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* 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 🤞 * another try 2 🤞 * 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 <[email protected]>
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