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mg-scripts
Knight Lab internal Metagenomic processing scripts for demultiplexing, QC and host removal
BSD 3-Clause "New" or "Revised" License
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allow configuration file to have resources per instrument type
#106
antgonza
opened
1 year ago
7
NuQCJob implementation
#105
charles-cowart
closed
1 year ago
10
WIP Added locking on run_directories
#104
charles-cowart
closed
1 year ago
3
Fixes_93, Updated to latest changes in metapool
#103
charles-cowart
closed
1 year ago
5
wallclock_time_in_hours -> wallclock_time_in_minutes
#102
charles-cowart
closed
1 year ago
1
Added support for replicates. Test needed.
#101
charles-cowart
closed
1 year ago
4
Small change to include metatranscriptomic
#100
charles-cowart
closed
1 year ago
2
Update get_sample_names() to filter by project
#99
charles-cowart
closed
1 year ago
2
Added get_sample_names() method
#98
charles-cowart
closed
1 year ago
2
Add Metatranscriptomic assay-type
#97
charles-cowart
closed
1 year ago
1
Fixes bug when validating bad sample-sheets.
#96
charles-cowart
closed
1 year ago
1
Modifications to support plugin refactoring
#95
charles-cowart
closed
1 year ago
2
Fix read csv
#94
wasade
closed
1 year ago
2
Differentiate exceptions by objects not messages
#93
wasade
closed
1 year ago
1
fixes error where errors detected by metapool aren't reported.
#92
charles-cowart
closed
1 year ago
4
Sample-sheet assay-type will now be verified.
#91
charles-cowart
closed
1 year ago
5
Update Assay-type in sample-sheets to respond to 'Metagenomic'
#90
charles-cowart
closed
1 year ago
1
Updated generate_sample_information_files()
#89
charles-cowart
closed
1 year ago
4
Preserve prep-file output paths from successful jobs
#88
charles-cowart
closed
1 year ago
2
Update based on additional testing on qiita-rc
#87
charles-cowart
closed
1 year ago
1
Updates based on testing
#86
charles-cowart
closed
1 year ago
1
Amplicon support
#85
charles-cowart
closed
1 year ago
3
MultiQC configuration updated
#84
charles-cowart
closed
1 year ago
3
fix sacct array cmd
#83
antgonza
closed
2 years ago
1
mv to slurm
#82
antgonza
closed
2 years ago
1
Added success confirmation for child jobs in arrays
#81
charles-cowart
closed
2 years ago
8
Handle case where all input fastq files to FastQCJob are zero_length.
#80
charles-cowart
closed
2 years ago
3
Update mg-scripts to take advantage of Illumina file spec
#79
charles-cowart
opened
2 years ago
0
Add early abort and notification when a job-step yields zero files.
#78
charles-cowart
opened
2 years ago
0
Calculate metrics for each job step
#77
charles-cowart
opened
2 years ago
0
Define the minimum length of reads for fastp invocation w/in config file
#76
charles-cowart
opened
2 years ago
0
Added support for kraken2
#75
charles-cowart
closed
2 years ago
2
Refactored QCJob
#74
charles-cowart
closed
2 years ago
5
min_bytes = 3.1K
#73
antgonza
closed
2 years ago
1
Prepend run-id to blanks.tsv files
#72
charles-cowart
closed
2 years ago
2
Wrap sample-sheet path in double-quotes.
#71
charles-cowart
closed
2 years ago
1
Convert underscores in sample-sheets to dots
#70
charles-cowart
closed
2 years ago
2
Updated run() method to accept callback function.
#69
charles-cowart
closed
2 years ago
1
Sample tracking3
#68
charles-cowart
closed
2 years ago
1
Detect when a sample failed processing in the pipeline.
#67
charles-cowart
closed
2 years ago
2
WIP: Tracking sample processing failures in pipeline
#66
charles-cowart
closed
2 years ago
2
Modified RTAComplete.txt and RunInfo.xml file-check
#65
charles-cowart
closed
2 years ago
2
reuse blanks for multiple projects in the same plate
#64
antgonza
opened
2 years ago
0
Use RTAComplete.txt to confirm that the folder is fully sync
#63
antgonza
closed
2 years ago
2
Use tube_id as sample_name
#62
antgonza
closed
2 years ago
1
include the number of reads at each state to the preparation information files
#61
antgonza
closed
2 years ago
4
report the samples that didn't make it to the end
#60
antgonza
closed
2 years ago
2
Add callback
#59
charles-cowart
closed
2 years ago
2
Real world test fixes
#58
charles-cowart
closed
2 years ago
1
Real world test fixes
#57
charles-cowart
closed
2 years ago
0
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