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updated the manta workflow\r\n\r\n* updated the whamg workflow\r\n\r\n* added versions to whamg\r\n\r\n* added some additional test data\r\n\r\n* updated the test data\r\n\r\n* updated the test data\r\n\r\n* updated the test data\r\n\r\n* updated the test data\r\n\r\n* overal updates and improvements\r\n\r\n* small updates\r\n\r\n* small updates\r\n\r\n* metrics part 1\r\n\r\n* metrics part 2\r\n\r\n* Module  evidence qc (#3)\r\n\r\n* make bincov matrix part 1\r\n\r\n* added ploidy and parts of calcmedcov\r\n\r\n* added WGD\r\n\r\n* removed delly and added a reheader to MANTA\r\n\r\n* added all code to the module (some parts are still broken)\r\n\r\n* small updates\r\n\r\n* small ploidy matrix fix\r\n\r\n* small updates to evidenceQC + re-added delly\r\n\r\n* Module gather batch evidence (#4)\r\n\r\n* added groundwork for the module\r\n\r\n* added groundwork for the module\r\n\r\n* more work done\r\n\r\n* removed commented lines\r\n\r\n* Continue module gather batch evidence 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fix stubs\r\n\r\n* fully add gridss\r\n\r\n* add tests\r\n\r\n* copy fix?\r\n\r\n* add gridss test to ci\r\n\r\n* exclude gridss vcfs from metrics (not supported)\r\n\r\n* update min nextflow version to fix caching issue\r\n\r\n* update gridss\r\n\r\n* remove TODOs [no ci]\r\n\r\n* Add genotyping (#26)\r\n\r\n* update scattering\r\n\r\n* update delly\r\n\r\n* bump commit\r\n\r\n* add --output_callers parameter\r\n\r\n* small fix to --output_callers\r\n\r\n* fix schema and test config\r\n\r\n* removed reheadering from manta\r\n\r\n* update bcftools/sort\r\n\r\n* update bcftools/sort\r\n\r\n* update headers after jasmine merge\r\n\r\n* small fix\r\n\r\n* finished genotyping\r\n\r\n* fix for paragraph/multigrmpy\r\n\r\n* updated the samplesheet conversion\r\n\r\n* removed some unused modules\r\n\r\n* add merging of samples from the same family\r\n\r\n* removed scattering from whamg\r\n\r\n* Updated jasmine (added support for bgzip to the module)\r\n\r\n* fix prettier\r\n\r\n* fix tests\r\n\r\n* fix tests again and remove black CI\r\n\r\n* add linting ci to nf-core.yml\r\n\r\n* Adopted SVINSSEQ as uniform ins sequence info key\r\n\r\n* disabled whamg for now\r\n\r\n* add missing format header\r\n\r\n* add patch for delly\r\n\r\n* fix header typo\r\n\r\n* remove local test profile\r\n\r\n* updated test profiles and added big tests\r\n\r\n* add delly args\r\n\r\n* add new args to schema and config\r\n\r\n* Add annotation + viola + join checks + cleanup (#29)\r\n\r\n* add join checks\r\n\r\n* fix delly mismatches\r\n\r\n* Added viola\r\n\r\n* fix header issues in single caller runs\r\n\r\n* header fix?\r\n\r\n* appease eclint\r\n\r\n* add stub to reverse_bed\r\n\r\n* fix for gridss?\r\n\r\n* appease eclint again!\r\n\r\n* typo\r\n\r\n* fix permissions\r\n\r\n* fix shebang\r\n\r\n* fix shebang again\r\n\r\n* disable gridss\r\n\r\n* fix tests\r\n\r\n* remove old code from gatk-sv\r\n\r\n* Add VEP to the pipeline\r\n\r\n* add some QOL parameters\r\n\r\n* update tests\r\n\r\n* QOL changes (variables and joins)\r\n\r\n* disable scattering for delly\r\n\r\n* remove unused gatk modules\r\n\r\n* update modules\r\n\r\n* made BED files optional\r\n\r\n* add metro map and update readme\r\n\r\n* forgot to save svg\r\n\r\n* fix linting\r\n\r\n* fix vep test\r\n\r\n* free up CI space?