NCI-CGR GEMSCAN issues - Githubissues

NCI-CGR / GEMSCAN

Joint variant calling with GATK4 HaplotypeCaller, Google DeepVariant 1.0.0 and Strelka2, coordinated via Snakemake.

https://nci-cgr.github.io/GEMSCAN/

MIT License

7 stars 8 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

changed the temp directory for bcftools sort

#45 shukwong closed 6 months ago
0
temp directory is having issues

#44 shukwong opened 6 months ago
1
updated docker images (issue 42)

#43 shukwong closed 6 months ago
0
some docker images are out of date

#42 shukwong closed 6 months ago
3
Merge pull request #1 from NCI-CGR/main

#41 shukwong closed 6 months ago
0
implement Harmonize mode only

#40 shukwong opened 1 year ago
0
The workflow skips many steps if the bed file contains only 1 line

#39 shukwong opened 1 year ago
0
Biowulf

#38 wresch closed 1 year ago
2
Update README.md

#37 komaljain3 closed 2 years ago
0
move Docker registry from quay.io to ghcr.io

#36 shukwong opened 2 years ago
0
prepend_labels for strelka calls runs longer than 2 hours

#35 shukwong opened 2 years ago
2
fixing the symlinks in strelka2_AddSampleName rule

#34 shukwong opened 2 years ago
1
GLnexus merge memory requirements calculation

#33 shukwong opened 2 years ago
0
force samples.txt columns to be str

#32 shukwong closed 2 years ago
0
when sampleID in samples.txt is an integer the workflow fails

#31 shukwong closed 2 years ago
1
handle alternate contigs and scaffolds in bed file

#30 shukwong opened 3 years ago
0
write a script to generate the samples.txt from a directory with BAM/cram files

#29 shukwong opened 3 years ago
0
set default path to glnexus_strelka2_config

#28 shukwong opened 3 years ago
0
fixed rule logic when user wants to run by sample

#27 shukwong closed 3 years ago
0
HaplotypeCaller bySample option error at HC_create_each_sample_manifest

#26 shukwong closed 3 years ago
0
add support for remote files on object store as input on Biowulf

#25 shukwong opened 3 years ago
2
Issue23

#24 shukwong closed 3 years ago
0
add time limit and multithreading to norm_left_align_split rules

#23 shukwong closed 3 years ago
1
create conda wrapper for GLnexus merge

#22 shukwong opened 3 years ago
0
use 90% of the memory allocated to GLnexus to avoid jobs being killed

#21 shukwong closed 3 years ago
0
increase default wall time for slurm config

#20 shukwong closed 3 years ago
1
use bedtools merge to check to see if bed file is sorted

#19 shukwong closed 3 years ago
0
make bed file (and gzipped bed file) optional

#18 shukwong opened 3 years ago
1
make GLnexus memory limit slightly less than glnexus_memGB

#17 shukwong closed 3 years ago
1
bedtools validation only check to make sure the bedfile is sorted

#16 shukwong closed 3 years ago
0
Have option to specify number of cpus by rule in CCAD

#15 shukwong opened 3 years ago
0
Non-clickable link in user document

#14 Binz-Z closed 3 years ago
2
convert runtime in minutes to be number of seconds for ccad profile

#13 shukwong closed 3 years ago
0
runtime not properly mapped in ccad profile

#12 shukwong closed 3 years ago
1
bebops docker image causes "kernel too old" error in CCAD

#11 shukwong closed 3 years ago
1
add checks to make sure the samples.txt file is tab delimited

#10 shukwong opened 3 years ago
2
Issue6

#9 shukwong closed 3 years ago
0
Issue6: added bed file validation rule

#8 shukwong closed 3 years ago
0
Use glnexus for all 3 callers (Issue4)

#7 shukwong closed 3 years ago
0
check for valid bed file before running the pipeline

#6 shukwong closed 3 years ago
1
Which vcf/gvcf files to keep?

#5 shukwong closed 3 years ago
3
Test using glnexus merge to merge HaploytypeCaller gvcf files (instead of combineGVCFs)

#4 shukwong closed 3 years ago
1
allow user to use cram files as input

#3 shukwong closed 3 years ago
1
Reference access permission and GRCh38

#2 Binz-Z closed 3 years ago
0
need to make sure outputDir in config has "/" at the end

#1 shukwong closed 3 years ago
2