant_calling_manta/main.nf.test
+++ b/tests/subworkflows/local/bam_variant_calling_manta/main.nf.test
@@ -31,6 +31,7 @@ nextflow_workflow {
input[3] = Channel.value([
file(params.manta_config, checkIfExists: true)
])
+ input[4] = Channel.fromPath("\${params.svync_configs}/*.yaml", checkIfExists:true).collect()
"""
}
}
diff --git a/tests/subworkflows/local/bam_variant_calling_qdnaseq/main.nf.test b/tests/subworkflows/local/bam_variant_calling_qdnaseq/main.nf.test
index 6dc4043e..f017b86a 100644
--- a/tests/subworkflows/local/bam_variant_calling_qdnaseq/main.nf.test
+++ b/tests/subworkflows/local/bam_variant_calling_qdnaseq/main.nf.test
@@ -40,6 +40,7 @@ nextflow_workflow {
[id:"female_ref"],
file(params.qdnaseq_female, checkIfExists: true)
])
+ input[5] = Channel.fromPath("\${params.bedgovcf_configs}/*.yaml", checkIfExists:true).collect()
"""
}
}
diff --git a/tests/subworkflows/local/bam_variant_calling_smoove/main.nf.test b/tests/subworkflows/local/bam_variant_calling_smoove/main.nf.test
index 192c4d2c..5767731d 100644
--- a/tests/subworkflows/local/bam_variant_calling_smoove/main.nf.test
+++ b/tests/subworkflows/local/bam_variant_calling_smoove/main.nf.test
@@ -26,6 +26,7 @@ nextflow_workflow {
[id:"fai"],
file(params.fai, checkIfExists: true)
])
+ input[3] = Channel.fromPath("\${params.svync_configs}/*.yaml", checkIfExists:true).collect()
"""
}
}
diff --git a/tests/subworkflows/local/bam_variant_calling_smoove/main.nf.test.snap b/tests/subworkflows/local/bam_variant_calling_smoove/main.nf.test.snap
index 2d970b5f..db1c1efb 100644
--- a/tests/subworkflows/local/bam_variant_calling_smoove/main.nf.test.snap
+++ b/tests/subworkflows/local/bam_variant_calling_smoove/main.nf.test.snap
@@ -13,8 +13,8 @@
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.02.0"
+ "nextflow": "24.03.0"
},
- "timestamp": "2024-03-11T14:24:00.029162632"
+ "timestamp": "2024-05-06T15:56:29.455835249"
}
}
\ No newline at end of file
diff --git a/tests/subworkflows/local/bam_variant_calling_wisecondorx/main.nf.test b/tests/subworkflows/local/bam_variant_calling_wisecondorx/main.nf.test
index d60a132a..63c33162 100644
--- a/tests/subworkflows/local/bam_variant_calling_wisecondorx/main.nf.test
+++ b/tests/subworkflows/local/bam_variant_calling_wisecondorx/main.nf.test
@@ -33,6 +33,7 @@ nextflow_workflow {
file(params.wisecondorx_reference, checkIfExists:true)
]
input[4] = [[],[]]
+ input[5] = Channel.fromPath("\${params.bedgovcf_configs}/*.yaml", checkIfExists:true).collect()
"""
}
}
diff --git a/tests/subworkflows/local/bam_variant_calling_wisecondorx/main.nf.test.snap b/tests/subworkflows/local/bam_variant_calling_wisecondorx/main.nf.test.snap
index b0f13b58..d5584ace 100644
--- a/tests/subworkflows/local/bam_variant_calling_wisecondorx/main.nf.test.snap
+++ b/tests/subworkflows/local/bam_variant_calling_wisecondorx/main.nf.test.snap
@@ -9,7 +9,7 @@
"sex": "male",
"caller": "wisecondorx"
},
- "test_aberrations.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+ "test.wisecondorx_aberrations.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
[
@@ -20,7 +20,7 @@
"sex": "male",
"caller": "wisecondorx"
},
- "test_bins.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+ "test.wisecondorx_bins.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
[
@@ -31,7 +31,7 @@
"sex": "male",
"caller": "wisecondorx"
},
