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poreCov
SARS-CoV-2 workflow for nanopore sequence data
https://case-group.github.io/
GNU General Public License v3.0
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Add del to json
#126
DataSpott
closed
3 years ago
1
Expand test_fastq-profile to generate json-outputs
#125
DataSpott
closed
2 years ago
1
Add Deletions to json-output
#124
DataSpott
closed
3 years ago
0
Running pipeline on Bascalled/Demultiplexed samples
#123
IFIK-virology
closed
3 years ago
3
Split fasta improvment
#122
DataSpott
closed
3 years ago
2
Dev myc
#121
replikation
closed
3 years ago
0
rewrote json-parser in python & integrated it
#120
DataSpott
closed
3 years ago
0
Covarplot & Reference BAM output
#119
hoelzer
closed
3 years ago
7
new pangolin version with new "column names"
#118
replikation
closed
3 years ago
4
V1200 read length parameter & guppy update
#117
replikation
closed
3 years ago
6
--minLength and --maxLength are overwritten when using the 1200 bp amplicon scheme (--primerV V1200) flag
#116
k8r3l
closed
3 years ago
7
Guppy CPU
#115
hoelzer
closed
3 years ago
6
rki_report patch
#114
DataSpott
closed
3 years ago
0
report - column header states mutations (on spike), but lists other genes
#113
oliverdrechsel
closed
3 years ago
2
Slurm support
#112
KevinMenden
closed
3 years ago
2
all_consensi vs all_consensus
#111
oliverdrechsel
closed
3 years ago
4
Update president QC
#110
hoelzer
closed
2 years ago
6
fixed typo
#109
RaverJay
closed
3 years ago
0
merge PRs
#108
RaverJay
closed
3 years ago
0
auto get latest pangolin container / Add pangolearn version
#107
RaverJay
closed
3 years ago
3
auto get latest pangolin container -> release 0.8.0
#106
replikation
closed
3 years ago
14
Guppy sequ kit
#105
DataSpott
closed
3 years ago
2
update pangoLEARN
#104
hoelzer
closed
3 years ago
0
latest pangolin
#103
replikation
closed
3 years ago
5
Update guppy GPU and CPU version
#102
hoelzer
closed
3 years ago
5
Singularity allow "--userns"
#101
KeyTals
closed
3 years ago
4
auto detect if fastq_pass was basecalled or not
#100
replikation
closed
3 years ago
0
Additional coverage visualization w/ ARTIC amplicon positions
#99
hoelzer
closed
3 years ago
0
dry-run for gitaction
#98
replikation
closed
3 years ago
0
wrong alignment view in IGV when there is a deletion in the SARS-CoV-2 samples
#97
natinreg
closed
3 years ago
5
Parameter optimization
#96
replikation
closed
3 years ago
4
nanopolish wo basecalling, improv errorhandling
#95
replikation
closed
3 years ago
5
Provide `--fastq_pass` AND `--fast5` to`--nanopolish`
#94
iferres
closed
3 years ago
4
Add all samples from samples.csv to report table
#93
RaverJay
closed
3 years ago
8
samples from samplesheet.yml are not reported
#92
oliverdrechsel
closed
3 years ago
3
Add raw data table output
#91
RaverJay
closed
3 years ago
3
Nanopolish implement
#90
replikation
closed
3 years ago
4
Warning when older version of pipeline is used
#89
hoelzer
closed
3 years ago
4
Summary report also in text table format
#88
hoelzer
closed
3 years ago
5
nanopolish addition beside medaka
#87
replikation
closed
3 years ago
1
more verbose error messages if the sample input is faulty or wrong
#86
replikation
closed
3 years ago
0
up pangolin
#85
hoelzer
closed
3 years ago
0
up pangolin
#84
hoelzer
closed
3 years ago
0
store singletons that passed qc
#83
hoelzer
closed
3 years ago
0
Report Insertions as well
#82
hoelzer
closed
2 years ago
13
Local cloud
#81
replikation
closed
3 years ago
1
Create .gitattributes
#80
RaverJay
closed
3 years ago
0
fixed kreport aggregation
#79
RaverJay
closed
3 years ago
1
Fixes error with only integer-like sample names
#78
RaverJay
closed
3 years ago
0
Module and subworkflow structure
#77
hoelzer
closed
3 years ago
2
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