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stjude
/
XenoCP
A cloud-based tool for mouse read cleansing in xenograft samples
Apache License 2.0
5
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3
forks
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Remove extra quotes and name derived table
#54
mellypop
closed
1 week ago
0
Explicitly declare insert columns
#53
mellypop
closed
1 week ago
0
Job keeps failing
#52
bounlu
closed
9 months ago
0
Add Singularity support
#51
mcrusch
closed
11 months ago
1
Fixed local build.
#50
mcrusch
closed
12 months ago
0
Recent Issues
#49
adthrasher
closed
11 months ago
1
No space left on device
#48
zhaowsong
closed
11 months ago
6
Add build.gradle version update
#47
adthrasher
closed
12 months ago
0
Update build to work with gradle >= 7
#46
mcrusch
closed
12 months ago
1
Tie BAM is too large
#45
mcrusch
closed
11 months ago
1
Limit the memory usage of Xenocp
#44
zhaowsong
closed
11 months ago
5
Update sample_data to reflect merged tie bams and contam lists
#43
mcrusch
closed
11 months ago
0
Clean BAM is larger than raw BAM files
#42
zhaowsong
closed
12 months ago
5
input yaml file
#41
zhaowsong
closed
1 year ago
0
fix: remove root dependency
#40
adthrasher
closed
1 year ago
0
Run command with Singularity will miss python packages.
#39
Autumn-Roy
closed
1 year ago
7
Rewrite BAM header
#38
adthrasher
opened
1 year ago
1
Point to updated STAR release
#37
adthrasher
closed
1 year ago
0
Bump action version. Update for master->main.
#36
adthrasher
closed
1 year ago
0
Update loadable refs to read_group refs
#35
mellypop
closed
1 week ago
1
Remove docker tag check from master.
#34
adthrasher
closed
2 years ago
0
Update bam insert statement to include new required data
#33
mellypop
closed
1 week ago
0
Commit missing CWL script
#32
adthrasher
closed
3 years ago
0
Combine tie bams and contam lists. Point WDL workflows to GitHub container registry.
#31
adthrasher
closed
3 years ago
0
Fix contamination list extension
#30
adthrasher
closed
3 years ago
0
Updated DX app for multiple mappers and references. Add memory requir…
#29
adthrasher
closed
3 years ago
0
wdl/tools: XenoCP 3.1.4 tasks use 3.1.0 container image
#28
zaeleus
closed
3 years ago
1
Update Docker build action to v2. Add release build to GitHub Container Registry.
#27
adthrasher
closed
3 years ago
0
Remove CIGAR strings for unmapped reads.
#26
claymcleod
closed
3 years ago
1
`MC` record data field not removed from unmapped records in final merged BAM
#25
zaeleus
closed
3 years ago
4
Add option at workflow level to skip duplicate marking
#24
adthrasher
closed
3 years ago
0
Wdl workflow
#23
adthrasher
closed
3 years ago
1
feat: add aligner options to DNAnexus app
#22
adthrasher
closed
3 years ago
0
fix: Explicitly sort contamination bams by queryname.
#21
adthrasher
closed
3 years ago
0
Docker builds
#20
adthrasher
closed
3 years ago
1
Add templates for issues and PRs
#19
adthrasher
closed
3 years ago
1
Adding support for multiple mappers
#18
adthrasher
closed
3 years ago
0
Updating schema.org URLs
#17
adthrasher
closed
3 years ago
0
Extract unmapped reads and pass through to merge step.
#16
adthrasher
closed
3 years ago
1
Singularity build of XenoCP
#15
adthrasher
closed
4 years ago
0
Identification of mouse reads
#14
RaphaelHablesreiter
closed
4 years ago
8
switch to https://schema.org/version/latest/schema.rdf
#13
mr-c
closed
4 years ago
0
running xenocp with singularity
#12
xinyuwen
closed
4 years ago
10
Error: Could not find or load main class org.stjude.compbio.sam.TweakSam
#11
lentaing
closed
4 years ago
3
Use sambamba to extract unmapped reads and then merge back in during …
#10
adthrasher
closed
3 years ago
2
Bug: unmapped read pairs are not preserved in output
#9
mcrusch
closed
3 years ago
2
docker: Install Python dependencies in builder stage
#8
zaeleus
closed
3 years ago
0
Readme and license
#7
adthrasher
closed
5 years ago
1
docker: Remove awk symlink
#6
zaeleus
closed
5 years ago
0
Added DNAnexus app files
#5
mcrusch
closed
5 years ago
0
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