- "test_segments.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+ "test.wisecondorx_segments.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
[
@@ -42,7 +42,7 @@
"sex": "male",
"caller": "wisecondorx"
},
- "test_chr_statistics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+ "test.wisecondorx_chr_statistics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
[
@@ -83,8 +83,8 @@
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.02.0"
+ "nextflow": "24.03.0"
},
- "timestamp": "2024-03-11T14:28:06.577335662"
+ "timestamp": "2024-05-06T15:54:06.8767855"
}
}
\ No newline at end of file
diff --git a/tests/subworkflows/local/vcf_annotate_vep_annotsv_vcfanno/main.nf.test b/tests/subworkflows/local/vcf_annotate_vep_annotsv_vcfanno/main.nf.test
index b6782038..2c0b469d 100644
--- a/tests/subworkflows/local/vcf_annotate_vep_annotsv_vcfanno/main.nf.test
+++ b/tests/subworkflows/local/vcf_annotate_vep_annotsv_vcfanno/main.nf.test
@@ -23,13 +23,14 @@ nextflow_workflow {
}
workflow {
"""
+ def meta = [id:"test", sample:"test", sex:"male", family: "test1", family_count:1, hpo:[]]
input[0] = Channel.of([
- [id:"test", sample:"test", sex:"male", variant_type:"sv", family: "test1", family_count:1],
+ meta + [variant_type:"sv"],
file(params.sv_vcf1, checkIfExists:true),
file(params.sv_tbi1, checkIfExists:true)
])
input[1] = Channel.of([
- [id:"test", sample:"test", sex:"male", family: "test1", family_count:1],
+ meta,
[]
])
input[2] = Channel.value([
@@ -48,6 +49,12 @@ nextflow_workflow {
input[9] = []
input[10] = []
input[11] = ["sv"]
+ input[12] = params.genome
+ input[13] = params.species
+ input[14] = params.vep_cache_version
+ input[15] = null
+ input[16] = []
+ input[17] = files("\${params.vcfanno_tomls}/*.toml", checkIfExists:true)
"""
}
}
@@ -56,7 +63,7 @@ nextflow_workflow {
assertAll(
{ assert workflow.success },
{ assert snapshot(
- workflow.out.vcfs[0][1..2].collect { file(it).name },
+ workflow.out.vcfs.collect { it.collect { it instanceof Map ? it : file(it).name } },
workflow.out.reports,
workflow.trace.succeeded().size(),
workflow.trace.failed().size()
@@ -78,13 +85,14 @@ nextflow_workflow {
}
workflow {
"""
+ def meta = [id:"test", sample:"test", sex:"male", family: "test1", family_count:1, hpo:[]]
input[0] = Channel.of([
- [id:"test", sample:"test", sex:"male", variant_type:"cnv", family: "test1", family_count:1],
+ meta + [variant_type:"cnv"],
file(params.sv_vcf1, checkIfExists:true),
file(params.sv_tbi1, checkIfExists:true)
])
input[1] = Channel.of([
- [id:"test", sample:"test", sex:"male", family: "test1", family_count:1],
+ meta,
[]
])
input[2] = Channel.value([
@@ -103,6 +111,12 @@ nextflow_workflow {
input[9] = []
input[10] = []
input[11] = ["cnv"]
+ input[12] = params.genome
+ input[13] = params.species
+ input[14] = params.vep_cache_version
+ input[15] = params.annotations_filter
+ input[16] = []
+ input[17] = files("\${params.vcfanno_tomls}/*.toml", checkIfExists:true)
"""
}
}
@@ -111,7 +125,7 @@ nextflow_workflow {
assertAll(
{ assert workflow.success },
{ assert snapshot(
- workflow.out.vcfs[0][1..2].collect { file(it).name },
+ workflow.out.vcfs.collect { it.collect { it instanceof Map ? it : file(it).name } },
workflow.out.reports,
workflow.trace.succeeded().size(),
workflow.trace.failed().size()
@@ -133,17 +147,18 @@ nextflow_workflow {
}
workflow {
"""
+ def meta = [id:"test", sample:"test", sex:"male", family: "test1", family_count:1, hpo:[]]
input[0] = Channel.of([
