issues
search
ohsu-cedar-comp-hub
/
WGS-nextflow-workflow
Apache License 2.0
3
stars
1
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Write Nextflow bcftools processes
#44
elisabethgoldman
closed
4 months ago
0
[WIP] Sliced fastq test
#43
rlancaster96
closed
5 months ago
0
Snpeff docker/singularity
#42
rlancaster96
closed
5 months ago
0
added mutect split by chromosome tool and workflow
#41
grie2448
opened
5 months ago
0
details to setup
#40
jordan2lee
closed
5 months ago
0
trimmomatic java -jar call in nf file
#39
rlancaster96
closed
5 months ago
1
trimmomatic docker/sif
#38
rlancaster96
closed
5 months ago
2
update bcftools dockerfile
#37
rlancaster96
closed
5 months ago
0
bcftools docker/sif image
#36
rlancaster96
closed
5 months ago
0
test files: chr19 and chr20 truth vcf liftover
#35
rlancaster96
closed
5 months ago
6
update gatk dockerfile
#34
rlancaster96
closed
5 months ago
4
fastqc image discrepancies
#33
rlancaster96
closed
5 months ago
6
calc contamination and get pileup summaries
#32
rlancaster96
closed
5 months ago
0
Mutect Scatter/Gather
#31
kellrott
closed
4 months ago
0
[WIP] Generate genomic interval files
#30
elisabethgoldman
closed
5 months ago
0
update mark_duplicates and bwamem
#29
rlancaster96
closed
5 months ago
0
run other vcf checks
#28
jordan2lee
closed
6 months ago
0
added bcftools workflow and tool
#27
grie2448
closed
6 months ago
0
allele frequency scripts
#26
jordan2lee
closed
6 months ago
0
Test docker
#25
rlancaster96
closed
5 months ago
0
Add sync to local script
#24
grie2448
closed
6 months ago
0
[WIP] Added variant calling and annotation workflow details to README
#23
elisabethgoldman
closed
5 months ago
0
Params templates for matched tumor and normal
#22
elisabethgoldman
closed
5 months ago
0
Params template
#21
elisabethgoldman
closed
6 months ago
1
FastQC Dockerfile
#20
elisabethgoldman
closed
6 months ago
0
add BCFtools to workflow
#19
elisabethgoldman
closed
6 months ago
0
Create templating script for params file
#18
elisabethgoldman
closed
5 months ago
1
[WIP] Outline alignment pipeline
#17
rlancaster96
closed
5 months ago
1
Outline variant calling pipeline
#16
elisabethgoldman
closed
5 months ago
1
Add Nextflow liinting for PR
#15
kellrott
closed
2 months ago
1
GATK docker image
#14
kellrott
closed
5 months ago
4
Outline Alignment Pipeline
#13
kellrott
closed
5 months ago
1
Document Fastqc workflow
#12
kellrott
closed
2 months ago
1
Cleanup tools directory
#11
kellrott
closed
6 months ago
0
[WIP] Cleanup
#10
kellrott
closed
6 months ago
0
Organize reference folder
#9
kellrott
closed
6 months ago
0
Setup new test files
#8
kellrott
closed
6 months ago
1
Mutect Dockerfile
#7
kellrott
closed
5 months ago
1
Fastqc Dockerfile
#6
kellrott
closed
6 months ago
1
BWA Dockerfile
#5
kellrott
closed
5 months ago
1
merge branches
#4
elisabethgoldman
closed
6 months ago
0
Cleanup and organize recently added files
#3
elisabethgoldman
closed
6 months ago
0
[WIP] Cleanup
#2
kellrott
closed
6 months ago
0
Update Full_script_build.nf
#1
elisabethgoldman
closed
6 months ago
0
Previous