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iqbal-lab-org
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clockwork
CRyPTIC data processing pipelines
MIT License
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#125
mbhall88
closed
1 month ago
2
Expose filter opts
#124
martinghunt
closed
2 months ago
0
Error running this command: fqtools count
#123
mansi-aai
closed
8 months ago
7
Some questions about the *.decontam.counts.tsv ?
#122
Huicen01
closed
10 months ago
4
Why map to the H37Rv reference genome twice using minimap?
#121
Huicen01
closed
10 months ago
6
ENA submission fixes
#120
martinghunt
closed
10 months ago
0
Error running this command: /bioinf-tools/cortex/scripts/calling/run_calls.pl
#119
Huicen01
closed
10 months ago
11
Add tag DP_ACGT to GVCF
#118
martinghunt
closed
1 year ago
0
Bug fix merging flags when not rmdup/markdup
#117
martinghunt
closed
1 year ago
0
AssertionError: When I run clockwork remove_contam command
#116
Huicen01
closed
1 year ago
5
Handle cortex fails in variant call script
#115
martinghunt
closed
1 year ago
0
Samples with a small number of reads causes Clockwork to crash
#114
marc-brouard
closed
1 year ago
1
enaDataGet not working: HTTP Error 400
#113
rpalcab
closed
1 year ago
2
Varcall no trim option
#112
martinghunt
closed
1 year ago
0
Make gvcf/fasta during var call one sample pipeline
#111
martinghunt
closed
1 year ago
0
force nextflow version 22.10.0 so dsl1 works
#110
martinghunt
closed
1 year ago
0
Update nextflow to scripts to use dsl2
#109
martinghunt
closed
1 year ago
0
update human assembly to CHM13
#108
mbhall88
closed
1 year ago
3
the minimum read depth for variant calling
#107
alantsangmb
closed
1 year ago
3
maximize cores and threads when running pipeline
#106
dhcvn
closed
1 year ago
7
Missed INH-R caused by deletion of the entire katG gene
#105
xrazmo
closed
1 year ago
6
approach to classify mutations
#104
alantsangmb
opened
1 year ago
5
QC pipeline with script only
#103
khoahoc0508
opened
1 year ago
4
ERROR : Unknown image format/type
#102
DOH-KEW4303
opened
1 year ago
4
gnuplot error libQt5Core.so.5: cannot open shared object file: No such file or directory
#101
mehc555
opened
1 year ago
1
HMPDACC downloads not working
#100
whottel
closed
1 year ago
2
rename VCF, instead of rsync and then delete
#99
martinghunt
closed
2 years ago
1
I don't know what's wrong
#98
s1df4i
closed
2 years ago
3
Error connecting to database
#97
pedrodcb
closed
1 year ago
1
GitHub actions
#96
martinghunt
closed
2 years ago
0
Software updates
#95
martinghunt
closed
2 years ago
0
Error when running qc.nf
#94
dpenas-u
closed
2 years ago
4
Download NTM reference database error
#93
khoahoc0508
closed
2 years ago
7
How to access the output?
#92
Mor-Rubinsteinn
closed
1 year ago
2
API rate limit exceeded -- Provide your GitHub user name and password to get a higher rate limit
#91
lily616
closed
2 years ago
1
error in download the reference data
#90
dhcvn
closed
2 years ago
7
bufio.Scanner: token too long
#89
YuanDaoDao001
opened
2 years ago
0
Upgrade enaBrowserTools to v1.6
#88
Zhicheng-Liu
opened
3 years ago
0
Fix gramtools build
#87
martinghunt
closed
3 years ago
0
Singularity Build gramtools issue
#86
mezewudo
closed
3 years ago
0
Error when removing contamination
#85
carolynzy
opened
3 years ago
0
Issue while reference_prepare
#84
carolynzy
closed
3 years ago
2
Installation error
#83
dhcvn
closed
1 year ago
8
Update minos to v0.11.0
#82
martinghunt
closed
3 years ago
0
Fix ENA rest api calls
#81
martinghunt
closed
3 years ago
0
Coverage QC stats
#80
jeff-k
opened
3 years ago
0
Clobber (and warn about) existing output directories instead of bailing
#79
jeff-k
opened
3 years ago
2
Multi-threading option for running decontamination analysis
#78
mezewudo
closed
4 years ago
2
Remove_contamination command throws up AssertionError
#77
mezewudo
closed
4 years ago
21
make NTMs contamination
#76
mbhall88
closed
4 years ago
1
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