- [id:"test", sample:"test", sex:"male", variant_type:"sv", family: "test1", family_count:1],
+ meta + [variant_type:"sv"],
file(params.sv_vcf1, checkIfExists:true),
file(params.sv_tbi1, checkIfExists:true)
], [
- [id:"test", sample:"test", sex:"male", variant_type:"cnv", family: "test1", family_count:1],
+ meta + [variant_type: "cnv"],
file(params.cnv_vcf1, checkIfExists:true),
file(params.cnv_tbi1, checkIfExists:true)
])
input[1] = Channel.of([
- [id:"test", sample:"test", sex:"male", family: "test1", family_count:1],
+ meta,
[]
])
input[2] = Channel.value([
@@ -162,6 +177,12 @@ nextflow_workflow {
input[9] = []
input[10] = []
input[11] = ["sv", "cnv"]
+ input[12] = params.genome
+ input[13] = params.species
+ input[14] = params.vep_cache_version
+ input[15] = null
+ input[16] = []
+ input[17] = files("\${params.vcfanno_tomls}/*.toml", checkIfExists:true)
"""
}
}
@@ -170,7 +191,7 @@ nextflow_workflow {
assertAll(
{ assert workflow.success },
{ assert snapshot(
- workflow.out.vcfs[0][1..2].collect { file(it).name },
+ workflow.out.vcfs.collect { it.collect { it instanceof Map ? it : file(it).name } },
workflow.out.reports,
workflow.trace.succeeded().size(),
workflow.trace.failed().size()
diff --git a/tests/subworkflows/local/vcf_annotate_vep_annotsv_vcfanno/main.nf.test.snap b/tests/subworkflows/local/vcf_annotate_vep_annotsv_vcfanno/main.nf.test.snap
index 82c97455..fc707522 100644
--- a/tests/subworkflows/local/vcf_annotate_vep_annotsv_vcfanno/main.nf.test.snap
+++ b/tests/subworkflows/local/vcf_annotate_vep_annotsv_vcfanno/main.nf.test.snap
@@ -2,8 +2,21 @@
"homo_sapiens - sv, no_filter": {
"content": [
[
- "test.sv.vcf.gz",
- "test.sv.vcf.gz.tbi"
+ [
+ {
+ "id": "test",
+ "sample": "test",
+ "sex": "male",
+ "family": "test1",
+ "family_count": 1,
+ "hpo": [
+
+ ],
+ "variant_type": "sv"
+ },
+ "test.sv.vcf.gz",
+ "test.sv.vcf.gz.tbi"
+ ]
],
[
"test.vep.summary.html:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -13,15 +26,43 @@
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.02.0"
+ "nextflow": "24.04.2"
},
- "timestamp": "2024-03-12T10:16:55.291447426"
+ "timestamp": "2024-06-05T16:01:35.19225934"
},
"homo_sapiens - sv & cnv": {
"content": [
[
- "test.cnv.vcf.gz",
- "test.cnv.vcf.gz.tbi"
+ [
+ {
+ "id": "test",
+ "sample": "test",
+ "sex": "male",
+ "family": "test1",
+ "family_count": 1,
+ "hpo": [
+
+ ],
+ "variant_type": "cnv"
+ },
+ "test.cnv.vcf.gz",
+ "test.cnv.vcf.gz.tbi"
+ ],
+ [
+ {
+ "id": "test",
+ "sample": "test",
+ "sex": "male",
+ "family": "test1",
+ "family_count": 1,
+ "hpo": [
+
+ ],
+ "variant_type": "sv"
+ },
+ "test.sv.vcf.gz",
+ "test.sv.vcf.gz.tbi"
+ ]
],
[
"test.vep.summary.html:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -32,15 +73,28 @@
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.02.0"
+ "nextflow": "24.04.2"
},
- "timestamp": "2024-03-12T10:17:27.514868326"
+ "timestamp": "2024-06-05T16:04:50.892603799"
},
"homo_sapiens - cnv, filter": {
"content": [
[
- "test.cnv.vcf.gz",
- "test.cnv.vcf.gz.tbi"
+ [
+ {
+ "id": "test",
+ "sample": "test",
+ "sex": "male",
+ "family": "test1",
+ "family_count": 1,
+ "hpo": [
+
+ ],
+ "variant_type": "cnv"
+ },
+ "test.cnv.vcf.gz",
+ "test.cnv.vcf.gz.tbi"
+ ]
],
[
"test.vep.summary.html:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -50,8 +104,8 @@
],
"meta": {
"nf-test": "0.8.4",
- "nextflow": "24.02.0"
+ "nextflow": "24.04.2"
},
- "timestamp": "2024-03-12T11:04:12.980338516"
