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moiexpositoalonsolab
/
grenepipe
A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles.
http://grene-net.org
GNU General Public License v3.0
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more problems with version 0.13.1
#58
ospfsg
opened
6 days ago
2
Columns in output file don't add up
#57
Easybel
closed
2 weeks ago
3
problem in running v0.13.1
#56
ospfsg
opened
3 weeks ago
5
Feature request: GenomicsDBImport
#55
DuttaAnik
opened
1 month ago
1
SLURM No wall time information given
#54
RvV1979
opened
1 month ago
1
rerun after deleting input files & server update
#53
RvV1979
closed
1 month ago
5
Workflow fails with contig-group-size != 0
#52
lczech
opened
2 months ago
1
SLURM cluster_config not recognized
#51
meixilin
opened
2 months ago
3
--rerun-incomplete flag repeat mapping step for all samples
#50
athenasyarifa
closed
3 months ago
6
not sure what the issue is
#49
Leovar101
closed
1 month ago
16
permission denied error
#48
Leovar101
closed
3 months ago
5
another type of error
#47
ospfsg
closed
3 months ago
11
a new type of error
#46
ospfsg
closed
6 months ago
1
a new type of error
#45
ospfsg
closed
6 months ago
2
problem with dedup
#44
ospfsg
closed
6 months ago
4
greenepipe run error
#43
ospfsg
closed
6 months ago
5
config file
#42
ospfsg
closed
7 months ago
5
Feature Request: Download reference genome and known variation
#41
pettyalex
closed
3 months ago
2
mamba is difficult to install in grenepipe environment
#40
wangshuangyi
closed
5 months ago
6
merging calls from multiple pipeline runs?
#39
RvV1979
closed
9 months ago
2
Write full executed command for each step to log files for reproducibility
#38
uzbit
closed
10 months ago
3
ModuleNotFoundError: No module named 'chardet'
#37
RvV1979
closed
10 months ago
2
restrict-regions and short contigs
#36
RvV1979
opened
11 months ago
2
Make "trimming-tool" optional
#35
coolkom
closed
3 months ago
4
GRENEPIPE v12.1
#34
mrese001
closed
1 year ago
5
java.lang.OutOfMemoryError: Java heap space
#33
RvV1979
closed
1 year ago
2
PID error
#32
Kkaholoaa
closed
1 year ago
9
MissingRuleException
#31
mrese001
closed
1 year ago
13
Error running toy example
#30
celianeto
closed
1 year ago
6
threads for bwa-mem2 via slurm
#29
RvV1979
closed
1 year ago
2
bwa-mem2 "{tmp}.0000.bam": File exists
#28
RvV1979
closed
1 year ago
5
Error in mapping on cluster
#27
AxelVaillant
closed
1 year ago
6
config file error
#26
BFeldmeyer
closed
1 year ago
5
Versions specified in conda env files and snakemake wrappers lead to conflicts/are not available
#25
akriese
closed
1 year ago
11
Conda installation error
#24
Samarth-T-Setty
closed
2 years ago
7
Run snakemake on Cluster
#23
orangelc1221
closed
2 years ago
3
CondaMemoryError when creating conda envs in cluster
#22
orangelc1221
closed
2 years ago
3
Error while running example
#21
andrewSharo
closed
2 years ago
6
BaseRecalibrator error - needs more readgroup info?
#20
mvdloosdrecht
closed
2 years ago
2
Change link in wiki
#19
Tatianabellagio
closed
2 years ago
1
Call variants being rerun when adding new samples
#18
Brent-Saylor-Canopy
closed
2 years ago
3
freebayes causes early error about number of threads
#17
bensprung
closed
2 years ago
12
Error in picard_collectmultiplemetrics
#16
Brent-Saylor-Canopy
closed
2 years ago
4
support for haploid genomes?
#15
bensprung
closed
2 years ago
8
Updating run with new reads
#14
Brent-Saylor-Canopy
closed
3 years ago
12
feature request: pass local reference genome database to snpEff
#13
bensprung
closed
2 years ago
2
snpEff download directory only works with a trailing slash
#12
bensprung
closed
2 years ago
3
Picard environment not created
#11
henriquevf
closed
2 years ago
8
FastQC on one set of reads only
#10
bensprung
closed
3 years ago
7
CollectMultipleMetrics: there is no package called ‘tidyverse’
#9
bensprung
closed
3 years ago
6
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