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exomeseq-gatk4
Whole Exome Sequencing in CWL using GATK4
MIT License
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Look into using bio-cwl-tools for tool definitions
#31
johnbradley
opened
4 years ago
0
switch to https://schema.org/version/latest/schema.rdf
#30
johnbradley
closed
4 years ago
1
switch to https://schema.org/version/latest/schema.rdf
#29
mr-c
closed
4 years ago
0
variant recalibration annotation parameters
#28
johnbradley
closed
4 years ago
0
Convert BWA output to BAM and sort simultaneously
#27
jprnz
closed
4 years ago
2
Enabling adapter detection to fastp-pe by default
#26
jprnz
closed
4 years ago
0
fix workflow version strings
#25
johnbradley
closed
4 years ago
0
update version to 2.1.0
#24
johnbradley
closed
4 years ago
0
Increase memory requirements
#23
johnbradley
closed
4 years ago
0
Updates to use fastp instead of fastqc+trim_galore
#22
dleehr
closed
4 years ago
1
remove DP flag from generate_annotations steps
#21
johnbradley
closed
4 years ago
0
save mark duplicate metric reports
#20
johnbradley
closed
4 years ago
0
Record total CPU hours and total storage needed
#19
johnbradley
opened
4 years ago
4
use FastP instead of FastQC and trim_galore
#18
johnbradley
closed
4 years ago
4
Use samtools multithreading capability
#17
johnbradley
closed
4 years ago
2
Keep mark duplicates reports
#16
johnbradley
closed
4 years ago
0
Toil and slurm compatibility changes
#15
johnbradley
closed
4 years ago
0
Sets pipefail on combinefiles.sh script
#14
dleehr
closed
5 years ago
0
Add pipefail to concat-gz-files
#13
dleehr
closed
5 years ago
0
Publish on Dockstore
#12
dleehr
closed
4 years ago
1
Concern over DP annotation used in VariantRecalibration
#11
johnbradley
closed
4 years ago
1
create v2.0.1
#10
johnbradley
closed
5 years ago
0
Update fastqc, trim_galore to improve cache-ability in preprocessing
#9
dleehr
closed
5 years ago
1
joint genotyping fixes
#8
johnbradley
closed
5 years ago
2
User request to workflow stop after initial VCF file
#7
johnbradley
opened
5 years ago
0
gatk4 exomseq error in joint-genotyping
#6
johnbradley
closed
5 years ago
14
Update changelog on 2.0 branch
#5
dleehr
closed
5 years ago
0
Update CHANGELOG with descriptive header and link to original repo
#4
dleehr
closed
5 years ago
0
Add CircleCI config and simple validate script
#3
dleehr
closed
5 years ago
0
Add Changelog
#2
dleehr
closed
5 years ago
1
Organizes exomeseq-gatk4 into new repo structure as 2.0.0
#1
dleehr
closed
5 years ago
2