PR for Release 1.4 #300

apeltzer · 2019-10-09T13:00:10Z

This is the dev to master PR for making a release 1.4 for nf-core/rnaseq. Lots of changes, so please have a look and review 👍

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

First pass update of relevant files for Salmon addition

Bug fixes for Salmon addition

Minor edit: the docker container name does not have a hyphen

Minor edit to installation.md

Minor: Update other singularity-related docs to reference the correct docker image.

Update adding_your_own.md

add tximport and summarizeexperiment

Fix template merge

Major overhaul of Salmon requirements

Add tximport function

apeltzer · 2019-10-14T08:15:30Z

apeltzer · 2019-10-14T14:07:12Z

I guess the tools 1.7.1 release is something I will wait for (when we release very soon?) ...

@drpatelh

* Remove ToDo string from README * Template update for nf-core/tools version 1.8.dev0 * Fix multiqc stuff * Remove png, include fix by @drpatelh

olgabot

Whooo so exciting! I had a few suggestions to make the documentation a little easier to understand. I'm also still confused about when the edgeR stuff is Euclidean distances vs Pearson's correlation.. maybe you can help?

CHANGELOG.md

assets/heatmap_header.txt

docs/usage.md

Co-Authored-By: Olga Botvinnik <[email protected]>

olgabot

Yay it's all "Pearson's Correlation" now! phew I was really confused

ewels · 2019-10-15T06:06:05Z

Can’t remember why we didn’t just use Pearson’s in the first place... Sorry for any trauma that this decision caused over the years 😂

olgabot · 2019-10-15T06:51:57Z

Eventually I think one could replace some k-mer based methods for sample similarity over the edgeR stuff and also make an MDS or UMAP plot but that is not in the scope of this release ...

@drpatelh

* Remove ToDo string from README * Template update for nf-core/tools version 1.8.dev0 * Fix multiqc stuff * Remove png, include fix by @drpatelh * Add Memory adjustments

apeltzer · 2019-10-15T09:42:04Z

Will get the container updated once more - preseq has been upgraded at bioconda now, rsem also compiling with R 3.6.1 now, so once this is done this is really good to go I believe 👍

Will then need another approval, e.g. @ewels or @drpatelh :-)

drpatelh · 2019-10-15T10:52:18Z

Oh. Ok then. Ill have a look 👍

apeltzer · 2019-10-15T10:52:57Z

See #314

drpatelh

Breezed over it @apeltzer given the reviews that have come before. Just a couple of minor comments/corrections 👍

I have to say we may need to think about splitting this pipeline up at some point because its gone way beyond the simplicity required to work out whats going on!

main.nf

@drpatelh

* Remove ToDo string from README * Template update for nf-core/tools version 1.8.dev0 * Fix multiqc stuff * Remove png, include fix by @drpatelh * Add Memory adjustments * Final Dependency updates for PR 1.4 * Let's get RSEM in once we add it :-)

Not up2date anymore - all things resolved 🎉

olgabot · 2019-10-15T07:13:23Z

docs/usage.md

--fasta '[path to Fasta reference]' \
--gtf '[path to GTF file]' \
--bed12 '[path to bed12 file]'
+--star_index '/path/to/STAR/index' \


Suggested change

--star_index '/path/to/STAR/index' \

--star_index '/path/to/star_index_directory/' \

Make it more obvious that this is a folder

olgabot · 2019-10-15T07:13:43Z

docs/usage.md

--gtf '[path to GTF file]' \
--bed12 '[path to bed12 file]'
+--star_index '/path/to/STAR/index' \
+--hisat2_index '/path/to/HISAT2/index' \


Suggested change

--hisat2_index '/path/to/HISAT2/index' \

--hisat2_index '/path/to/hisat2_index_directory/' \

Make it more obvious that this is a folder

oops I thought I submitted this!! next time ..

Something for V1.5 :-)

drpatelh and others added 30 commits June 10, 2019 12:42

First pass update of relevant files

162ec29

Fix lint errors and warnings

d795658

Reorder parameters

4523b87

Rename Salmon processes

66a586c

Use correct strandedness

d563371

Reorder validate inputs

c891083

Merge pull request #223 from drpatelh/salmon

c234717

First pass update of relevant files for Salmon addition

Bug fixes

a7536c1

Merge pull request #224 from drpatelh/salmon

3f664e2

Bug fixes for Salmon addition

Update installation.md

29be92b

Minor edit: the docker container name does not have a hyphen

Merge pull request #225 from jburos/patch-1

6e6f397

Minor edit to installation.md

Update adding_your_own.md

2571767

Minor: Update other singularity-related docs to reference the correct docker image.