+ "timestamp": "2024-06-05T16:02:48.492322238"
}
}
\ No newline at end of file
diff --git a/tests/subworkflows/local/vcf_annotate_vep_annotsv_vcfanno/nextflow.config b/tests/subworkflows/local/vcf_annotate_vep_annotsv_vcfanno/nextflow.config
index 65252546..963c69ea 100644
--- a/tests/subworkflows/local/vcf_annotate_vep_annotsv_vcfanno/nextflow.config
+++ b/tests/subworkflows/local/vcf_annotate_vep_annotsv_vcfanno/nextflow.config
@@ -6,7 +6,11 @@ process {
}
withName: ANNOTSV_ANNOTSV {
- ext.args = "-SVminSize 20"
+ ext.args = {[
+ "-SVminSize 20",
+ "-vcf 1",
+ meta.hpo ? "-hpo ${meta.hpo}" : ""
+ ].join(" ")}
ext.prefix = {"${meta.id}.annot"}
}
diff --git a/workflows/structural.nf b/workflows/structural.nf
index ff0f45d0..614acbdd 100644
--- a/workflows/structural.nf
+++ b/workflows/structural.nf
@@ -9,43 +9,6 @@ include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pi
include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_structural_pipeline'
-// Check callers (see lib/GlobalVariables.groovy for the list of supported callers)
-def callers = params.callers.tokenize(",")
-
-for (caller in callers) {
- if(!(caller in GlobalVariables.allCallers)) { error("The caller '${caller}' is not supported please specify a comma delimited list with on or more of the following callers: ${GlobalVariables.allCallers}".toString()) }
-}
-
-def sv_callers_to_use = callers.intersect(GlobalVariables.svCallers)
-def cnv_callers_to_use = callers.intersect(GlobalVariables.cnvCallers)
-
-if (sv_callers_to_use && params.sv_callers_support > sv_callers_to_use.size()) {
- error("The --sv_callers_support parameter (${params.sv_callers_support}) is higher than the amount of SV callers in --callers (${sv_callers_to_use.size()}). Please adjust --sv_callers_support to a value lower of equal to the amount of SV callers to use.")
-}
-
-if (cnv_callers_to_use && params.cnv_callers_support > cnv_callers_to_use.size()) {
- error("The --cnv_callers_support parameter (${params.cnv_callers_support}) is higher than the amount of CNV callers in --callers (${cnv_callers_to_use.size()}). Please adjust --cnv_callers_support to a value lower of equal to the amount of CNV callers to use.")
-}
-
-if ("qdnaseq" in callers && (!params.qdnaseq_male || !params.qdnaseq_female)) {
- error("Please give the QDNAseq references using --qdnaseq_male and --qdnaseq_female")
-}
-
-if ("wisecondorx" in callers && !params.wisecondorx_reference) {
- error("Please give the WisecondorX reference using --wisecondorx_reference")
-}
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- CONFIG FILES
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
-ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
-ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT LOCAL MODULES/SUBWORKFLOWS
@@ -90,7 +53,47 @@ include { MULTIQC } from '../modules/nf-core/multiqc/m
workflow STRUCTURAL {
take:
- ch_samplesheet // channel: samplesheet read in from --input
+ // channels
+ ch_samplesheet // channel: samplesheet read in from --input
+ ch_multiqc_config
+ ch_multiqc_custom_config
+ ch_multiqc_logo
+ ch_multiqc_custom_methods_description
+
+ // file inputs
+ fasta // The fasta file to use
+ fai // The index of the fasta file
+ expansionhunter_catalog // The expansionhunter catalog
+ qdnaseq_female // The QDNAseq annotations for female samples
+ qdnaseq_male // The QDNAseq annotations for male samples
+ wisecondorx_reference // The WisecondorX annotations file
