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wodanaz
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Assembling_viruses
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pangolin from conda version causing issues.
#82
wodanaz
closed
2 years ago
5
Prevent malware warning for pillow
#81
johnbradley
opened
2 years ago
2
Fix uploading failure
#80
johnbradley
closed
2 years ago
0
Do not upload log for upload-output-data.sh script
#79
johnbradley
closed
2 years ago
0
Support running on a single node with local storage
#78
johnbradley
closed
2 years ago
0
Use 4 cores for trim_galore
#77
johnbradley
closed
2 years ago
2
Speed up remove_adapters step
#76
johnbradley
closed
2 years ago
0
Create snakemake report
#75
johnbradley
closed
2 years ago
0
Add report generation
#74
johnbradley
closed
2 years ago
1
Run coverage steps in parallel
#73
johnbradley
closed
2 years ago
0
Allow custom conda cache directory
#72
johnbradley
closed
2 years ago
0
Allow specifying snakemake conda directory
#71
johnbradley
closed
2 years ago
0
Fixes sam file not found error
#70
johnbradley
closed
2 years ago
0
Fix sam file not found error
#69
johnbradley
closed
2 years ago
0
Fix MissingOutputException when FASTQ files are in a subdirectory
#68
johnbradley
opened
2 years ago
0
Switch to Snakemake
#67
johnbradley
closed
2 years ago
0
Zip log files
#66
johnbradley
closed
2 years ago
0
Improve samtools coverage step
#65
johnbradley
closed
2 years ago
0
Remove mode argument
#64
johnbradley
closed
2 years ago
0
Remove duplicate sample names check
#63
johnbradley
closed
2 years ago
0
Remove sample date requirement from the pipeline
#62
johnbradley
closed
2 years ago
0
Add option to disable modules
#61
johnbradley
closed
2 years ago
0
Speed up creating escapevariants environment
#60
johnbradley
closed
2 years ago
4
Add support for running on Azure
#59
johnbradley
closed
2 years ago
0
Handle duplicate sample names
#58
johnbradley
closed
2 years ago
0
Adds 3 tabs to spreadsheet
#57
johnbradley
closed
2 years ago
1
Include barplot in pipeline
#56
johnbradley
opened
2 years ago
2
Spreadsheet changes
#55
johnbradley
closed
2 years ago
2
Simplify to duke and nc_state modes
#54
johnbradley
closed
2 years ago
1
Add a filename checking step
#53
johnbradley
closed
2 years ago
0
Simplify run scripts
#52
johnbradley
closed
2 years ago
0
issues with pangolin upgrade
#51
wodanaz
closed
3 years ago
7
Add snakemake slurm config
#50
johnbradley
closed
3 years ago
0
Add Snakefile to setup genome
#49
johnbradley
closed
3 years ago
1
Add ability to upload to DDS
#48
johnbradley
closed
2 years ago
1
Prompt for trim adapter type
#47
johnbradley
opened
3 years ago
0
Add support for restarting the pipeline
#46
johnbradley
closed
2 years ago
15
run-dds-escape-variants.sh deprecation?
#45
wodanaz
opened
3 years ago
4
Adds config.sh and remove hard coded tmpdir
#44
johnbradley
closed
3 years ago
0
issues with picard
#43
wodanaz
opened
3 years ago
10
Adds supermetadata step and filters using spike.bed
#42
johnbradley
closed
3 years ago
1
pangolin update
#41
wodanaz
opened
3 years ago
2
Fix out of memory errors when using a conda environment
#40
johnbradley
closed
3 years ago
5
Adds conda environment to scripts
#39
johnbradley
closed
3 years ago
0
make supermetadata table and modify titles
#38
johnbradley
closed
3 years ago
16
Adds -j numjobs argument
#37
johnbradley
closed
3 years ago
0
Provide all tools used by the pipeline
#36
johnbradley
closed
3 years ago
1
Adds pangolin step
#35
johnbradley
closed
3 years ago
0
Add pangolin step
#34
johnbradley
closed
3 years ago
4
Allow configuration of MAX_ARRAY_JOBS
#33
johnbradley
closed
3 years ago
0
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