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biowdl
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070cbb252016d18f59d52e4919a2a267f1c18671
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20
5.29_update
5.31_update
BIOWDL-208
BIOWDL-213
BIOWDL-216
BIOWDL-232
BIOWDL-245
BIOWDL-247
BIOWDL-253
BIOWDL-258
BIOWDL-259
BIOWDL-261
BIOWDL-265
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BIOWDL-279
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17
v5.2.0
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phhv1reassembly
phhv1assembly
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Created with Raphaël 2.2.0
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Merge remote-tracking branch 'origin/develop' into sage
increase resources GRIDSS
Have more records in ram
addPicardDedup
addPicardDedup
Add option to assume sort order
Update Picard and reevaluate use of intel inflater/defaler
Set xmx value properly for UmiAwareMarkDuplicatesWithMateCigar
Use proper encoding
Use set_tag call from pysam
Add format parameter to macs2
Use more conventional list unpacking for clarity
Update changelog
Correct output files
Also create directories
Dedent overindented code
Add umiTagName flag
Add script to extract umi from read name
Allow multiple bam inputs
Make sure task is consistent
update changelog
samtoolsAddOpti…
samtoolsAddOptionalIndexFileAsInput
Merge branch 'develop' into samtoolsAddOptionalIndexFileAsInput
add annotateBamWithUmi
add umiAwareMarkDuplicate
Use mamba-forge and mamba to install dependencies
Merge pull request #295 from biowdl/BIOWDL-576
More correct evaluation of controlBams input
Update changelog
Add time minutes parameter
Add parameter_meta for macs2
Require 5 minutes
BIOWDL-576
BIOWDL-576
Add sampleposition in array task
give dictionary and index to virusbreakend
Merge branch 'develop' into samtoolsAddOptionalIndexFileAsInput
make recovery sv vcf optional in purple
gridss more memory
change gridss runtime settings
use alternative gridss image for virusbreakend
increase gridss memory
increase memory gridss
upgrade gridss to 2.12.2
try version 2.11.1 for gridss
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