ThreeKings

What's Changed

• Merge pull request #157 from genomic-medicine-sweden/dev by @Lucpen in #158
• Update vep to 112 and references encode 46 by @Lucpen in #159
• Adds possibility to make drop database by @Lucpen in #147
• Template update for nf-core/tools version 3.0.2 by @Lucpen in #167
• add parameter --skip_variant_calling by @Lucpen in #169
• make module_to_export_counts_folder by @Lucpen in #172
• Fix versions in multiqc and ymls for drop modules by @Lucpen in #174
• Sex info to DROP by @Jakob37 in #168
• Prepare release 3.0.0 by @Lucpen in #177
• Add documentation by @Lucpen in #178
• bump to version 3.0.0 by @Lucpen in #180
• fix bug running variant calling gatk and fix dev bug in bcf norm by @Lucpen in #182
• change way of adding variant caller to vcf by @Lucpen in #184
• Release 3.0.0 - three kings by @Lucpen in #181
• Merge pull request #181 from genomic-medicine-sweden/dev by @Lucpen in #185

New Contributors

• @Jakob37 made their first contribution in #168

Full Changelog: 2.2.1...3.0.0

Scrooge

What's Changed

• Merge pull request #154 from genomic-medicine-sweden/dev by @Lucpen in #155
• fixing multiqc by @Lucpen in #156

Full Changelog: 2.2.0...2.2.1

TioDeNadal

What's Changed

• Merge pull request #142 from genomic-medicine-sweden/dev by @Lucpen in #143
• fix bootstrapann input by @Lucpen in #151
• Added possibility to download refs by @Lucpen in #149
• Prepare release 2.2.0 by @Lucpen in #153

Full Changelog: 2.1.0...2.2.0

Elf

What's Changed

• Merge pull request #116 from genomic-medicine-sweden/dev by @Lucpen in #117
• Template update nf-core/tools version 2.14.1 by @Lucpen in #123
• Update CODEOWNERS by @pbiology in #118
• Adapt vcf to scout by @Lucpen in #127
• fix bug allelic imbalance by @Lucpen in #129
• camelize drop output column names and update gnu-wget container by @Lucpen in #132
• fix GATKs ASEReadCounter by @Lucpen in #137
• Remove unnecessary tabix by @Lucpen in #140
• Prepare release 2.1.0 by @Lucpen in #141
• Release 2.1.0 by @Lucpen in #142

New Contributors

• @pbiology made their first contribution in #118

Full Changelog: 2.0.1...2.1.0

Grinch

What's Changed

• Merge pull request #113 from genomic-medicine-sweden/dev by @Lucpen in #114
• Publish research file vep by @Lucpen in #115
• Patch release 2.0.1 - Grinch by @Lucpen in #116

Full Changelog: 2.0.0...2.0.1

Santa

What's Changed

• Merge pull request #87 from genomic-medicine-sweden/dev by @Lucpen in #92
• feat updated zenodo by @Lucpen in #94
• fix switch subsampling and downsampling bug by @Lucpen in #97
• Added ci test with all switches off by @Lucpen in #100
• Adding meta by @Lucpen in #101
• fixed asereadcounter by @Lucpen in #103
• Master by @Lucpen in #95
• feat add args to AE and AS by @Lucpen in #104
• Reformatted prepare references subworkflow by @Lucpen in #105
• Update FastQC by @fellen31 in #106
• Make function to branches references into compressed or uncompressed by @Lucpen in #107
• changed parameter names from switch to skip by @Lucpen in #108
• removed vep_filters parameter will now be generated from clinical panel by @Lucpen in #109
• Updated modules by @Lucpen in #110
• feat prepare for release by @Lucpen in #112
• Release 2.0.0 by @Lucpen in #113

Full Changelog: 1.1.0...2.0.0

Rudolph

Added

• switch_vep, switch_build_tracks and switch_stringtie to make the pipeline more versatile #61
• Updated template and nf-tools #65
• Use nf-validation plugin for parameter and samplesheet validation #66
• Installed the nf-core version of ensemblvep/vep module #67
• A new parameter vep_plugin_files to supply files required by vep plugins #67
• The possibility of using igenomes_base to point to a path where genome specific reference files are placed (fasta, fai, gtf, star_index, salmon_index, subsample_bed) #76
• Merging of case's vcf files #80
• Reference list to MultiQC report #88
• Added module to calculate insert size and added results to MultiQC report #90
• Added Zenodo

Fixed

• Renamed the other switches (subsample_region_switch, downsample_switch, run_drop_ae_switch and run_drop_as_switch) so that they all start with switch* (switch_subsample_region, switch_downsample, switch_drop_ae and switch_drop_as) #61
• Separated modules.config into smaller configs #61
• Missing fasta_fai channel when fai file is given #63
• DROP output file columns, removing duplicate column and adding same ids to both AE and AS #68
• Patch tools update and case ID parsing #71
• Naming of DROP output files #72
• VEP plugin schema to allow for directories #74
• Made params.platform into a channel #75
• Changed name of salmon's quant.nf to include sample id #78
• Shortened name of DROP output files #79
• Merging of vcfs has been moved to after bootstrapAnn #81
• Substituted bgzip and tabix modules by bgzip_tabix module #85
• Updated module input channels in the GATK variant calling subworkflow #89

Nisse

First release of tomte!