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wtsi-npg
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p4
Process and Pipe Pipeline Panacea
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Stage2 init options
#349
dozy
closed
2 days ago
1
P4 stage2 init options
#348
dozy
opened
2 weeks ago
0
prep release 0.40.0
#347
dozy
closed
1 month ago
0
update container labels
#346
avnishsinghh
closed
1 month ago
0
Docker with bwa mem2, new bambi
#345
dozy
closed
1 month ago
0
add bwa-mem2 to Dockerfile
#344
dozy
closed
1 month ago
1
Fix various missing items
#343
kjsanger
closed
2 months ago
1
Allow a more recent Test::Compile
#342
kjsanger
closed
2 months ago
0
Very old Test::Compile being used
#341
kjsanger
opened
2 months ago
2
Container needs adjustments for PATH so viv.pl and vtfp.pl are available
#340
jmtcsngr
opened
3 months ago
0
Container may need explicit export PERL5LIB
#339
jmtcsngr
opened
3 months ago
0
Publish docker image
#338
avnishsinghh
closed
3 months ago
0
Add Dockerfile installing p4 and a variety of tools
#337
kjsanger
closed
3 months ago
1
extend chmod of STAR directory to use g-s
#336
dozy
closed
3 months ago
0
prep release 0.39.0
#335
dozy
closed
6 months ago
0
first try at adding stage2 preprocessing options
#334
dozy
opened
7 months ago
0
prep for release 0.38.0 (merge devel to master)
#333
dozy
closed
9 months ago
0
bam and cram index creation changes
#332
dozy
closed
7 months ago
1
add optional stage1 methods to allow analysis using product crams as input (instead of default BCL)
#331
dozy
opened
9 months ago
0
inheritance of undef parameter values bug
#330
dozy
opened
9 months ago
1
produce cram index files with samtools
#329
dozy
closed
8 months ago
1
add additional autosome specific coverage threshold
#328
ces
closed
10 months ago
0
add primer_clip_unmap_len_flag and primer_clip_arbitrary_flags to sam…
#327
dozy
opened
11 months ago
0
release 0.37.2 prep
#326
dozy
closed
11 months ago
0
change bambi i2b command (--nocall-quality)
#325
dozy
closed
1 year ago
0
release 0.37.1 prep (merge devel to master)
#324
dozy
closed
1 year ago
0
amend markdup_duplexseq (nanoseq) method to use:
#323
dozy
closed
1 year ago
0
devel to master (release 0.37.0 prep)
#322
dozy
closed
1 year ago
0
add i2b_nocall_qual_switch to control the i2b_nocall_qual_flag. Chang…
#321
dozy
closed
1 year ago
0
add --nocall-quality flag (with default value 2) to bambi i2b command
#320
dozy
closed
1 year ago
0
merge devel branch to master branch (release 0.36.0 prep)
#319
dozy
closed
1 year ago
0
add optical duplicates flag for biobambam markdup method
#318
dozy
closed
1 year ago
0
fix non-consented human split with bwa-mem2 target alignment
#317
dozy
closed
1 year ago
0
prep release 0.35.0
#316
dozy
closed
1 year ago
0
remove scramble use from pipeline templates
#315
dozy
closed
1 year ago
1
merge devel to master (release 0.34.0 prep)
#314
dozy
closed
1 year ago
0
add calmd to biobambam,samtools and duplexseq markdup methods
#313
dozy
closed
1 year ago
0
merge devel to master (v0.33.1 prep)
#312
dozy
closed
1 year ago
0
Move from cache@v2 to @v3
#311
kjsanger
closed
1 year ago
0
Move from checkout@v2 to @v3
#310
kjsanger
closed
1 year ago
0
use ubuntu latest in github runners
#309
jmtcsngr
closed
1 year ago
0
prep for release 0.33.0
#308
dozy
closed
1 year ago
0
extend list of preserved auxtags in realignment bamreset
#307
dozy
closed
1 year ago
1
prep for release 0.32.4
#306
dozy
closed
1 year ago
0
prep 0.32.3 release
#305
dozy
closed
1 year ago
0
markdup_method:none for phix and non-consented human split
#304
dozy
closed
2 years ago
0
add maxreadlen flag to bamstreamingduplicates
#303
dozy
closed
1 year ago
0
0.32.2 release prep (devel merge to master)
#302
dozy
closed
2 years ago
0
markdup_none assumes target alignment
#301
dozy
opened
2 years ago
0
Merge aligned samtools
#300
jidur
closed
1 year ago
0
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