+ vep_cache // The VEP cache directory
+ annotsv_annotations // The annotations directory for AnnotSV
+ annotsv_candidate_genes // A file containing the AnnotSV candidate genes
+ annotsv_gene_transcripts // A file containing the AnnotSV gene transcripts
+ vcfanno_lua // A Lua script to use with vcfanno
+ vcfanno_resources // A comma delimited list of paths to vcfanno resource files
+ vcfanno_toml // The vcfanno config to
+ blacklist // A BED file of blacklisted regions
+ manta_config // A configuration file to be used in Manta
+ svync_dir // A directory containing svync configs (they must end in '.yaml' and contain the full name of the caller)
+ bedgovcf_dir // A directory containing bedgovcf configs (they must end in '.yaml' and contain the full name of the caller)
+ vcfanno_default_dir // A directory containing the default vcfanno configs (they must end in '.toml')
+
+ // boolean inputs
+ annotate // Run annotation on SV and CNV data
+ concat_output // Concatenate all output files
+
+ // value inputs
+ callers // All callers to be used
+ sv_callers_support // How many SV callers are needed to support the variant
+ cnv_callers_support // How many CNV callers are needed to support the variant
+ genome // The genome to use
+ species // The species to be used by VEP
+ vep_assembly // The genome assembly to be downloaded for VEP
+ vep_cache_version // The version of the VEP cache to use
+ annotations_filter // The filter pattern to use after annotation
+ outdir // The output directory of the pipeline
main:
@@ -104,37 +107,81 @@ workflow STRUCTURAL {
count_types = 0 // The amount of different variant types that can be concatenated
//
- // Create input channels from parameters
+ // Input validation
//
- ch_fasta = Channel.fromPath(params.fasta).map{[[id:'fasta'], it]}.collect()
- ch_annotsv_candidate_genes = params.annotsv_candidate_genes ? Channel.fromPath(params.annotsv_candidate_genes).map{[[], it]}.collect() : [[],[]]
- ch_annotsv_gene_transcripts = params.annotsv_gene_transcripts ? Channel.fromPath(params.annotsv_gene_transcripts).map{[[], it]}.collect() : [[],[]]
- ch_vcfanno_lua = params.vcfanno_lua ? Channel.fromPath(params.vcfanno_lua).collect() : []
- ch_catalog = params.expansionhunter_catalog ? Channel.fromPath(params.expansionhunter_catalog).map{[[id:'catalog'], it]}.collect() : [[id:'catalog'],[file("https://github.com/Illumina/ExpansionHunter/raw/master/variant_catalog/grch38/variant_catalog.json", checkIfExists:true)]]
- ch_qdnaseq_male = params.qdnaseq_male ? Channel.fromPath(params.qdnaseq_male).map{[[id:'qdnaseq'], it]}.collect() : [[],[]]
- ch_qdnaseq_female = params.qdnaseq_female ? Channel.fromPath(params.qdnaseq_female).map{[[id:'qdnaseq'], it]}.collect() : [[],[]]
- ch_wisecondorx_reference = params.wisecondorx_reference ? Channel.fromPath(params.wisecondorx_reference).map{[[id:'wisecondorx'], it]}.collect() : [[],[]]
- ch_blacklist = params.blacklist ? Channel.fromPath(params.blacklist).map{[[id:'blacklist'], it]}.collect() : [[],[]]
- ch_manta_config = Channel.fromPath(params.manta_config ?: "${projectDir}/assets/manta_config.ini").collect()
+ // When making changes here, make sure to also update the following files: conf/modules.config
+ def List svCallers = ["delly", "manta", "smoove"] //, "gridss"
+ def List cnvCallers = ["qdnaseq", "wisecondorx"]
+ def List repeatsCallers = ["expansionhunter"]
