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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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Confirm Qiita Study sample-templates do not already contain well_id_384 and other reserved columns.
#150
charles-cowart
opened
1 week ago
0
WIP: Add tellread
#149
charles-cowart
opened
3 weeks ago
1
WIP: Seqpro refactor
#148
charles-cowart
opened
1 month ago
1
Updated get_project_info()
#147
charles-cowart
closed
1 month ago
2
Add production change
#146
charles-cowart
closed
2 months ago
2
ConvertJob.copy_sequences() method added.
#145
charles-cowart
opened
2 months ago
8
Production updates
#144
charles-cowart
closed
2 months ago
2
added get_sample_names() method that's replicate compliant
#143
charles-cowart
closed
2 months ago
1
parameter must now be a list once again.
#142
charles-cowart
closed
2 months ago
1
Updates from production, Support for new human-filtering impl
#141
charles-cowart
closed
2 months ago
15
Replace sacct polling
#140
charles-cowart
opened
3 months ago
0
Update fastq file parsing regexes in util.py
#139
charles-cowart
opened
3 months ago
0
on job-restart the failed_samples.html could be incomplete.
#138
antgonza
closed
4 months ago
1
latest updates based on testing
#137
charles-cowart
closed
5 months ago
1
dynamically adjust various run parameters based on bin sizes
#136
charles-cowart
closed
5 months ago
2
Removed default profile functionality
#135
charles-cowart
closed
5 months ago
1
Update job polling mechanism
#134
charles-cowart
opened
5 months ago
0
incorporates the latest changes from production testing.
#133
charles-cowart
closed
5 months ago
2
bugfix for subset project names
#132
charles-cowart
closed
6 months ago
1
Update GenPrepFileJob()
#131
charles-cowart
closed
6 months ago
1
readd /dev/shm and rm SLURM_ARRAY_TASK_MIN check
#130
antgonza
closed
6 months ago
2
Added support for restarting jobs
#129
charles-cowart
closed
6 months ago
2
add KATHAROseq samples to SIFs.
#128
charles-cowart
opened
6 months ago
6
log-parsing
#127
charles-cowart
closed
6 months ago
3
For runs w/multiple projects, manage adapter-trimmed files
#126
charles-cowart
closed
6 months ago
1
Loader fix
#125
charles-cowart
closed
6 months ago
1
InstrumentUtils() types should be vetted by IGM, Illumina
#124
charles-cowart
opened
6 months ago
0
Multi configuration
#123
charles-cowart
closed
6 months ago
3
improve error reporting on run-id
#122
antgonza
opened
6 months ago
0
Add other wet-lab added samples make it to the sample info file.
#121
antgonza
opened
6 months ago
0
using the wkdir as the processing folder and rm gres
#120
antgonza
closed
7 months ago
1
Updated tests
#119
charles-cowart
closed
7 months ago
1
Save adapter-filtered-only data
#118
wasade
closed
7 months ago
7
Fixes #106
#117
charles-cowart
closed
6 months ago
4
shm and se changes
#116
antgonza
closed
8 months ago
1
Updates based on qiita-rc testing + changes to metapool
#115
charles-cowart
closed
8 months ago
3
shm and se operation changes
#114
wasade
opened
9 months ago
1
More updates, based on qp-klp changes
#113
charles-cowart
closed
9 months ago
1
Updates based on testing in Qiita-RC
#112
charles-cowart
closed
9 months ago
2
Fixes bug w/non 'install -e .' installs.
#111
charles-cowart
closed
9 months ago
1
Updates to support proper function and testing of code in qp-klp.
#110
charles-cowart
closed
9 months ago
2
Fixes issue with fastq.gz files having _I1_ etc.
#109
charles-cowart
opened
10 months ago
1
Pipeline.get_sample_names() fix for plate-replicates
#108
charles-cowart
opened
10 months ago
4
changes for replicates
#107
antgonza
closed
11 months ago
1
allow configuration file to have resources per instrument type
#106
antgonza
opened
11 months ago
7
NuQCJob implementation
#105
charles-cowart
closed
10 months ago
10
WIP Added locking on run_directories
#104
charles-cowart
closed
12 months ago
3
Fixes_93, Updated to latest changes in metapool
#103
charles-cowart
closed
12 months 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
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