\r\n\r\n* use another cache for vep\r\n\r\n* edit PosCon3 samplesheet_big.csv (#30)\r\n\r\n* Add bcftools sort (#31)\r\n\r\n* add join checks\r\n\r\n* fix delly mismatches\r\n\r\n* Added viola\r\n\r\n* fix header issues in single caller runs\r\n\r\n* header fix?\r\n\r\n* appease eclint\r\n\r\n* add stub to reverse_bed\r\n\r\n* fix for gridss?\r\n\r\n* appease eclint again!\r\n\r\n* typo\r\n\r\n* fix permissions\r\n\r\n* fix shebang\r\n\r\n* fix shebang again\r\n\r\n* disable gridss\r\n\r\n* fix tests\r\n\r\n* remove old code from gatk-sv\r\n\r\n* Add VEP to the pipeline\r\n\r\n* add some QOL parameters\r\n\r\n* update tests\r\n\r\n* QOL changes (variables and joins)\r\n\r\n* disable scattering for delly\r\n\r\n* remove unused gatk modules\r\n\r\n* update modules\r\n\r\n* made BED files optional\r\n\r\n* add metro map and update readme\r\n\r\n* forgot to save svg\r\n\r\n* fix linting\r\n\r\n* fix vep test\r\n\r\n* free up CI space?\r\n\r\n* use another cache for vep\r\n\r\n* add bcftools sort\r\n\r\n* fix smoove output (#33)\r\n\r\n* fix smoove output\r\n\r\n* update according to other modules\r\n\r\n* Fully implement annotation (#35)\r\n\r\n* Template update for nf-core/tools version 2.6\r\n\r\n* Template update for nf-core/tools version 2.7.2\r\n\r\n* first steps\r\n\r\n* fully implement the annotation\r\n\r\n* update test\r\n\r\n* offer a lamb to the linting gods\r\n\r\n* bug fix\r\n\r\n* offer a virgin to the linting gods (hope this is enough)\r\n\r\n* Add dynamic VCFanno config creation\r\n\r\n* go on a pilgrimage to the mountain of the linting gods and make a blood sacrifice\r\n\r\n* fix and update annotate test to stub\r\n\r\n* update vep container on stub runs\r\n\r\n* add postannotations support to the configs\r\n\r\n* simplified the vcfanno config code and made it smarter\r\n\r\n* added new fields from the annotsv vcf to the default configs\r\n\r\n* added a param for the default annotsv file name\r\n\r\n* fix small bug with param\r\n\r\n* fix small bug with param\r\n\r\n* Add all default configs\r\n\r\n* sacrificing my firstborn child to the linting gods\r\n\r\n* Moved the unused configs to a separate folder\r\n\r\n* update configs\r\n\r\n* update vep config\r\n\r\n* add option to annotate on small variants with AnnotSV (real test files should still be added)\r\n\r\n* Remove unused VEP parameters\r\n\r\n* fix issues\r\n\r\n* add tests for small variants vcfs\r\n\r\n* add an option to also output the annotsv outputs\r\n\r\n* Merge wrongly placed commits (#40)\r\n\r\n* fixes for big tests\r\n\r\n* metro map update\r\n\r\n* Template update for nf-core/tools version 2.8\r\n\r\n* black linting\r\n\r\n* update modules\r\n\r\n* update modules\r\n\r\n* fix local modules\r\n\r\n* bump\r\n\r\n* eclint\r\n\r\n* update genome in docs\r\n\r\n* update vcfanno configs retina and rpe\r\n\r\n* fix rpe bed file