- val_vcfanno_resources = params.vcfanno_resources ? params.vcfanno_resources.split(",").collect{file(it, checkIfExists:true)}.flatten() : []
+ def List allCallers = svCallers + cnvCallers + repeatsCallers
+ def List annotationCallers = svCallers + cnvCallers
- ch_vep_extra_files = []
+ // Callers that need the sex
+ def List sexCallers = ["expansionhunter", "qdnaseq"]
+
+ def lower_cased_callers = callers.toLowerCase()
+ def callers = lower_cased_callers.tokenize(",").collect {
+ if(it == "all") {return allCallers}
+ if(it == "sv") {return svCallers}
+ if(it == "cnv") {return cnvCallers}
+ if(it == "rre") {return repeatsCallers}
+ return it
+ }.flatten()
+
+ for (caller in callers) {
+ if(!(caller in allCallers)) { error("The caller '${caller}' is not supported please specify a comma delimited list with on or more of the following callers: ${allCallers}".toString()) }
+ }
+
+ def sv_callers_to_use = callers.intersect(svCallers)
+ def cnv_callers_to_use = callers.intersect(cnvCallers)
+ def rre_callers_to_use = callers.intersect(repeatsCallers)
- if(params.vep_phenotypes && params.phenotypes && params.phenotypes_tbi) {
- ch_vep_extra_files.add(file(params.phenotypes, checkIfExists:true))
- ch_vep_extra_files.add(file(params.phenotypes_tbi, checkIfExists:true))
+ if (sv_callers_to_use && sv_callers_support > sv_callers_to_use.size()) {
+ error("The 'sv_callers_support' option (${sv_callers_support}) is higher than the amount of SV callers given (${sv_callers_to_use.size()}). Please adjust 'sv_callers_support' to a value lower of equal to the amount of SV callers to use.")
}
- else if(params.vep_phenotypes) {
- error("Please specify '--phenotypes PATH/TO/PHENOTYPES/FILE' and '--phenotypes_tbi PATH/TO/PHENOTYPES/INDEX/FILE' to use the Phenotypes VEP plugin.")
+
+ if (cnv_callers_to_use && cnv_callers_support > cnv_callers_to_use.size()) {
+ error("The 'cnv_callers_support' option (${cnv_callers_support}) is higher than the amount of CNV callers given (${cnv_callers_to_use.size()}). Please adjust 'cnv_callers_support' to a value lower of equal to the amount of CNV callers to use.")
}
+ if ("qdnaseq" in callers && (!qdnaseq_male || !qdnaseq_female)) {
+ error("Please give the QDNAseq references using 'qdnaseq_male' and 'qdnaseq_female'")
+ }
+
+ if ("wisecondorx" in callers && !wisecondorx_reference) {
+ error("Please give the WisecondorX reference using 'wisecondorx_reference'")
+ }
+
+ //
+ // Create input channels from parameters
+ //
+
+ ch_fasta = Channel.fromPath(fasta).map{[[id:'fasta'], it]}.collect()
+ ch_annotsv_candidate_genes = annotsv_candidate_genes ? Channel.fromPath(annotsv_candidate_genes).map{[[], it]}.collect() : [[],[]]
+ ch_annotsv_gene_transcripts = annotsv_gene_transcripts ? Channel.fromPath(annotsv_gene_transcripts).map{[[], it]}.collect() : [[],[]]
+ ch_vcfanno_lua = vcfanno_lua ? Channel.fromPath(vcfanno_lua).collect() : []
+ ch_catalog = expansionhunter_catalog ? Channel.fromPath(expansionhunter_catalog).map{[[id:'catalog'], it]}.collect() : [[],[]]
+ ch_qdnaseq_male = qdnaseq_male ? Channel.fromPath(qdnaseq_male).map{[[id:'qdnaseq'], it]}.collect() : [[],[]]
+ ch_qdnaseq_female = qdnaseq_female ? Channel.fromPath(qdnaseq_female).map{[[id:'qdnaseq'], it]}.collect() : [[],[]]
+ ch_wisecondorx_reference = wisecondorx_reference ? Channel.fromPath(wisecondorx_reference).map{[[id:'wisecondorx'], it]}.collect() : [[],[]]
