Clinical-Genomics-Lund nextflow_wgs issues

Clinical-Genomics-Lund / nextflow_wgs

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annotsv if-statement fixes

#218 ViktorHy closed 2 days ago
0
Test mimisbrunnr as a extra layer of clinical significance for CNVs

#217 ViktorHy opened 3 days ago
2
Order of VCFs to SVDB merge not consistent between subsequent reruns of same sample

#216 alkc opened 4 days ago
0
Downsample mito bams to prevent eklipse crashes

#215 alkc opened 6 days ago
0
Add restart rules to processes

#214 alkc opened 6 days ago
0
Add flag to only output BAM files

#213 alkc opened 2 weeks ago
0
Add flag to stop pipeline when bam + qc has been generated

#212 alkc opened 3 weeks ago
0
Optimizations 202407

#211 ViktorHy closed 1 month ago
1
Custom intervals in update_bed.pl

#210 Jakob37 opened 1 month ago
4
Don't load cases with removed panels

#209 Jakob37 opened 1 month ago
0
Updated deploy script

#208 Jakob37 closed 1 month ago
4
modycf post verification updates

#207 Jakob37 closed 1 month ago
0
Restore GERP annotations

#206 alkc opened 1 month ago
0
GERP annotations missing

#205 alkc opened 1 month ago
0
Enable Chanjo2

#204 Jakob37 closed 2 months ago
0
Profile for solid tumors

#203 Jakob37 opened 2 months ago
0
Disable Chanjo2

#202 Jakob37 closed 2 months ago
0
Mody CF (clean)

#201 Jakob37 closed 2 months ago
2
Memory usage markdup and dnascope

#200 ViktorHy opened 2 months ago
0
Iterating on mody cf

#199 Jakob37 closed 2 months ago
1
Mody-CF update

#198 Jakob37 closed 2 months ago
0
Control CPU / memory allocations from config

#197 Jakob37 opened 2 months ago
0
Update bed file to include custom intervals

#196 Jakob37 opened 3 months ago
0
D4 full coverage

#195 Jakob37 closed 3 months ago
1
Trim checklist template and add validation samples

#194 Jakob37 closed 3 months ago
1
D4 in yaml

#193 Jakob37 closed 3 months ago
0
Added GQ to format field of all individuals via filter_mutect2

#192 ViktorHy closed 3 months ago
8
Verification

#191 Jakob37 closed 1 month ago
0
Revert "Verification"

#190 Jakob37 closed 4 months ago
0
added csv-file path to onComplete

#189 ViktorHy closed 4 months ago
0
Overlapping inversions and deletions

#188 ViktorHy opened 4 months ago
1
Chanjo2 middleman

#187 Jakob37 closed 4 months ago
0
Add rerun custom flag to bjorn+wgs to prevent re-upload into loqusdb

#186 Jakob37 opened 4 months ago
3
For onco, `default_gene_panels` are not included in `gene_panels` in the yaml output

#185 Jakob37 opened 4 months ago
0
myeloid-const fixes to match clarity reanalysis

#184 ViktorHy closed 4 months ago
2
Add VEP111 annotations to rank models

#183 alkc closed 4 months ago
0
WGS trio rank model misses `FILTER` PASS rule found in wgs SNV single rank model

#182 alkc opened 4 months ago
0
Gnomad v4

#181 Jakob37 opened 4 months ago
0
Update rank models with new VEP consequence annotations

#180 alkc opened 5 months ago
0
Streamline PR template

#179 alkc closed 3 months ago
1
d4 coverage calculations into production ol' wgs

#178 Jakob37 closed 4 months ago
0
Update Gnomad SV version

#177 Jakob37 opened 5 months ago
0
Rank model updates for VEP 111

#176 alkc closed 4 months ago
0
Dealing with committed lab IDs in mody cf

#175 Jakob37 opened 5 months ago
0
GQC issue

#174 Jakob37 closed 5 months ago
1
Load MT frequencies into loqusdb

#173 Jakob37 closed 2 months ago
2
Reproducibility issue within same sample/group due to order of inputs to SVDB_merge

#172 alkc opened 5 months ago
1
GATK GQC always cast to int to prevent genmod from ignoring it

#171 alkc closed 5 months ago
3
`GQC` encoded as `float` disables `GATK` caller penalty

#170 alkc closed 5 months ago
0
Starting from bam with modified group/sample ids fails at `build_mitochondrial_qc_json`

#169 alkc opened 5 months ago
1