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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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Update fastp version
#70
HarryHung
closed
1 year ago
1
Add missing process labels to GET_KRAKEN2_DB
#69
HarryHung
closed
1 year ago
0
Improve schema for NF Tower
#68
HarryHung
closed
1 year ago
0
Update ARIBA Module AMR Detection Mechanism
#67
HarryHung
closed
1 year ago
0
Add information about Nextflow Tower
#66
HarryHung
closed
1 year ago
0
Update ARIBA reference sequences
#65
HarryHung
closed
1 year ago
0
Databases Consolidation
#64
HarryHung
closed
1 year ago
0
Proper Nextflow Tower Support
#63
HarryHung
closed
1 year ago
0
Update mlst image with latest database
#62
HarryHung
closed
1 year ago
0
Improve the robustness of LSF profile
#61
HarryHung
closed
1 year ago
0
Update `README.md` and workflow chart to include Virulence
#60
HarryHung
closed
1 year ago
0
Fix error when Nextflow tries to collect metrics in Python container
#59
HarryHung
closed
1 year ago
0
Revamp output logic and other code improvements
#58
HarryHung
closed
1 year ago
0
Switch other AMR detection to ARIBA-based; Databases saving improvements
#57
HarryHung
closed
1 year ago
0
Release 0.8.2
#56
HarryHung
closed
1 year ago
0
Add SeroBA failure protection and Update SeroBA image
#55
HarryHung
closed
1 year ago
0
Release 0.8.1
#54
HarryHung
closed
1 year ago
0
Bump pipeline version to 0.8.1
#53
HarryHung
closed
1 year ago
0
ERROR ~ Error executing process > 'PIPELINE:SEROTYPE (NP-0087-IDRL-AKU_S92_trimmed)'
#52
Samiah-Kanwar
closed
1 year ago
14
Alternative assembly publish mode
#51
HarryHung
closed
1 year ago
0
Assembler failure protection
#50
HarryHung
closed
1 year ago
0
Revert Clindamycin back to CLI
#49
HarryHung
closed
1 year ago
0
Prevent output column shift caused by , in values
#48
HarryHung
closed
1 year ago
0
Improve workflow chart
#47
HarryHung
closed
1 year ago
0
Update included Nextflow to 23.04.1
#46
HarryHung
closed
1 year ago
0
Release 0.8.0
#45
HarryHung
closed
1 year ago
0
Bump pipeline version to 0.8.0
#44
HarryHung
closed
1 year ago
0
Include container engine information in `info.txt`
#43
HarryHung
closed
1 year ago
0
Reduce Pipeline Storage Footprint and Experimental Storage Reduction Option
#42
HarryHung
closed
1 year ago
0
Update AMR output, abbreviations, and order
#41
HarryHung
closed
1 year ago
0
Change default Kraken 2 database
#40
HarryHung
closed
1 year ago
0
Include storage details in `README.md`
#39
HarryHung
closed
1 year ago
0
Remove SeroBA comment column in `results.csv`
#38
HarryHung
closed
1 year ago
0
Group QC columns together in `result.csv`
#37
HarryHung
closed
1 year ago
0
Add Read QC after preprocess module and before all other modules
#36
HarryHung
closed
1 year ago
0
Proper workaround for SeroBA + Singularity issue
#35
HarryHung
closed
1 year ago
0
Improve LSF stability
#34
HarryHung
closed
1 year ago
0
Add workaround for Seroba + Singularity issue
#33
HarryHung
closed
1 year ago
0
Bugfix/proper-retry
#32
HarryHung
closed
1 year ago
0
Bugfix/amr-determinants
#31
HarryHung
closed
1 year ago
0
Release 0.7.1
#30
HarryHung
closed
1 year ago
0
Clarify local DB paths do not accept existing DBs
#29
HarryHung
closed
1 year ago
0
Contigs Filtering
#28
HarryHung
closed
1 year ago
0
Singularity and Sanger Farm Capacity, Bash scripts Re-organisation
#27
HarryHung
closed
1 year ago
0
Remove Nextflow workaround for Docker CPU Limit
#26
HarryHung
closed
1 year ago
0
Pipeline Overhaul
#25
HarryHung
closed
1 year ago
0
Set CPU/threads of processess based on CPUs available to their containers
#24
HarryHung
closed
1 year ago
0
process LINEAGE fatal error when not all CPUs set to available to Docker
#23
HarryHung
closed
1 year ago
0
Fix files being generated by Nextflow Docker Containers own by root
#22
HarryHung
closed
1 year ago
0
Add initialisation only workflow
#21
HarryHung
closed
1 year ago
0
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