in config\r\n\r\n* Cnv support (#50)\r\n\r\n* Template update for nf-core/tools version 2.6\r\n\r\n* Template update for nf-core/tools version 2.7.2\r\n\r\n* first steps\r\n\r\n* fully implement the annotation\r\n\r\n* update test\r\n\r\n* offer a lamb to the linting gods\r\n\r\n* bug fix\r\n\r\n* offer a virgin to the linting gods (hope this is enough)\r\n\r\n* Add dynamic VCFanno config creation\r\n\r\n* go on a pilgrimage to the mountain of the linting gods and make a blood sacrifice\r\n\r\n* fix and update annotate test to stub\r\n\r\n* update vep container on stub runs\r\n\r\n* add postannotations support to the configs\r\n\r\n* simplified the vcfanno config code and made it smarter\r\n\r\n* added new fields from the annotsv vcf to the default configs\r\n\r\n* added a param for the default annotsv file name\r\n\r\n* fix small bug with param\r\n\r\n* fix small bug with param\r\n\r\n* Add all default configs\r\n\r\n* sacrificing my firstborn child to the linting gods\r\n\r\n* Moved the unused configs to a separate folder\r\n\r\n* update configs\r\n\r\n* update vep config\r\n\r\n* add option to annotate on small variants with AnnotSV (real test files should still be added)\r\n\r\n* Remove unused VEP parameters\r\n\r\n* fix issues\r\n\r\n* add tests for small variants vcfs\r\n\r\n* add an option to also output the annotsv outputs\r\n\r\n* Merge wrongly placed commits (#40)\r\n\r\n* fixes for big tests\r\n\r\n* metro map update\r\n\r\n* Template update for nf-core/tools version 2.8\r\n\r\n* black linting\r\n\r\n* update modules\r\n\r\n* update modules\r\n\r\n* fix local modules\r\n\r\n* bump\r\n\r\n* eclint\r\n\r\n* update genome in docs\r\n\r\n* update vcfanno configs retina and rpe\r\n\r\n* fix rpe bed file in config\r\n\r\n* adjust test to new data\r\n\r\n* remove unused data from workflows\r\n\r\n* remove simple event annotation\r\n\r\n* update modules config\r\n\r\n* remove unused modules\r\n\r\n* fix compile error\r\n\r\n* another compile error\r\n\r\n* remove comments in config\r\n\r\n* guess what! another compile error\r\n\r\n* small fixes to annotsv\r\n\r\n* update viola\r\n\r\n* circumvent a annotsv bug\r\n\r\n* add gridss genotyping\r\n\r\n* filter out variants with 0/0 genotype from gridss\r\n\r\n* move ref variants filtering to before annotsv\r\n\r\n* update tests\r\n\r\n* fix linting and add meta to references\r\n\r\n* black\r\n\r\n* install expansionhunter\r\n\r\n* fix merge conflict issues\r\n\r\n* fix linting\r\n\r\n* fix config\r\n\r\n* fix stub\r\n\r\n* add expansionhunter\r\n\r\n* some concurrency debugging\r\n\r\n* add nf-validation support\r\n\r\n* revert to using linkedhashmap for now\r\n\r\n* fix jasmine issue\r\n\r\n* update tests\r\n\r\n* fix typos\r\n\r\n* fix linting\r\n\r\n* there you go editorconfig\r\n\r\n* let's make it pretty\r\n\r\n* update nf-test config\r\n\r\n* fix even more tests\r\n\r\n* add concat output and fix tests\r\n\r\n* fix schema\r\n\r\n* now be nice please\r\n\r\n* i'm pretty again\r\n\r\n* update big test samplesheet [no ci]\r\n\r\n* fix max_time pattern [no ci]\r\n\r\n* add bcftools sort to single runs\r\n\r\n* only apply