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RNA-Seq Workflow v2.0 #1

Merged
merged 38 commits into from
Oct 2, 2019
Merged

RNA-Seq Workflow v2.0 #1

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18a49ed
Copy template for rnaseq-workflow-v2.0.
claymcleod Jun 24, 2019
fdb1f1b
First draft of the RNA-Seq workflow v2.0 RFC.
claymcleod Jun 24, 2019
93b4c2d
Update conda channels.
claymcleod Jun 24, 2019
56446b5
Add `conda` environment creation command.
claymcleod Jun 24, 2019
24fca5c
Add various questions and TODO items.
claymcleod Jun 24, 2019
e36a8b5
Additional discussion points added to the RFC.
claymcleod Jun 24, 2019
303f0e8
Multiple updates to RFC.
claymcleod Jun 24, 2019
0589874
Added example to the header cleanup suggestion.
claymcleod Jun 24, 2019
d4453cf
Changed title of TODO section.
claymcleod Jun 24, 2019
b46a495
Fix title cases.
claymcleod Jun 24, 2019
50db0ad
Updates to table of contents structure.
claymcleod Jun 24, 2019
5e0521c
Move one TODO item to outstanding questions.
claymcleod Jun 24, 2019
1db067d
Expand PAR macro so there is no ambiguity on what we're discussing here.
claymcleod Jun 24, 2019
c2defb6
Fix two mistakes and two broken links.
lnason Jun 25, 2019
0cce7d8
Added information about installing Rust and `fqlib`.
claymcleod Jun 26, 2019
eb7e8e2
Missing backslash in command.
claymcleod Jun 26, 2019
cc9ed76
Added more information about motivation to remove the ERCC SpikeIn se…
claymcleod Jun 27, 2019
c43bfed
Added new QC steps for qualimap and rseqc.
claymcleod Jun 27, 2019
8972442
Add FastQC information.
claymcleod Jun 27, 2019
7711865
Cleaned up doc by adding some items and updating status of some items.
claymcleod Jun 27, 2019
a69e568
Added an outstanding question about `qualimap counts`.
claymcleod Jun 27, 2019
b9a08c6
Various clarifications before sending to the broader group.
claymcleod Jun 27, 2019
9e92935
Updated to GENCODE v31, which was released today.
claymcleod Jul 3, 2019
f1094f3
Overhaul of RFC after internal discussion.
claymcleod Jul 4, 2019
0b1f725
Incremental updates to the RFC.
claymcleod Jul 6, 2019
d2a8a37
Added resources directory and Jupyter notebook for "RNA-Seq Workflow
claymcleod Jul 7, 2019
dfbaab7
Added sequence dictionaries to future-proof things.
claymcleod Jul 7, 2019
161d62b
Updated RFC with latest on the GENCODE compatibility investigation.
claymcleod Jul 7, 2019
66be22e
Cleaned up section for known feature filtering of GTF.
claymcleod Jul 7, 2019
f41478f
Added .gitkeep to hide expansion of resources folder in Github.
claymcleod Jul 7, 2019
0d33994
Various changes to workflow:
claymcleod Jul 7, 2019
587f0b3
Addressed Andrew and Alex's comments on the PR.
claymcleod Jul 8, 2019
b81d35e
Adding Picard SamToFastq step to convert split bams to fastqs
adthrasher Jul 11, 2019
8d7dd49
Merge branch 'master' into cmcleod/rnaseq-workflow-v2
claymcleod Aug 26, 2019
7fa344b
Improve introduction paragraph and link to PR
claymcleod Aug 26, 2019
5c8dba9
Updating RFC to reflect the pipeline as implemented.
adthrasher Aug 26, 2019
a17092f
Adding additional todo items and updating the text on gene model post…
adthrasher Aug 27, 2019
0018357
Adding bigwig step and updating introduction the the correct build co…
adthrasher Sep 24, 2019
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