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LCR-BCCRC
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lcr-modules
Collection of standard analytical pipelines for genomic and transcriptomic data
https://lcr-modules.rtfd.io
MIT License
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7
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Conda environment reproducibility
#329
lkhilton
opened
3 days ago
0
Level 3 modules: correct version in op.setup_module
#328
gillissierra
closed
4 days ago
0
New opv12 env yaml file
#327
lkhilton
closed
1 week ago
0
LymphGen Updates
#326
lkhilton
opened
3 weeks ago
0
Level3 modules new directory for prepare step
#325
gillissierra
closed
1 week ago
1
svar_master liftover step checks that file isn't only header
#324
gillissierra
closed
1 month ago
0
Update documentation
#323
Kdreval
closed
1 month ago
0
Module/rainstorm/1.1 md5sum tracking update
#322
gillissierra
closed
1 month ago
0
vcf2maf can't handle empty deblacklisted maf
#321
Kdreval
closed
1 month ago
1
cutadapt module
#320
Kdreval
closed
1 month ago
1
cutadapt module
#319
Kdreval
closed
1 month ago
0
Updates to bwa and utils modules
#318
Kdreval
closed
1 month ago
2
Ega download module
#317
Kdreval
closed
2 months ago
2
Module/fishhook/1.1 - can now use covariates supplied in yaml
#316
gillissierra
closed
2 months ago
0
Restore missing reference_files changes to oncodrivefml reference rules
#315
lkhilton
closed
3 months ago
0
Add `--vanilla` arg to all `Rscript` commands
#314
lkhilton
closed
4 months ago
0
Small patch for better cram compatibility
#313
lkhilton
closed
4 months ago
0
Introducing: mm10 compatibility!
#312
lkhilton
closed
4 months ago
1
Wrap vcf2maf vep_cache in ancient
#311
lkhilton
closed
4 months ago
0
Fix assertion errors
#310
lkhilton
closed
3 months ago
1
Add ancient flag to cache input
#309
lkhilton
closed
4 months ago
0
Minor patches to lymphgen-2.0
#308
lkhilton
closed
4 months ago
0
Module/fishhook/1.1
#307
gillissierra
closed
5 months ago
0
fishHook - add covariates option
#306
gillissierra
closed
2 months ago
0
fishHook - add gene list
#305
gillissierra
closed
5 months ago
3
Add oncodrivefml env to envs directory
#304
mannycruz
closed
5 months ago
0
Module/igv/1.0
#303
mannycruz
opened
5 months ago
1
Add genome build wildcard to _hotmaps_input_maf rule
#302
mannycruz
closed
5 months ago
0
Module/hotmaps/1.0
#301
mannycruz
closed
5 months ago
1
Module/oncodrivefml/1.0
#300
mannycruz
closed
6 months ago
1
Typo in default config of module/oncodriveclustl/1.0
#299
mannycruz
closed
6 months ago
0
Module/oncodriveclustl/1.0
#298
mannycruz
closed
6 months ago
0
Module/mutsig/1.1
#297
gillissierra
closed
7 months ago
0
Revert "Module/mutsig/1.1"
#296
gillissierra
closed
7 months ago
0
Module/mutsig/1.1
#295
gillissierra
closed
7 months ago
1
restore dnds 1.0
#294
gillissierra
closed
7 months ago
0
Revert "Module/dnds/1.1"
#293
gillissierra
closed
7 months ago
0
Module/dnds/1.1
#292
gillissierra
closed
7 months ago
0
bug fix: handle non-standard bed files in reference workflow
#291
Kdreval
closed
4 months ago
0
Bug fix in QC module
#290
Kdreval
closed
8 months ago
0
bug fix: add missing key in default cnvkit config
#289
Kdreval
closed
9 months ago
0
Demo doesn't dry-run as documented
#288
Pranav-Garg
closed
1 week ago
16
Patch: Changed functions in cnvkit and controlfreec to remove reliance on re…
#287
Jwong684
closed
9 months ago
1
Path sent to liftover has wildcards populated
#286
gillissierra
closed
9 months ago
0
Housekeeping
#285
Kdreval
closed
9 months ago
0
ichorCNA 1.1 update patch
#284
Jwong684
opened
10 months ago
3
Svar fix - empty files are not sent through liftover
#283
gillissierra
closed
10 months ago
0
Small fix needed or annotate rule errors
#282
gillissierra
closed
10 months ago
0
Error handling in svar_master workflow
#281
gillissierra
closed
10 months ago
0
Module/specshla/1.0
#280
Jwong684
closed
10 months ago
0
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