viola on gridss VCFs and change prefixes\r\n\r\n* remove unused comment [no ci]\r\n\r\n* fix input pattern\r\n\r\n* improve the efficiency of viola\r\n\r\n* black\r\n\r\n* added a sort step to gridss\r\n\r\n* updated the gridss label\r\n\r\n* patch gridss module\r\n\r\n* remove estimate_read_length\r\n\r\n* remove unused code\r\n\r\n* small typo\r\n\r\n* add -ends to vcfanno\r\n\r\n* add full test config\r\n\r\n* fix full test description\r\n\r\n* update samplesheet\r\n\r\n* add exists tags to the samplesheet schema\r\n\r\n* specify advised resources for gridss\r\n\r\n* possible fix for gridss OOM?\r\n\r\n* remove code duplication\r\n\r\n* remove an unused parameter\r\n\r\n* added a check for callers support being higher than the amount of sv callers\r\n\r\n* update metro map\r\n\r\n* increase gridss memory\r\n\r\n* try to optimize gridss part 2\r\n\r\n* try to optimize gridss part 3\r\n\r\n* oops\r\n\r\n* oops 2\r\n\r\n* oops 3\r\n\r\n* update to advised amounts\r\n\r\n* increase viola time\r\n\r\n* discourage the use of gridss for now\r\n\r\n* typo\r\n\r\n* linting fix\r\n\r\n* rename SV subworkflow\r\n\r\n* fix expansionhunter catalog and add qdnaseq ref\r\n\r\n* add qdnaseq\r\n\r\n* add a check for the qdnaseq reference\r\n\r\n* fixed some issues with qdnaseq\r\n\r\n* add cram merging and index creation\r\n\r\n* update resources for qdnaseq\r\n\r\n* update resources for qdnaseq\r\n\r\n* update resources for qdnaseq\r\n\r\n* fix resources qdnaseq\r\n\r\n* add wisecondorx\r\n\r\n* updated the metro map\r\n\r\n* fix background of metro map\r\n\r\n* update resolution\r\n\r\n* update resolution\r\n\r\n* remove old samplesheet conversion script\r\n\r\n* moved available callers to a groovy script\r\n\r\n* removed the manual check for file exists (now fully uses nf-validation)\r\n\r\n* fix a bug with concat when a cnv caller has been supplied\r\n\r\n* added some comments for the last fix\r\n\r\n* update optional input handling\r\n\r\n* fix small issue with annotsv annotations\r\n\r\n* fix a no process matching selector warning\r\n\r\n* revert last changes\r\n\r\n* temp fix for warning\r\n\r\n* improve vep cache handling + update modules\r\n\r\n* typo\r\n\r\n* fix container declaration\r\n\r\n* fix for manta issue?\r\n\r\n* undo last commit\r\n\r\n* version bump expansionhunter\r\n\r\n* added support for manta configs\r\n\r\n* made qdnaseq references gender specific\r\n\r\n* update manta resources\r\n\r\n* add contig input to manta\r\n\r\n* moved the contigs file creation to the manta subwf\r\n\r\n* fix vep params in schema\r\n\r\n* fix linting with no template update\r\n\r\n* fix nf-test tests\r\n\r\n* fix eclint\r\n\r\n* fix eclint\r\n\r\n* change gender to sex\r\n\r\n* typo\r\n\r\n* added the sex arg to expansionhunter\r\n\r\n* fix nf-test config for v0.8.0\r\n\r\n* revert nf-test to 0.7.3\r\n\r\n* prettier\r\n\r\n* set default sex to female instead of male\r\n\r\n* fix tests samplesheet\r\n\r\n* Fix vep container issue (#52)\r\n\r\n* add dynamic container fetching for vep\r\n\r\n* linting fix\r\n\r\n* moved the function to the process itself\r\n\r\n* fix conda issue\r\n\r\n* eclint\r\n\r\n* fix params schema\r\n\r\n* fix linting\r\n\r\n* fix for vep issue?