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sanger-bentley-group
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gps-pipeline
Nextflow Pipeline for processing Streptococcus pneumoniae sequencing raw reads (FASTQ files) by the GPS Project (Global Pneumococcal Sequencing Project)
GNU General Public License v3.0
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Bump version to 1.0.0-rc10
#120
HarryHung
closed
3 weeks ago
0
Release Version 1.0.0-rc10
#119
HarryHung
closed
3 weeks ago
0
Update bundled Nextflow to 24.04.4
#118
HarryHung
closed
3 weeks ago
0
Updating mlst image with MLST database built in 2024 July
#117
HarryHung
closed
3 weeks ago
0
Nextflow update to 24.04.3
#116
HarryHung
closed
3 weeks ago
0
.refs is no longer required for PopPUNK database
#115
HarryHung
closed
3 weeks ago
0
Update PopPUNK Database to GPS v9
#114
HarryHung
closed
3 weeks ago
0
Shovill Appears to be Not Working
#113
fugunokaraage
opened
1 month ago
5
Bump version to 1.0.0-rc9
#112
HarryHung
closed
2 months ago
0
Release Version 1.0.0-rc9
#111
HarryHung
closed
2 months ago
0
Switch to Docker Compose v2
#110
HarryHung
closed
2 months ago
0
Fix minor issues in ARIBA database and logic
#109
HarryHung
closed
2 months ago
0
Issue with running GPS pipeline
#108
TNVN2022
closed
2 months ago
22
Hotfix: Fix incorrect thread count issue of LSF profile
#107
HarryHung
closed
2 months ago
0
Release Version 1.0.0-rc8
#106
HarryHung
closed
2 months ago
0
Update bundled Nextflow executable to `24.04.2`
#105
HarryHung
closed
2 months ago
0
Save actual assembler thread count when all available are used
#104
HarryHung
closed
2 months ago
0
Change to a safer version matching operator
#103
HarryHung
closed
3 months ago
0
Fix empty unpaired reads crashing Unicycler
#102
HarryHung
closed
3 months ago
0
Use `workflow.container` introspection to acquire image/container information
#101
HarryHung
closed
3 months ago
0
suggestions to singularity preflight
#100
Phuong-Le
closed
3 months ago
3
Release Version 1.0.0-rc7
#99
HarryHung
closed
4 months ago
0
Fixing GPSC assignment for samples with filename with dot
#98
HarryHung
closed
4 months ago
0
Release Version 1.0.0-rc6
#97
HarryHung
closed
4 months ago
0
Proper 23s rRNA mutation-based ERY+CLI resistance detection
#96
HarryHung
closed
4 months ago
0
Cannot download seroBA database
#95
fugunokaraage
closed
5 months ago
1
Release Version 1.0.0-rc5
#94
HarryHung
closed
5 months ago
0
Allow optional assembler thread count option
#93
HarryHung
closed
5 months ago
0
Update SeroBA and its database to v1.0.7
#92
HarryHung
closed
5 months ago
1
Release Version 1.0.0-rc4
#91
HarryHung
closed
6 months ago
0
Input File Validation
#90
HarryHung
closed
6 months ago
0
Hotfix: Update on storage details
#89
HarryHung
closed
7 months ago
0
Update on storage details
#88
HarryHung
closed
7 months ago
0
Release Version 1.0.0-rc3
#87
HarryHung
closed
7 months ago
0
Proper implementation of dynamic retry directive
#86
HarryHung
closed
7 months ago
0
Update PopPUNK database to GPS v8 (reference only) database
#85
HarryHung
closed
7 months ago
0
Add inferred Minimum Inhibitory Concentration to Other AMR
#84
HarryHung
closed
8 months ago
0
Change name to `GPS Pipeline` from `GPS Unified Pipeline`
#83
HarryHung
closed
8 months ago
0
Release Version 1.0.0-rc2
#82
HarryHung
closed
9 months ago
0
Optional test input
#81
HarryHung
closed
9 months ago
0
Fix: ref_start and ref_end could be non-numeric
#80
HarryHung
closed
9 months ago
0
Improve variant detection
#79
HarryHung
closed
10 months ago
0
Update the included Nextflow Executable to 23.10.0
#78
HarryHung
closed
10 months ago
0
SeroBA v1.0.5 update
#77
HarryHung
closed
10 months ago
0
Unify relational operators
#76
HarryHung
closed
10 months ago
0
Add top non-Strep genus check as extra Taxonomy QC
#75
HarryHung
closed
10 months ago
0
Update SeroBA and spn-pbp-amr images, rework SeroBA database creation
#74
HarryHung
closed
10 months ago
0
Add mapped read depth check for gene detection
#73
HarryHung
closed
10 months ago
0
Improve stability of report generation
#72
HarryHung
closed
11 months ago
0
Correct folP variant nucleotide range
#71
HarryHung
closed
11 months ago
0
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