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[Feature Addition: Salmon] #221

Merged
merged 166 commits into from
Jul 8, 2019
Merged

[Feature Addition: Salmon] #221

merged 166 commits into from
Jul 8, 2019

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apeltzer
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@apeltzer apeltzer commented Jun 8, 2019

This is basically @olgabot @lpantano and partially (I Think) @kerimoff 's work.

PR checklist

  • This comment contains a description of changes (with reason)
  • If you've fixed a bug or added code that should be tested, add tests!
  • If necessary, also make a PR on the nf-core/rnaseq branch on the nf-core/test-datasets repo
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Make sure your code lints (nf-core lint .).
  • Documentation in docs is updated
  • CHANGELOG.md is updated
  • README.md is updated

I guess there are a couple of things that could be updated beforehand in separate packages:

  • Documentation
  • README to include @kerimoff as contributor too

olgabot and others added 30 commits May 29, 2019 11:58
@olgabot
Addhtseq to environment requirements
8fb4041
@olgabot
Add HTSeq to changelog
71bcd9f
@olgabot
small change to trigger build
2727392
@olgabot
Add v1.4dev section and move change there
74c004c
@apeltzer
Merge branch 'dev' into patch-1
8369cc4
@apeltzer
Merge pull request #209 from olgabot/patch-1
9d44294 
Add htseq to environment requirements
@olgabot
Add salmon to requirements
eccbec3
@olgabot
Update changelog with salmon=0.14.0
eeb85c6
@olgabot
Add salmon index
2a3e6b4
@olgabot
Add transcriptome to test config
5dd9a14
@olgabot
fa --> fasta
10d0d6d
@olgabot
Less character width to specify transcriptome in summary
6252606
@olgabot
Add salmon quant
c1a4dfb
@olgabot
add raw_salmon channel
6aa3689
@olgabot
Add salmon index to changelog
2d6c85b
@olgabot
Add salmon to usage
1eeea23
@olgabot
Output salmon index to reference_transcriptome folder
362304a
@olgabot
write out more docs for salmon index
110fc45
@olgabot
Add cpus for salmon quant
23e5821
@olgabot
Add gtf for gene summarization
da96b5a
@olgabot
use BOTH salmon_quant and salmon_index configs
ad0791a
@olgabot
use same cpu, memory for both salmon quant and index
f344819
@olgabot
semicolon, not comma -_-;;;
5b5424d
@olgabot
Add merging of salmon gene and transcript counts
5ab4b4d
@olgabot
Don't need salmon quant twice
be6eafc
@olgabot
Add merging of transcript id to gene name mapping
eff09b2
@lpantano
Merge pull request #210 from czbiohub/olgabot/add-salmon
24edf8c 
Add salmon to requirements
@olgabot
Move salmon to after featurecounts to use featurecounts output
faf2b32
@olgabot
Add scraping software versions
49b694a
@olgabot
Separate transcript and gene count merging
4267ba9
olgabot and others added 17 commits June 27, 2019 08:58
@olgabot @drpatelh
Use @drpatelh's wording
ac2b2a2 
Co-Authored-By: Harshil Patel <drpatelh@users.noreply.github.com>
@olgabot
remove random fenced code
11276af
@olgabot
Use 7th column for gene namec
beab23f
@olgabot
Shorten name of biotype field in summary for brevity
32a37fd
@olgabot
use 0'th item not 1th
7d84ba2
@olgabot
Add sample name to output
17dd8fe
@olgabot
use tximport for each sample and then merge individually
0028728
@olgabot
properly merge gene counts and tpm files
f1f3b8a
@olgabot
actually use the gene counts to merge ..
2be0b27
@olgabot
Add transcript_id and gene_id to salmon output csv
70bb37c
@olgabot
Add --gencode flag to usage and summary output
3bef844
@olgabot
Don't need salmon RDS files
41c58f8
@olgabot
Add gtf_qualimap
5c13cc0
@apeltzer
Merge pull request #242 from czbiohub/olgabot/salmon-gencode
3c72549 
GENCODE annotation compatibility with salmon
@apeltzer
Merge pull request #243 from czbiohub/olgabot/featurecounts-merge-memory
034ee2a 
Minimize memory footprint of `merge_featurecounts`
@apeltzer
Merge pull request #244 from pilm-bioinformatics/lpantano-salmon-txim…
848241a 
…port-patch

fix mismatch between tx2gene and quant.sf
@apeltzer
Remove trailing slash
d1b6d34
@olgabot
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olgabot commented Jul 7, 2019

FWIW In case it's useful, I've been successfully using a merged version of this salmon branch and all it's PRs: https://github.com/czbiohub/rnaseq/tree/olgabot/merged-salmon

@apeltzer
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apeltzer commented Jul 7, 2019

I guess we should add the "fancy readgroup" stuff here too and then we're good 👍 Feedback that this works fine is always nice to know 👍

@drpatelh
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drpatelh commented Jul 7, 2019

@apeltzer Let's just merge the open PR we have open already for the read group addition. I'll add a separate process in when I add RSEM.

@apeltzer
Merge pull request #241 from apeltzer/salmon-readgroups
ad7e743 
Add in ReadGroups for QualiMap compatibility
@apeltzer
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apeltzer commented Jul 8, 2019

Ok whoever has time: @drpatelh @olgabot @lpantano - please final round of reviews and then I'll merge this to dev.

@apeltzer apeltzer merged commit e9284af into dev Jul 8, 2019
@apeltzer apeltzer deleted the salmon branch July 8, 2019 13:23
@drpatelh drpatelh mentioned this pull request Jul 8, 2019
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@olgabot olgabot olgabot left review comments

@lpantano lpantano lpantano requested changes

@kerimoff kerimoff kerimoff left review comments

@drpatelh drpatelh drpatelh approved these changes

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5 participants
@apeltzer @lpantano @drpatelh @olgabot @kerimoff