\r\n\r\n* fix for missing singularity container\r\n\r\n* Add filtering on annotations + fix linting (#55)\r\n\r\n* Add filtering on annotations\r\n\r\n* fix linting\r\n\r\n* begone trailing whitespace\r\n\r\n* add annotation filter to test\r\n\r\n* CNV VCFs (#58)\r\n\r\n* add vcf creation to wisecondorx\r\n\r\n* add qdnaseq vcfs\r\n\r\n* update tests\r\n\r\n* add a simple qdnaseq filter\r\n\r\n* small fix in the wisecondorx config\r\n\r\n* small naming fix\r\n\r\n* add jasmine\r\n\r\n* fix for config?\r\n\r\n* fix tests\r\n\r\n* prettier\r\n\r\n* fix tests again\r\n\r\n* fix output logic\r\n\r\n* fix jasmine + add annotation\r\n\r\n* eclint\r\n\r\n* more output logic fixes\r\n\r\n* eclint (again)\r\n\r\n* more output logic fixes\r\n\r\n* fix cnv outputs\r\n\r\n* remove obsolete if statement\r\n\r\n* fix issue with meta joining\r\n\r\n* Family merging (#61)\r\n\r\n* add vcf creation to wisecondorx\r\n\r\n* add qdnaseq vcfs\r\n\r\n* update tests\r\n\r\n* add a simple qdnaseq filter\r\n\r\n* small fix in the wisecondorx config\r\n\r\n* small naming fix\r\n\r\n* add jasmine\r\n\r\n* fix for config?\r\n\r\n* fix tests\r\n\r\n* prettier\r\n\r\n* fix tests again\r\n\r\n* fix output logic\r\n\r\n* fix jasmine + add annotation\r\n\r\n* eclint\r\n\r\n* more output logic fixes\r\n\r\n* eclint (again)\r\n\r\n* more output logic fixes\r\n\r\n* fix cnv outputs\r\n\r\n* remove obsolete if statement\r\n\r\n* fix issue with meta joining\r\n\r\n* add family name to the samplesheet and meta\r\n\r\n* changes to jasmine subwf + add family merging subwf\r\n\r\n* add correct reheadering\r\n\r\n* add family merging (does not work rn)\r\n\r\n* some more work\r\n\r\n* fix repeat  VCF error\r\n\r\n* add z-score to VCF header\r\n\r\n* small fixes to sex defining\r\n\r\n* Add proper testing + fix some issues found (#64)\r\n\r\n* add vcf creation to wisecondorx\r\n\r\n* add qdnaseq vcfs\r\n\r\n* update tests\r\n\r\n* add a simple qdnaseq filter\r\n\r\n* small fix in the wisecondorx config\r\n\r\n* small naming fix\r\n\r\n* add jasmine\r\n\r\n* fix for config?\r\n\r\n* fix tests\r\n\r\n* prettier\r\n\r\n* fix tests again\r\n\r\n* fix output logic\r\n\r\n* fix jasmine + add annotation\r\n\r\n* eclint\r\n\r\n* more output logic fixes\r\n\r\n* eclint (again)\r\n\r\n* more output logic fixes\r\n\r\n* fix cnv outputs\r\n\r\n* remove obsolete if statement\r\n\r\n* fix issue with meta joining\r\n\r\n* add family name to the samplesheet and meta\r\n\r\n* changes to jasmine subwf + add family merging subwf\r\n\r\n* add correct reheadering\r\n\r\n* add family merging (does not work rn)\r\n\r\n* some more work\r\n\r\n* fix repeat  VCF error\r\n\r\n* first commit\r\n\r\n* add z-score to VCF header\r\n\r\n* small fixes to sex defining\r\n\r\n* add test for bam_cnv_calling\r\n\r\n* test bam_prepare_samtools\r\n\r\n* test bam_repeat_estimation_expansionhunter\r\n\r\n* test bam_sv_calling\r\n\r\n* test bam_variant_calling_delly\r\n\r\n* test bam_variant_calling_gridss\r\n\r\n* test bam_variant_calling_manta\r\n\r\n* test