tomte - Snowball

What's Changed

• Add nf-test alignment subworkflow by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/209
• Add nf-test prepare_references subworkflow by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/214
• nf-test subworklow analyse transcript by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/217
• nf-test call_variant by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/218
• nf-test bam_qc by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/219
• nf-test allele specific calling by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/220
• nf-test annotate_snv by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/221
• nf-test download references and fixed stubs by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/223
• nf-test igv tracks by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/222
• add nf-tests for modules part i by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/225
• add nf-tests for modules part ii - drop by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/226
• Change local module for nf core ones by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/227
• add nf-tests for modules part iii - downloads by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/228
• Run tests only when something changes by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/231
• nf-test callvariantsgatk by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/229
• remove extwhen i - prepare_references by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/232
• remove extwhen ii - download_references by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/233
• remove extwhen iii - alignment by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/234
• remove extwhen iv - analyse_transcripts by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/235
• remove extwhen v - annotate_snv by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/236
• Remove remaining extwhen by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/237
• fix nextflow language local modules/subworkflow by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/239
• Merging template updates 3.3.1 by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/242
• Nf core template merge 3.3.1 by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/241
• Merging template updates v3.3.2 by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/245
• Nf core template merge 3.3.2 by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/243
• updated output.md and parameter.md by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/246
• Prepare release 4.0.0 by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/247
• Solve conflicts release 4.0.0 by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/250
• Reviewing release 4.0.0 by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/254
• Release 4.0.0 by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/248

Full Changelog: https://github.com/genomic-medicine-sweden/tomte/compare/3.0.1...4.0.0

- Nextflow
Published by Lucpen 7 months ago

tomte - Snowman

What's Changed

• Making a release to fix to the bug solved in #206. DROP expression outliers previously returned max 20 lowest p-value entries. Now it returns those classified as having aberrant expression first, and then fills up to 20 from those with lowest p-values. #210

Full Changelog: https://github.com/genomic-medicine-sweden/tomte/compare/3.0.0...3.0.1

- Nextflow
Published by Lucpen 11 months ago

tomte - ThreeKings

What's Changed

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

New Contributors

• @Jakob37 made their first contribution in https://github.com/genomic-medicine-sweden/tomte/pull/168

Full Changelog: https://github.com/genomic-medicine-sweden/tomte/compare/2.2.1...3.0.0

- Nextflow
Published by Lucpen over 1 year ago

tomte - Scrooge

What's Changed

• Merge pull request #154 from genomic-medicine-sweden/dev by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/155
• fixing multiqc by @Lucpen in https://github.com/genomic-medicine-sweden/tomte/pull/156

Full Changelog: https://github.com/genomic-medicine-sweden/tomte/compare/2.2.0...2.2.1

- Nextflow
Published by Lucpen over 1 year ago

tomte - TioDeNadal

What's Changed

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

Full Changelog: https://github.com/genomic-medicine-sweden/tomte/compare/2.1.0...2.2.0

- Nextflow
Published by Lucpen over 1 year ago

tomte - Elf

What's Changed

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

New Contributors

• @pbiology made their first contribution in https://github.com/genomic-medicine-sweden/tomte/pull/118

Full Changelog: https://github.com/genomic-medicine-sweden/tomte/compare/2.0.1...2.1.0

- Nextflow
Published by Lucpen over 1 year ago

tomte - Grinch

What's Changed

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

Full Changelog: https://github.com/genomic-medicine-sweden/tomte/compare/2.0.0...2.0.1

- Nextflow
Published by Lucpen almost 2 years ago

tomte - Santa

What's Changed

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

Full Changelog: https://github.com/genomic-medicine-sweden/tomte/compare/1.1.0...2.0.0

- Nextflow
Published by Lucpen almost 2 years ago

tomte - Rudolph

Added

• switchvep, switchbuildtracks and switchstringtie 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, starindex, salmonindex, 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 (subsampleregionswitch, downsampleswitch, rundropaeswitch and rundropasswitch) so that they all start with switch* (switchsubsampleregion, switchdownsample, switchdropae and switchdropas) #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

- Nextflow
Published by Lucpen almost 2 years ago

tomte - Nisse

First release of tomte!

- Nextflow
Published by Lucpen over 2 years ago