bespin-workflows exomeseq-gatk4 issues

bespin-workflows / 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