bam_variant_calling_qdnaseq\r\n\r\n* test bam_variant_calling_smoove\r\n\r\n* test bam_variant_calling_wisecondorx\r\n\r\n* uniformize config\r\n\r\n* test vcf_annotate_vep_annotsv_vcfanno\r\n\r\n* test vcf_concat_bcftools\r\n\r\n* test vcf_merge_callers_jasmine\r\n\r\n* fix header\r\n\r\n* update vep annotations\r\n\r\n* oops\r\n\r\n* add gnomad to vep\r\n\r\n* revert vep container changes\r\n\r\n* add sift\r\n\r\n* fix merge crams with families\r\n\r\n* fix join duplication for replicates\r\n\r\n* fully test jasmine family merge\r\n\r\n* uniformize tests\r\n\r\n* fix duplication glitch\r\n\r\n* add pipeline tests for callers\r\n\r\n* add families tests\r\n\r\n* add duplicates tests\r\n\r\n* remove old tests and add new tests to ci\r\n\r\n* fix linting\r\n\r\n* use nf-core dev for linting\r\n\r\n* update minimum nextflow version\r\n\r\n* revert nf-core version to latest\r\n\r\n* upload artifacts\r\n\r\n* fix artifacts\r\n\r\n* only upload nf-test folder\r\n\r\n* fix artifact again?\r\n\r\n* fix artifact again?\r\n\r\n* fix artifact again?\r\n\r\n* prettier\r\n\r\n* only get artifacts on failure\r\n\r\n* only get artifacts on failure\r\n\r\n* only get artifacts on failure\r\n\r\n* fix qdnaseq test\r\n\r\n* set nf-test to v0.8.1\r\n\r\n* try to fix permission errors\r\n\r\n* update family jasmine tests\r\n\r\n* small clarification in the header\r\n\r\n* Fix annotsv TCL error (#69)\r\n\r\n* add vcf creation to wisecondorx\r\n\r\n* add qdnaseq vcfs\r\n\r\n* update tests\r\n\r\n* add a simple qdnaseq filter\r\n\r\n* small fix in the wisecondorx config\r\n\r\n* small naming fix\r\n\r\n* add jasmine\r\n\r\n* fix for config?\r\n\r\n* fix tests\r\n\r\n* prettier\r\n\r\n* fix tests again\r\n\r\n* fix output logic\r\n\r\n* fix jasmine + add annotation\r\n\r\n* eclint\r\n\r\n* more output logic fixes\r\n\r\n* eclint (again)\r\n\r\n* more output logic fixes\r\n\r\n* fix cnv outputs\r\n\r\n* remove obsolete if statement\r\n\r\n* fix issue with meta joining\r\n\r\n* add family name to the samplesheet and meta\r\n\r\n* changes to jasmine subwf + add family merging subwf\r\n\r\n* add correct reheadering\r\n\r\n* add family merging (does not work rn)\r\n\r\n* some more work\r\n\r\n* fix repeat  VCF error\r\n\r\n* first commit\r\n\r\n* add z-score to VCF header\r\n\r\n* small fixes to sex defining\r\n\r\n* add test for bam_cnv_calling\r\n\r\n* test bam_prepare_samtools\r\n\r\n* test bam_repeat_estimation_expansionhunter\r\n\r\n* test bam_sv_calling\r\n\r\n* test bam_variant_calling_delly\r\n\r\n* test bam_variant_calling_gridss\r\n\r\n* test bam_variant_calling_manta\r\n\r\n* test bam_variant_calling_qdnaseq\r\n\r\n* test bam_variant_calling_smoove\r\n\r\n* test bam_variant_calling_wisecondorx\r\n\r\n* uniformize config\r\n\r\n* test vcf_annotate_vep_annotsv_vcfanno\r\n\r\n* test vcf_concat_bcftools\r\n\r\n* test vcf_merge_callers_jasmine\r\n\r\n* fix header\r\n\r\n* update vep annotations\r\n\r\n* oops\r\n\r\n* add gnomad to vep\r\n\r\n* revert vep container changes\r\n\r\n* add sift\r\n\r\n* fix merge crams with families\r\n\r\n* fix join duplication for replicates\r\n\r\n* fully test jasmine