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maxplanck-ie
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snakepipes
Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
MIT License
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Question regarding spikeIns
#925
sunta3iouxos
closed
9 months ago
1
no spikeIn chromosomes found with extention _spikein
#924
sunta3iouxos
opened
11 months ago
12
Removed mode Gruen from scRNAseq entirely
#923
katsikora
closed
11 months ago
0
updated documentation after moving SalmonIndex
#922
katsikora
closed
11 months ago
0
rename `--skipVelocyto` to sth like `--skipVelocityCounts`
#921
katsikora
closed
11 months ago
0
reason: Missing output files
#920
sunta3iouxos
closed
11 months ago
2
WorkflowError in line 187
#919
sunta3iouxos
closed
11 months ago
2
possibility to have readable envs?
#918
sunta3iouxos
closed
11 months ago
1
how does snakePipes find and reports contaminations?
#917
sunta3iouxos
closed
11 months ago
7
Fix docs build
#916
adRn-s
closed
11 months ago
0
noncoding-RNA-seq test data
#915
roddypr
closed
11 months ago
2
difference in conda env hashes between snakePipes and snakemake
#914
katsikora
opened
11 months ago
1
Move salmon index from mRNAseq/scRNAseq to createIndices
#913
katsikora
closed
11 months ago
1
Fix 857
#912
katsikora
closed
12 months ago
0
Fix 880
#911
katsikora
closed
12 months ago
0
ATAC example miss /bamCoverage/*.filtered.seq_depth_norm.bw files
#910
HamletShaoE
opened
1 year ago
5
setting for cutandrun
#909
sunta3iouxos
closed
12 months ago
2
createIndices: error: unrecognized arguments: h38
#908
Ci-TJ
closed
1 year ago
1
DNA-mapping workflow gives an error related to number of CPUs per node
#907
re-rosales
closed
12 months ago
2
CICD updates
#906
WardDeb
closed
1 year ago
0
Fix895 ks
#905
katsikora
closed
1 year ago
0
Fix889
#904
katsikora
closed
1 year ago
0
conda envs get re-created by another user of the same group
#903
katsikora
opened
1 year ago
1
old GH action was deprecated
#902
adRn-s
closed
1 year ago
0
CI dag test
#901
WardDeb
opened
1 year ago
1
Develop
#900
katsikora
closed
1 year ago
0
Dev wd
#899
WardDeb
closed
1 year ago
0
Error in WGBS workflow (invalid 'times' argument)
#898
kaznt
closed
12 months ago
12
Update column offset nearestGene.R
#897
rbrauning
opened
1 year ago
0
snakePipes createEnvs - missing mamba not reported. mamba in base
#896
mirax87
closed
12 months ago
11
revisit qc when using spikein for norm/ cutntag
#895
katsikora
closed
12 months ago
0
3primeseq question
#894
sunta3iouxos
closed
12 months ago
1
3primeseq ks
#893
katsikora
closed
1 year ago
0
Merge the latest bugfix release into develop
#892
katsikora
closed
1 year ago
0
3primeseq
#891
dkoppstein
closed
1 year ago
0
DAG printing breaks for ChIP-seq with --cutntag --useSpikeInForNorm
#890
katsikora
closed
12 months ago
1
Sambamba flagstat (sorted)
#889
katsikora
closed
12 months ago
0
update snakemake and implement native slurm support
#888
katsikora
opened
1 year ago
0
DNA-mapping pipeline gets stuck at origFASTQ rule when using a custom cluster config yaml
#887
TobiasHohl
opened
1 year ago
4
Error with DNA mapping workflow: [main_samview] fail to read the header from "-"
#886
chondammab
closed
1 year ago
3
Fix #884
#885
katsikora
closed
1 year ago
3
createEnvs fails when channel_priority set to 'strict'
#884
isaacvock
closed
1 year ago
2
Conda dir
#883
katsikora
closed
1 year ago
0
bumped bugfix version
#882
katsikora
closed
1 year ago
0
Check for valid fastq files before workflow execution
#881
WardDeb
closed
1 year ago
2
How is memory allocation propagated?
#880
half-adder
closed
12 months ago
1
Develop
#879
katsikora
closed
1 year ago
0
update and reformat documentation
#878
katsikora
opened
1 year ago
0
Fix871 ks
#877
katsikora
opened
1 year ago
0
Config ks
#876
katsikora
closed
1 year ago
0
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