+ ch_blacklist = blacklist ? Channel.fromPath(blacklist).map{[[id:'blacklist'], it]}.collect() : [[],[]]
+ ch_manta_config = manta_config ? Channel.fromPath(manta_config).collect() : [[]]
+ ch_svync_configs = svync_dir ? Channel.fromPath("${svync_dir}/*.yaml", checkIfExists:true).collect() : []
+ ch_bedgovcf_configs = bedgovcf_dir ? Channel.fromPath("${bedgovcf_dir}/*.yaml", checkIfExists:true).collect() : []
+
+ val_vcfanno_resources = vcfanno_resources ? vcfanno_resources.split(",").collect{file(it, checkIfExists:true)}.flatten() : []
+ val_default_vcfanno_tomls = vcfanno_default_dir ? files("${vcfanno_default_dir}/*.toml", checkIfExists:true) : []
+ val_vcfanno_toml = vcfanno_toml ? file(vcfanno_toml, checkIfExists:true) : []
+
+ ch_vep_extra_files = []
+
//
// Create optional inputs
//
- if(!params.fai){
+ if(!fai){
SAMTOOLS_FAIDX(
ch_fasta
)
@@ -143,37 +190,37 @@ workflow STRUCTURAL {
ch_fai = SAMTOOLS_FAIDX.out.fai.map{[[id:'fai'], it]}.collect()
}
else {
- ch_fai = Channel.fromPath(params.fai).map{[[id:"fai"],it]}.collect()
- }
-
- if(!params.bwa && "gridss" in callers){
- BWA_INDEX(
- ch_fasta
- )
-
- ch_versions = ch_versions.mix(BWA_INDEX.out.versions)
- ch_bwa_index = BWA_INDEX.out.index.map{[[id:'bwa'], it[1]]}.collect()
- }
- else if(params.bwa && "gridss" in callers) {
- ch_bwa_index_input = Channel.fromPath(params.bwa).map{[[id:"bwa"],it]}.collect()
- if(params.bwa.endsWith(".tar.gz")) {
- UNTAR_BWA(
- ch_bwa_index_input
- )
- ch_versions = ch_versions.mix(UNTAR_BWA.out.versions)
-
- UNTAR_BWA.out.untar
- .collect()
- .set { ch_bwa_index }
- } else {
- ch_bwa_index = ch_bwa_index_input
- }
- }
- else {
- ch_bwa_index = Channel.empty()
+ ch_fai = Channel.fromPath(fai).map{[[id:"fai"],it]}.collect()
}
- if(params.annotate && !params.annotsv_annotations && callers.intersect(GlobalVariables.annotationCallers)) {
+ // if(!bwa && "gridss" in callers){
+ // BWA_INDEX(
+ // ch_fasta
+ // )
+
+ // ch_versions = ch_versions.mix(BWA_INDEX.out.versions)
+ // ch_bwa_index = BWA_INDEX.out.index.map{[[id:'bwa'], it[1]]}.collect()
+ // }
+ // else if(bwa && "gridss" in callers) {
+ // ch_bwa_index_input = Channel.fromPath(bwa).map{[[id:"bwa"],it]}.collect()
+ // if(bwa.endsWith(".tar.gz")) {
+ // UNTAR_BWA(
+ // ch_bwa_index_input
+ // )
+ // ch_versions = ch_versions.mix(UNTAR_BWA.out.versions)
+
+ // UNTAR_BWA.out.untar
+ // .collect()
+ // .set { ch_bwa_index }
+ // } else {
+ // ch_bwa_index = ch_bwa_index_input
+ // }
+ // }
+ // else {
+ // ch_bwa_index = Channel.empty()
+ // }
+
+ if(annotate && !annotsv_annotations && callers.intersect(annotationCallers)) {
ANNOTSV_INSTALLANNOTATIONS()
ch_versions = ch_versions.mix(ANNOTSV_INSTALLANNOTATIONS.out.versions)
@@ -182,9 +229,9 @@ workflow STRUCTURAL {
.collect()
.set { ch_annotsv_annotations }
}
- else if(params.annotate && callers.intersect(GlobalVariables.annotationCallers)) {
- ch_annotsv_annotations_input = Channel.fromPath(params.annotsv_annotations).map{[[id:"annotsv_annotations"], it]}.collect()
- if(params.annotsv_annotations.endsWith(".tar.gz")){
+ else if(annotate && callers.intersect(annotationCallers)) {
+ ch_annotsv_annotations_input = Channel.fromPath(annotsv_annotations).map{[[id:"annotsv_annotations"], it]}.collect()
+ if(annotsv_annotations.endsWith(".tar.gz")){
UNTAR_ANNOTSV(
ch_annotsv_annotations_input
)
@@ -194,23 +241,23 @@ workflow STRUCTURAL {
.collect()
.set { ch_annotsv_annotations }
} else {