family merge\r\n\r\n* uniformize tests\r\n\r\n* fix duplication glitch\r\n\r\n* add pipeline tests for callers\r\n\r\n* add families tests\r\n\r\n* add duplicates tests\r\n\r\n* remove old tests and add new tests to ci\r\n\r\n* fix linting\r\n\r\n* use nf-core dev for linting\r\n\r\n* update minimum nextflow version\r\n\r\n* revert nf-core version to latest\r\n\r\n* upload artifacts\r\n\r\n* fix artifacts\r\n\r\n* only upload nf-test folder\r\n\r\n* fix artifact again?\r\n\r\n* fix artifact again?\r\n\r\n* fix artifact again?\r\n\r\n* prettier\r\n\r\n* only get artifacts on failure\r\n\r\n* only get artifacts on failure\r\n\r\n* only get artifacts on failure\r\n\r\n* fix qdnaseq test\r\n\r\n* set nf-test to v0.8.1\r\n\r\n* try to fix permission errors\r\n\r\n* update family jasmine tests\r\n\r\n* split annotsv input files by svtype and merge them back\r\n\r\n* small clarification in the header\r\n\r\n* fix bcftools concat issue\r\n\r\n* fix linting\r\n\r\n* don't lint .prettierignore\r\n\r\n* Add Svync standardization + other fixes (#72)\r\n\r\n* add vcf creation to wisecondorx\r\n\r\n* add qdnaseq vcfs\r\n\r\n* update tests\r\n\r\n* add a simple qdnaseq filter\r\n\r\n* small fix in the wisecondorx config\r\n\r\n* small naming fix\r\n\r\n* add jasmine\r\n\r\n* fix for config?\r\n\r\n* fix tests\r\n\r\n* prettier\r\n\r\n* fix tests again\r\n\r\n* fix output logic\r\n\r\n* fix jasmine + add annotation\r\n\r\n* eclint\r\n\r\n* more output logic fixes\r\n\r\n* eclint (again)\r\n\r\n* more output logic fixes\r\n\r\n* fix cnv outputs\r\n\r\n* remove obsolete if statement\r\n\r\n* fix issue with meta joining\r\n\r\n* add family name to the samplesheet and meta\r\n\r\n* changes to jasmine subwf + add family merging subwf\r\n\r\n* add correct reheadering\r\n\r\n* add family merging (does not work rn)\r\n\r\n* some more work\r\n\r\n* fix repeat  VCF error\r\n\r\n* first commit\r\n\r\n* add z-score to VCF header\r\n\r\n* small fixes to sex defining\r\n\r\n* add test for bam_cnv_calling\r\n\r\n* test bam_prepare_samtools\r\n\r\n* test bam_repeat_estimation_expansionhunter\r\n\r\n* test bam_sv_calling\r\n\r\n* test bam_variant_calling_delly\r\n\r\n* test bam_variant_calling_gridss\r\n\r\n* test bam_variant_calling_manta\r\n\r\n* test bam_variant_calling_qdnaseq\r\n\r\n* test bam_variant_calling_smoove\r\n\r\n* test bam_variant_calling_wisecondorx\r\n\r\n* uniformize config\r\n\r\n* test vcf_annotate_vep_annotsv_vcfanno\r\n\r\n* test vcf_concat_bcftools\r\n\r\n* test vcf_merge_callers_jasmine\r\n\r\n* fix header\r\n\r\n* update vep annotations\r\n\r\n* oops\r\n\r\n* add gnomad to vep\r\n\r\n* revert vep container changes\r\n\r\n* add sift\r\n\r\n* fix merge crams with families\r\n\r\n* fix join duplication for replicates\r\n\r\n* fully test jasmine family merge\r\n\r\n* uniformize tests\r\n\r\n* fix duplication glitch\r\n\r\n* add pipeline tests for callers\r\n\r\n* add families tests\r\n\r\n* add duplicates tests\r\n\r\n* remove old tests and add new tests to ci\r\n\r\n* fix linting\r\n\r\n* use nf-core dev for linting\r\n\r\n* update minimum nextflow version\r\n\r\n* revert nf-core version to latest\r\n\r\n* upload artifacts\r\n\r\n* fix artifacts\r\n\r\n* only upload nf-test folder\r\n\r\n* fix artifact again?