Quality Checking Pipeline#23

Draft

claymcleod wants to merge 69 commits intomainfrom

rfcs/qc-workflow

Commits on Feb 19, 2020

ci: replace Travis with Github Actions
claymcleod
committed
Add rudimentary draft for quality assurance pipeline RFC

acchiao
authored and
claymcleod
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Remove tool options from workflow table

acchiao
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claymcleod
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Add table row for infer_experiment

acchiao
authored and
claymcleod
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Add table rows for junction_annotation and junction_saturation

acchiao
authored and
claymcleod
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Remove reference to rseqc junction_annotation

acchiao
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claymcleod
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Add in-progress section and update goals

acchiao
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claymcleod
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Add important metrics section with some brief justifications

acchiao
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claymcleod
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Update text/0000-quality-assurance-pipeline.md

acchiao
and
claymcleod
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Remove junction_annotation

acchiao
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claymcleod
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Update 0000-quality-assurance-pipeline.md

dfinkels
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claymcleod
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Updated language for clarity

dfinkels
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claymcleod
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Further clarification /language edits

dfinkels
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claymcleod
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Adjust outline to look like rnseq workflow

dfinkels
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claymcleod
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Spelling Corrections outstanding questions

dfinkels
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claymcleod
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Added draft Metrics for WGS,WES,RNAseq

dfinkels
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claymcleod
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Edited language in "Metrics for" sections

dfinkels
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claymcleod
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Correct spelling errors "Outstanding Questions"

dfinkels
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claymcleod
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Mapping Percentage to % Aligned

dfinkels
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claymcleod
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Expanded introduction

dfinkels
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claymcleod
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Edits Intro, Motivation and Discussion

dfinkels
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claymcleod
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Two spaces after period

dfinkels
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claymcleod
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Two spaces after periods full doc

dfinkels
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claymcleod
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Added Thresholds section

dfinkels
authored and
claymcleod
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Added commands for QC steps

dfinkels
authored and
claymcleod
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Changed bash code syntax

dfinkels
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claymcleod
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Edited text under St Jude Genomics QC Process

dfinkels
authored and
claymcleod
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Various updates to the QC RFC
claymcleod
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Change all 'RNA-Seq' to 'RNA-seq'
claymcleod
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improve: updates to the QC RFC
claymcleod
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Assign RFC a number of 0002.
claymcleod
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Tool versions reverted back to what we use in RNA-seq v2.
claymcleod
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Add fastq_screen tool
claymcleod
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fix: correct conda package name
claymcleod
committed

Commits on Mar 15, 2020

Commits on Mar 23, 2020

further WIP
claymcleod
committed

Commits on Nov 18, 2020

Commits on Jul 6, 2021

Commits on Jul 7, 2021

fix: typo and CI exclusion
a-frantz
committed

Commits on Jun 27, 2023