Merge pull request #226 from jburos/patch-1

3e37864

Update adding_your_own.md

Add empty salmon_multiqc_logs channel

fbad8b6

add new dependcies for salmon

3e5baa6

upgrade to latest dependencies

24729d3

Merge pull request #228 from nf-core/lpantano-patch-tximport

507f2e4

add tximport and summarizeexperiment

deleted -M from the featureCounts command

4729278

Resolve merge conflicts with TEMPLATE

56dc76c

Fix merge conflicts

92d35ea

Fix template merge

de8691d

Merge pull request #230 from drpatelh/master

c2977ba

Fix template merge

Major overhaul of Salmon requirements

05e4eaf

Update CHANGELOG

a77dd45

Merge pull request #232 from drpatelh/salmon

039f771

Major overhaul of Salmon requirements

Add tximport function

6ff4577

add docs for tximport

ec4915a

update readme and changelog

fd6ab71

Merge pull request #233 from nf-core/lpantano-tximport

926a950

Add tximport function

fix variable and correct version to parse gtf

c65197d

apeltzer added 3 commits October 14, 2019 15:37

Merge remote-tracking branch 'upstream/dev' into dev

896d461

Template update for nf-core/tools version 1.8.dev0

46f2b76

Merge in template v1.7

9a8e635

apeltzer and others added 3 commits October 14, 2019 17:17

Fix multiqc stuff

46b8219

Remove png, include fix by @drpatelh

e064801

TEMPLATE v1.7 PR merged in (#310)

8f0b257

* Remove ToDo string from README * Template update for nf-core/tools version 1.8.dev0 * Fix multiqc stuff * Remove png, include fix by @drpatelh

olgabot requested changes Oct 14, 2019

View reviewed changes

apeltzer and others added 2 commits October 14, 2019 22:43

Apply suggestions from code review

0d25c3f

Co-Authored-By: Olga Botvinnik <[email protected]>

Apply suggestions from code review

13d436b

Co-Authored-By: Olga Botvinnik <[email protected]>

apeltzer requested a review from olgabot October 14, 2019 20:48

olgabot approved these changes Oct 15, 2019

View reviewed changes

apeltzer and others added 3 commits October 15, 2019 09:17

Merge branch 'dev' of https://github.com/nf-core/rnaseq into dev

f17e58b

Add Memory adjustments

bbb7146

Mini Memory Adjustments (#313)

43c0829

* Remove ToDo string from README * Template update for nf-core/tools version 1.8.dev0 * Fix multiqc stuff * Remove png, include fix by @drpatelh * Add Memory adjustments

Final Dependency updates for PR 1.4

733b51c

Let's get RSEM in once we add it :-)

f3ab509

drpatelh approved these changes Oct 15, 2019

View reviewed changes

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apeltzer and others added 3 commits October 15, 2019 13:17

Package updates for PR 1.4 (#314)

5678295

* Remove ToDo string from README * Template update for nf-core/tools version 1.8.dev0 * Fix multiqc stuff * Remove png, include fix by @drpatelh * Add Memory adjustments * Final Dependency updates for PR 1.4 * Let's get RSEM in once we add it :-)

Merge branch 'dev' of https://github.com/nf-core/rnaseq into dev

8399375

Requested changes from review by @drpatelh

052ef88

apeltzer merged commit 55eee0c into master Oct 15, 2019

olgabot reviewed Oct 15, 2019

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PR for Release 1.4 #300

PR for Release 1.4 #300

apeltzer commented Oct 9, 2019

apeltzer commented Oct 14, 2019

apeltzer commented Oct 14, 2019

olgabot left a comment

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ewels commented Oct 15, 2019

olgabot commented Oct 15, 2019

apeltzer commented Oct 15, 2019

drpatelh commented Oct 15, 2019

apeltzer commented Oct 15, 2019

drpatelh left a comment

olgabot Oct 15, 2019

olgabot Oct 15, 2019

olgabot Oct 15, 2019

apeltzer Oct 15, 2019

	--star_index '/path/to/STAR/index' \
	--star_index '/path/to/star_index_directory/' \

	--hisat2_index '/path/to/HISAT2/index' \
	--hisat2_index '/path/to/hisat2_index_directory/' \

PR for Release 1.4 #300

PR for Release 1.4 #300

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apeltzer commented Oct 9, 2019

PR checklist

apeltzer commented Oct 14, 2019

apeltzer commented Oct 14, 2019

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ewels commented Oct 15, 2019

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