\r\n\r\n* fix artifact again?\r\n\r\n* fix artifact again?\r\n\r\n* prettier\r\n\r\n* only get artifacts on failure\r\n\r\n* only get artifacts on failure\r\n\r\n* only get artifacts on failure\r\n\r\n* fix qdnaseq test\r\n\r\n* set nf-test to v0.8.1\r\n\r\n* try to fix permission errors\r\n\r\n* update family jasmine tests\r\n\r\n* split annotsv input files by svtype and merge them back\r\n\r\n* small clarification in the header\r\n\r\n* fix bcftools concat issue\r\n\r\n* fix linting\r\n\r\n* don't lint .prettierignore\r\n\r\n* deprecate gridss for now\r\n\r\n* implement delly svync\r\n\r\n* implement manta svync\r\n\r\n* implement smoove svync\r\n\r\n* add better headering to merge callers\r\n\r\n* small fix to bcftools annotate\r\n\r\n* fix headers for family merging\r\n\r\n* remove unused assets\r\n\r\n* fix some stability issues\r\n\r\n* simplify expansionhunter handling\r\n\r\n* reheader with bcftools/reheader again\r\n\r\n* fix the headering once and for all\r\n\r\n* add a quick view statement\r\n\r\n* change view to dump\r\n\r\n* rename dump tag\r\n\r\n* extra dump\r\n\r\n* fix join issue\r\n\r\n* fix header issues with annotsv\r\n\r\n* add missing header line for annotsv\r\n\r\n* fix callers info field\r\n\r\n* remove some views\r\n\r\n* add views for hpc debugging\r\n\r\n* a workaround for double variants in annotsv\r\n\r\n* a workaround for double variants in annotsv try 2\r\n\r\n* remove view statements\r\n\r\n* fix join error?\r\n\r\n* fix some linting issues\r\n\r\n* don't test gridss\r\n\r\n* drop pinned nf-test version\r\n\r\n* disable gridss tests for real\r\n\r\n* fix some tests\r\n\r\n* update subwf tests\r\n\r\n* update pipeline tests\r\n\r\n* fix annotate tests?\r\n\r\n* fix annotate tests again?\r\n\r\n* add views to annotation test\r\n\r\n* fix join error + fix test jasmine\r\n\r\n* revert join error changes?\r\n\r\n* another try to fix weird join error\r\n\r\n* join error fix try 3\r\n\r\n* join error fix try 4\r\n\r\n* join error fix try 5\r\n\r\n* join error fix try 6\r\n\r\n* join error fix try 7\r\n\r\n* Template v2.13.1 sync + update all modules (#73)\r\n\r\n* Template update for nf-core/tools version 2.6\r\n\r\n* Template update for nf-core/tools version 2.7.2\r\n\r\n* update pipeline name\r\n\r\n* update test-data repo name\r\n\r\n* update test data config name\r\n\r\n* update pipeline name\r\n\r\n* update pipeline name\r\n\r\n* update nf-core yaml\r\n\r\n* Template update for nf-core/tools version 2.13.1\r\n\r\n* Merge branch 'TEMPLATE' into template-v2.13.1-sync\r\n\r\n* fix some linting issues\r\n\r\n* update all modules\r\n\r\n* fix subwf in modules json\r\n\r\n* remove unused code\r\n\r\n* remove unused code\r\n\r\n* fix jasminesv\r\n\r\n* fix eclint\r\n\r\n* prettier\r\n\r\n* have nf-test in the CI\r\n\r\n* fix samtools convert stub\r\n\r\n* prettier\r\n\r\n* fix tabix outputs + tests\r\n\r\n* update test snapshots\r\n\r\n* remove views\r\n\r\n* rearrange 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