qiita-spots/qp-knight-lab-processing issues and pull requests

#144 - Refactor needed to remove duplicated lines after PacBio addition.

Issue - State: open - Opened by antgonza 2 days ago

#143 - PacBio

Pull Request - State: closed - Opened by antgonza 11 days ago - 1 comment

#142 - Do not add human filtering specific columns when host is not human

Issue - State: open - Opened by ackermag 28 days ago

#139 - QC_Analysis_TellReadJob.html

Pull Request - State: closed - Opened by antgonza 2 months ago

#138 - add subsample_reads

Pull Request - State: closed - Opened by antgonza 2 months ago

#137 - Expand SPP blanks handling to include katharoseq, other controls

Issue - State: open - Opened by AmandaBirmingham 2 months ago
Labels: enhancement

#134 - remove sequencer types info, instead get from kl-metapool

Pull Request - State: open - Opened by AmandaBirmingham 2 months ago

#132 - adding PrepNuQCWorkflow

Pull Request - State: closed - Opened by antgonza 4 months ago - 2 comments

#131 - test full runs in WorkflowFactory.py

Pull Request - State: open - Opened by antgonza 4 months ago

#129 - inserting data to qiita for testing

Pull Request - State: closed - Opened by antgonza 5 months ago - 1 comment

#128 - Update mg-scripts to take advantage of Illumina file spec

Issue - State: open - Opened by charles-cowart over 3 years ago

#126 - Calculate metrics for each job step

Issue - State: open - Opened by charles-cowart over 3 years ago

#125 - Define the minimum length of reads for fastp invocation w/in config file

Issue - State: open - Opened by charles-cowart over 3 years ago

#124 - reuse blanks for multiple projects in the same plate

Issue - State: open - Opened by antgonza over 3 years ago
Labels: urgent-need

#122 - replace _scan_fastq_files for 3 methods

Issue - State: open - Opened by antgonza almost 4 years ago

#121 - add code to be able to run tests via python

Issue - State: open - Opened by antgonza almost 4 years ago

#120 - Validate instrument model in sample sheet and run outputs

Issue - State: open - Opened by ElDeveloper over 5 years ago - 3 comments

#119 - allow configuration file to have resources per instrument type

Issue - State: open - Opened by antgonza almost 2 years ago - 7 comments

#118 - Add other wet-lab added samples make it to the sample info file.

Issue - State: open - Opened by antgonza over 1 year ago

#116 - InstrumentUtils() types should be vetted by IGM, Illumina

Issue - State: open - Opened by charles-cowart over 1 year ago

#114 - Update fastq file parsing regexes in util.py

Issue - State: open - Opened by charles-cowart over 1 year ago

#113 - Have Qiita/SPP automatically perform some Katharoseq processing.

Issue - State: open - Opened by charles-cowart 12 months ago

#112 - Revisit legacy fastq file search code

Issue - State: open - Opened by charles-cowart 7 months ago

#111 - Isn't this effectively a noop?

Issue - State: open - Opened by charles-cowart 7 months ago

#109 - raise an error if more than 20% of the reads get assigned to Undetermined

Issue - State: open - Opened by antgonza 5 months ago

#108 - improve error when there are no files that passed human-filtering

Issue - State: open - Opened by antgonza 5 months ago

#107 - fix-ci

Pull Request - State: closed - Opened by antgonza 5 months ago - 1 comment

#106 - merging mg-scripts

Pull Request - State: closed - Opened by antgonza 5 months ago - 1 comment

#105 - merging mg-scripts

Pull Request - State: closed - Opened by antgonza 5 months ago - 1 comment

#104 - rm duplicated execute_pipeline

Pull Request - State: closed - Opened by antgonza 5 months ago - 1 comment

#103 - mock out sbatch for pipeline testing

Issue - State: open - Opened by antgonza 6 months ago

#101 - add execute_pipeline to StandardMetatranscriptomicWorkflow

Pull Request - State: closed - Opened by antgonza 6 months ago - 1 comment

#100 - fixes after deploy 03.25

Pull Request - State: closed - Opened by antgonza 6 months ago - 1 comment

#99 - Fix for generating failed_samples.html reporting.

Pull Request - State: closed - Opened by charles-cowart 7 months ago

#98 - production hotfixes

Pull Request - State: closed - Opened by charles-cowart 8 months ago

#97 - Recent changes in testing

Pull Request - State: closed - Opened by charles-cowart 9 months ago - 1 comment

#96 - fixes issue encountered during testing.

Pull Request - State: open - Opened by charles-cowart 9 months ago

#95 - “Project” and “Failed at” column inputs are switched for the failed samples file

Issue - State: open - Opened by mmbryant23 9 months ago

#94 - WIP: Updates based on production testing

Pull Request - State: open - Opened by charles-cowart 10 months ago

#93 - Updates to bring plugin in-line w/mg-scripts

Pull Request - State: open - Opened by charles-cowart 11 months ago

#92 - Refactored SPP plugin w/tellread support.

Pull Request - State: closed - Opened by charles-cowart 12 months ago - 2 comments

#91 - WIP: Added Qiita study reserved-word check

Pull Request - State: closed - Opened by charles-cowart about 1 year ago

#90 - improve README

Pull Request - State: closed - Opened by antgonza about 1 year ago

#89 - Updates based on initial runs in production.

Pull Request - State: closed - Opened by charles-cowart about 1 year ago - 2 comments

#88 - WIP: Update sample-name validation

Pull Request - State: open - Opened by charles-cowart about 1 year ago