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Start writing STAT solo #4

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@olgabot olgabot commented May 28, 2019

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olgabot added 30 commits May 2, 2019 12:04
@olgabot
Rename all nfcore/nf-core/kerimoff --> czbiohub
2c7e255
@olgabot
base off of nfcore, author is Olga
d4cbf10
@olgabot
Add makefile for docker building
0608307
@olgabot
accept PRs to master from anywhere! mwah hahahaha"
58d1b68
@olgabot
Update docker image names
21c9e75
@olgabot
Merge pull request #1 from czbiohub/olgabot/rename-czbiohub
98c6740 
Olgabot/rename czbiohub
@olgabot
updating fastp
7eee68e
@olgabot
Update trimmer name, time and requirments
1dabc27
@olgabot
Fix parameter name for params.clip_r{1,2} --> params.five_prime_clip_…
7ee32d2 
…r{1,2}
@olgabot
Fix parameter name for params.clip_r{1,2} --> params.five_prime_clip_…
b4d3097 
…r{1,2} AGAIN
@olgabot
Separate fastqc on trimmed reads
4bbd28d
@olgabot
Fix naming of output trimming reports
ca5d350
@olgabot
fix test data'
7e42784
@olgabot
Don't lint the pipeline for now
044819b
@olgabot
Merge pull request #3 from czbiohub/olgabot/fastp
85474f8 
Use fastp for trimming instead of trimgalore
@olgabot
Add notes about fastp and htseq
a8a45cf
@olgabot
Remove subread (featureCounts) from requirements
e2628de
@olgabot
Initial try of htseq-count
f96d082
@olgabot
Add notes in changelog
4553722
@olgabot
update regex for htseq-count version
24d7d15
@olgabot
Add test example for makefile
b3107a4
@olgabot
update biotypes header to htseq-count
2b0d50f
@olgabot
Rename to merge_htseq-count.py
c29fdde
@olgabot
specify memory for htseq-count
eab4f0a
@olgabot
Use czbiohub/rnaseq container
94665be
@olgabot
Update merging of htseq-count gene-cell tables"
1433132
@olgabot
Missing pipe characters
48d910c
@olgabot
Comment out sample correlation for now
2ee34d9
@olgabot
Try updating the edger similarity
1aca486
@olgabot
remove htseq-count merging python gscript
c479b86
olgabot added 27 commits May 22, 2019 11:46
@olgabot
Fix typo
2816e71
@olgabot
Show aws region and batch queue if aws specified
4633a76
@olgabot
increase padding for summary
ae44946
@olgabot
remove gtf printing
8dbcd8a
@olgabot
protect output with quotes
22c27d7
@olgabot
Remove sample correlation
ddb0337
@olgabot
add czbiohub logo to pipeline
3abaea7
@olgabot
Add aws batch info to summary
9e69752
@olgabot
Fix merge conflict
c3a75fb
@olgabot
Fix work dir specification
e7817e9
@olgabot
Add outdir for makefile
d2103b8
@olgabot
Fix merge conflict
4996594
@olgabot
remove comments
337c473
@olgabot
Add splicing, exon quant to testing
5771a9c
@olgabot
Test all aspects of pipelien
8349201
@olgabot
Also test hisat2 aligner
73b4338
@olgabot
remove git rebase cruft
d37868e
@olgabot
Don't test transcriptome for now
ea6d19f
@olgabot
Add pigz to dockerfile
735373b
@olgabot
Sort genome names, change fastp name
ab5b446
@olgabot
Use different base directory for dexseq prepare annotation
51598cb
@olgabot
Use home instead of for scripts
7e4712c
@olgabot
fastp --> trim_with_fastp
fba9eba
@olgabot
Move all utility scripts to be flat in bin/
57644c8
@olgabot
use latest docker image
2fd3bc6
@olgabot
start writing STARsolo
7c83074
@olgabot
Add storage options for star Genome generate container
62575d1
@olgabot olgabot closed this May 28, 2019
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olgabot commented May 28, 2019

ahh sorry again :(

@olgabot olgabot reopened this May 28, 2019
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