SciLifeLab Sarek issues

SciLifeLab / Sarek

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

https://nf-co.re/sarek

MIT License

132 stars 6 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

error running the test

#815 egenomics closed 4 years ago
4
Errors running sarek with Nextflow 19.07 - command 'ps' not found

#814 lconde-ucl closed 4 years ago
13
VEP only annotates Tumor samples

#813 nicweb closed 4 years ago
5
No variants IDs annotated

#812 silviamorins closed 4 years ago
1
Merge into dev fixes that were merged into master

#811 maxulysse closed 4 years ago
0
fix: Update link to ASCAT loci file for GRCh37

#810 maxulysse closed 5 years ago
0
ASCAT loci for download link timeout

#809 DoaneAS closed 5 years ago
2
BWA map error

#808 fw1121 closed 4 years ago
4
Huge problem with pipeline on Happlotype caller

#807 kokyriakidis closed 4 years ago
1
Error executing process ConcatVCF

#806 silviamorins closed 5 years ago
8
fix path to Rscript

#805 maxulysse closed 5 years ago
0
containerOverrides for AWS BATCH nextflow

#804 Dharmendra-G-1 closed 4 years ago
4
fix VEP containers

#803 maxulysse closed 5 years ago
0
RunVCFTools and RunBcftoolsStats are run twice for the same input

#802 alneberg closed 4 years ago
2
Better uppmax configs

#801 alneberg closed 5 years ago
0
Mutect2 GATK4 with filtering and Panel-Of-Normals

#800 szilvajuhos closed 4 years ago
3
Testing Jenkins

#799 maxulysse closed 5 years ago
3
Can handle both fastq.gz and fq.gz

#798 maxulysse closed 5 years ago
0
fq.gz extension

#797 apeltzer closed 5 years ago
2
Strange VCFTools graphs in MultiQC report

#796 silviamorins closed 4 years ago
1
Fix 0.0X Coverage for targeted Data

#795 apeltzer closed 5 years ago
1
Coverage 0.0X on whole exome sequencing data

#794 silviamorins closed 5 years ago
3
Improve munin configuration

#793 maxulysse closed 5 years ago
0
Annotation with both SnpEff and VEP

#792 kokyriakidis closed 4 years ago
1
Cannnot annotate using CADD

#791 kokyriakidis closed 4 years ago
1
Update docs

#790 maxulysse closed 5 years ago
0
one Conda environment to rule them all

#789 maxulysse closed 5 years ago
4
Fix some bugs on munin

#788 maxulysse closed 5 years ago
0
use -K 100000000 for bwa mem

#787 maxulysse closed 5 years ago
0
Target Bed for HaplotypeCaller

#786 kokyriakidis closed 4 years ago
13
Update GATK TO 4.1.1.0 and include CNN

#785 kokyriakidis closed 5 years ago
1
Update to VEP 96

#784 kokyriakidis closed 4 years ago
2
Mix SIngle end and Paired end data

#783 kokyriakidis closed 4 years ago
2
Missing hints for capital letters required

#782 silviamorins closed 4 years ago
1
Controlfreec

#781 maxulysse closed 5 years ago
3
ERROR: resolved path doesnt match with open path

#780 asura117 closed 4 years ago
17
Warning - access to undefined parameter related to annotation cache

#779 asura117 closed 5 years ago
5
add || true for all tools when gathering versions

#778 maxulysse closed 5 years ago
1
Further improvments on VEP

#777 maxulysse closed 5 years ago
1
CADD

#776 maxulysse closed 5 years ago
1
Update munin configuration

#775 maxulysse closed 5 years ago
0
Markdup java options

#774 maxulysse closed 5 years ago
0
Improve parallelization of preprocessing

#773 maxulysse closed 5 years ago
0
Should we include CADD annotations?

#772 kokyriakidis closed 4 years ago
2
Look into MultiQC report for multi patients TSV

#771 maxulysse closed 4 years ago
1
Should we use -Y option for bwa mem?

#770 maxulysse closed 4 years ago
1
Parallelisation of CreateRecalibrationTable

#769 kokyriakidis closed 4 years ago
3
add sorted list of empty process resource specification to the

#768 KochTobi closed 4 years ago
6
Max CPUs Workstation Utilization

#767 kokyriakidis closed 4 years ago
5
Added `ps` in `r-base` and `runallelecount` containers

#766 maxulysse closed 5 years ago
0