- ch_annotsv_annotations = Channel.fromPath(params.annotsv_annotations).map{[[id:"annotsv_annotations"], it]}.collect()
+ ch_annotsv_annotations = Channel.fromPath(annotsv_annotations).map{[[id:"annotsv_annotations"], it]}.collect()
}
}
else {
ch_annotsv_annotations = Channel.empty()
}
- if(!params.vep_cache && params.annotate && callers.intersect(GlobalVariables.annotationCallers)) {
+ if(!vep_cache && annotate && callers.intersect(annotationCallers)) {
ENSEMBLVEP_DOWNLOAD(
- Channel.of([[id:"vep_cache"], params.vep_assembly, params.species, params.vep_cache_version]).collect()
+ Channel.of([[id:"vep_cache"], vep_assembly, species, vep_cache_version]).collect()
)
ch_versions = ch_versions.mix(ENSEMBLVEP_DOWNLOAD.out.versions)
ch_vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.map{it[1]}.collect()
}
- else if (params.vep_cache && params.annotate && callers.intersect(GlobalVariables.annotationCallers)) {
- ch_vep_cache = Channel.fromPath(params.vep_cache).collect()
+ else if (vep_cache && annotate && callers.intersect(annotationCallers)) {
+ ch_vep_cache = Channel.fromPath(vep_cache).collect()
}
else {
ch_vep_cache = Channel.empty()
@@ -243,7 +290,7 @@ workflow STRUCTURAL {
// Determine the gender if needed
//
- if(callers.intersect(GlobalVariables.sexCallers)) {
+ if(callers.intersect(sexCallers)) {
ch_input_no_sex
.branch {
sex: it[0].sex
@@ -291,8 +338,9 @@ workflow STRUCTURAL {
ch_inputs.crams,
ch_fasta,
ch_fai,
- ch_bwa_index,
- ch_manta_config
+ ch_manta_config,
+ ch_svync_configs,
+ sv_callers_to_use
)
ch_versions = ch_versions.mix(BAM_SV_CALLING.out.versions)
@@ -317,7 +365,9 @@ workflow STRUCTURAL {
ch_qdnaseq_male,
ch_qdnaseq_female,
ch_wisecondorx_reference,
- ch_blacklist
+ ch_blacklist,
+ ch_bedgovcf_configs,
+ cnv_callers_to_use
)
ch_versions = ch_versions.mix(BAM_CNV_CALLING.out.versions)
ch_annotation_input = ch_annotation_input.mix(BAM_CNV_CALLING.out.vcfs)
@@ -327,7 +377,7 @@ workflow STRUCTURAL {
// Annotate the variants
//
- if(params.annotate) {
+ if(annotate) {
VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO(
ch_annotation_input,
ch_inputs.small_variants,
@@ -340,7 +390,13 @@ workflow STRUCTURAL {
ch_vep_extra_files,
ch_vcfanno_lua,
val_vcfanno_resources,
- variant_types
+ variant_types,
+ genome,
+ species,
+ vep_cache_version,
+ annotations_filter,
+ val_vcfanno_toml,
+ val_default_vcfanno_tomls
)
ch_reports = ch_reports.mix(VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO.out.reports)
@@ -354,7 +410,7 @@ workflow STRUCTURAL {
// Estimate repeat sizes
//
- if(callers.intersect(GlobalVariables.repeatsCallers)){
+ if(callers.intersect(repeatsCallers)){
count_types++
@@ -373,7 +429,7 @@ workflow STRUCTURAL {
// Concatenate the VCF files from different types of analysis
//
- if(count_types > 1 && params.concat_output) {
+ if(count_types > 1 && concat_output) {
ch_outputs
.map { meta, vcf, tbi ->
@@ -410,18 +466,15 @@ workflow STRUCTURAL {
// Collate and save software versions
//
softwareVersionsToYAML(ch_versions)
- .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true)
+ .collectFile(storeDir: "${outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true)
.set { ch_collated_versions }
//
// MODULE: MultiQC
//
ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
- ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
- ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
- ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)