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25 Open 14 Closed
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Issues list

qp-klp should read and populate OverrideCycles from the run.
#130 opened Apr 30, 2025 by antgonza
2
raise an error if more than 20% of the reads get assigned to Undetermined
#109 opened Apr 17, 2025 by antgonza
improve error when there are no files that passed human-filtering
#108 opened Apr 17, 2025 by antgonza
mock out sbatch for pipeline testing
#103 opened Mar 20, 2025 by antgonza
Looks almost identical to the prior job script except output location, why not parameterize and pass in on submission with --export?
#110 opened Feb 25, 2025 by charles-cowart
Isn't this effectively a noop?
#111 opened Feb 25, 2025 by charles-cowart
Revisit legacy fastq file search code
#112 opened Feb 25, 2025 by charles-cowart
“Project” and “Failed at” column inputs are switched for the failed samples file
#95 opened Dec 2, 2024 by mmbryant23
Have Qiita/SPP automatically perform some Katharoseq processing.
#113 opened Sep 23, 2024 by charles-cowart
Update fastq file parsing regexes in util.py
#114 opened May 20, 2024 by charles-cowart
@charles-cowart
Update _get_fastq_files() to handle I2 files
#85 opened Apr 2, 2024 by charles-cowart
@charles-cowart
Update job polling mechanism
#115 opened Mar 12, 2024 by charles-cowart
@charles-cowart
InstrumentUtils() types should be vetted by IGM, Illumina
#116 opened Feb 15, 2024 by charles-cowart
@charles-cowart
improve error reporting on run-id
#117 opened Feb 13, 2024 by antgonza
@charles-cowart
Add other wet-lab added samples make it to the sample info file.
#118 opened Feb 12, 2024 by antgonza
@charles-cowart
allow configuration file to have resources per instrument type
#119 opened Oct 10, 2023 by antgonza
@charles-cowart
7
Update mg-scripts to take advantage of Illumina file spec
#128 opened May 2, 2022 by charles-cowart
@charles-cowart
Add early abort and notification when a job-step yields zero files.
#127 opened May 2, 2022 by charles-cowart
@charles-cowart
Calculate metrics for each job step
#126 opened May 2, 2022 by charles-cowart
@charles-cowart
Define the minimum length of reads for fastp invocation w/in config file
#125 opened Apr 19, 2022 by charles-cowart
@charles-cowart
reuse blanks for multiple projects in the same plate urgent-need
#124 opened Jan 25, 2022 by antgonza
@charles-cowart
FastQCJob _scan_fastq_files() method needs reevaluation
#123 opened Oct 8, 2021 by charles-cowart
replace _scan_fastq_files for 3 methods
#122 opened Oct 6, 2021 by antgonza
@charles-cowart
add code to be able to run tests via python
#121 opened Oct 5, 2021 by antgonza
Validate instrument model in sample sheet and run outputs
#120 opened Feb 29, 2020 by ElDeveloper
3
ProTip! Exclude everything labeled bug with -label:bug.