add changes from additional fasta PR #419

pranathivemuri · 2020-05-22T20:30:16Z

Many thanks to contributing to nf-core/rnaseq!

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Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).

PR checklist

PR is to dev rather than master
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 .).
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CHANGELOG.md is updated
README.md is updated

Learn more about contributing: https://github.com/nf-core/rnaseq/tree/master/.github/CONTRIBUTING.md

main.nf

Co-authored-by: Olga Botvinnik <[email protected]>

…tf takes place

pranathivemuri · 2020-05-22T23:32:53Z

main.nf

@@ -298,9 +332,7 @@ if (params.gtf) {
    Channel
        .fromPath(params.gtf, checkIfExists: true)
        .ifEmpty { exit 1, "GTF annotation file not found: ${params.gtf}" }
-        .into { gtf_makeSTARindex; gtf_makeHisatSplicesites; gtf_makeHISATindex; gtf_makeSalmonIndex; gtf_makeBED12;


@olgabot I am not sure if this change is correct - But I did it to not have the channels called by the operator here and in the later steps as outputs.

.github/workflows/ci.yml

.travis.yml

pranathivemuri · 2020-05-26T18:44:31Z

same as PR - #208

bin/fasta2gtf.py

Co-authored-by: Olga Botvinnik <[email protected]>

Output concatenated genome fasta to RSEM reference

pranathivemuri · 2020-06-03T01:00:01Z

@olgabot please review?

olgabot

Excited to see this get in!

olgabot · 2020-06-03T17:18:41Z

main.nf

@@ -395,6 +417,9 @@ if (params.genome) summary['Genome'] = params.genome
 if (params.pico) summary['Library Prep'] = "SMARTer Stranded Total RNA-Seq Kit - Pico Input"
 summary['Strandedness'] = (unStranded ? 'None' : forwardStranded ? 'Forward' : reverseStranded ? 'Reverse' : 'None')
 summary['Trimming'] = "5'R1: $clip_r1 / 5'R2: $clip_r2 / 3'R1: $three_prime_clip_r1 / 3'R2: $three_prime_clip_r2 / NextSeq Trim: $params.trim_nextseq"
+if (params.additional_fasta){


Can this if statement be on one line?

apeltzer

Except for the Dockerfile / sysctl stuff, I'm happy with this 👍

Need to think about making all of this a bit more modular using DSLv2 soon, but thats something for a different discussion/PR :-)

apeltzer · 2020-06-03T17:57:20Z

Dockerfile

@@ -11,3 +11,4 @@ ENV PATH /opt/conda/envs/nf-core-rnaseq-1.4.3dev/bin:$PATH

 # Dump the details of the installed packages to a file for posterity
 RUN conda env export --name nf-core-rnaseq-1.4.3dev > nf-core-rnaseq-1.4.3dev.yml
+COPY assets/sysctl.conf /etc/sysctl.conf


Mhm, this seems to be changing stuff that might affect others too - maybe get rid of this?

apeltzer · 2020-06-03T17:57:31Z

assets/sysctl.conf

@@ -0,0 +1 @@
+vm.nr_hugepages=128


See above ;-)

pranathivemuri · 2020-06-03T21:09:06Z

@olgabot @apeltzer please review again and feel free to merge it!

pranathivemuri · 2020-06-08T03:40:51Z

@olgabot @apeltzer please review again and feel free to merge it!

apeltzer · 2020-06-08T08:28:08Z

Could you fix the markdown issues once more?

/home/runner/work/rnaseq/rnaseq/CHANGELOG.md:19 MD032/blanks-around-lists Lists should be surrounded by blank lines [Context: "* Builds are done on GitHub Ac..."]
/home/runner/work/rnaseq/rnaseq/CHANGELOG.md:20:1 MD004/ul-style Unordered list style [Expected: asterisk; Actual: dash]
/home/runner/work/rnaseq/rnaseq/CHANGELOG.md:20 MD032/blanks-around-lists Lists should be surrounded by blank lines [Context: "- Add option for `--additional..."]
/home/runner/work/rnaseq/rnaseq/CHANGELOG.md:22 MD012/no-multiple-blanks Multiple consecutive blank lines [Expected: 1; Actual: 2]
##[error]Process completed with exit code 1.

apeltzer

Thank you for fixing everything @pranathivemuri !

add changes from additional fasta PR

b746c2c

pranathivemuri requested a review from olgabot May 22, 2020 20:30

olgabot changed the base branch from master to dev May 22, 2020 20:31

pranathivemuri added 6 commits May 22, 2020 13:39

resolve merge conflicts from dev

b585d07

lint

44d9c52

lint

8343bd8

logs

5926df6

add another bracket

f4b7666

fixed ch_genome_gtf error. to fixg tf_makeSTARindex

3b9c962

olgabot reviewed May 22, 2020

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main.nf Show resolved Hide resolved

pranathivemuri and others added 3 commits May 22, 2020 15:17

Update main.nf

bad82e3

Co-authored-by: Olga Botvinnik <[email protected]>

write to genome_gtf instead of the big list, reorder when combining g…

7cc50b0

…tf takes place

make file executable

d5e615b

pranathivemuri commented May 22, 2020

View reviewed changes

fix tests

51bafe8

olgabot requested changes May 23, 2020

View reviewed changes

.github/workflows/ci.yml Outdated Show resolved Hide resolved

.travis.yml Outdated Show resolved Hide resolved

pranathivemuri added 4 commits May 22, 2020 19:13

Delete .travis.yml

40be1d7

remove additonal_fasta flag in ci

5b248ca

Merge branch 'master' of https://github.com/pranathivemuri/rnaseq

d39f483

additional fasta gz extension corrected

4b6d928

olgabot requested changes May 26, 2020

View reviewed changes

bin/fasta2gtf.py Outdated Show resolved Hide resolved

olgabot reviewed May 26, 2020

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bin/fasta2gtf.py Outdated Show resolved Hide resolved

pranathivemuri and others added 7 commits May 26, 2020 13:58

correct flag

c4ccb69

Apply suggestions from code review

d170b19

Co-authored-by: Olga Botvinnik <[email protected]>

correct flag

d0ab115

Merge branch 'master' of https://github.com/pranathivemuri/rnaseq

fa47a49

correct fasta2gtf name formatting

93a5456

correct fasta2gtf name formatting

79fdac8

correcting the formatting again

9d72d92

pranathivemuri and others added 16 commits May 30, 2020 16:55

ch_genome_gtf writing to

db77ef0

fix variables

3fe379e

fix variables

a53cc84

fix variables

69e2bc4

fix variables

ade0833

fix variables

87f377d

fix variables

a506d03

fix variables

ebf1a98

unclear how to fix this merge conflict

113185f

add gtfile into gtf_makeRSEMReference

b0319ac

setting in combine

3276397

adjust ch_genome_gtf flag

fc183db

Merge branch 'dev' into master

02324a5

Maybe fix rsem error

9224bba

Merge pull request #1 from nf-core/olgabot/additional-fasta-rsem

672d3d7

Output concatenated genome fasta to RSEM reference

Update CHANGELOG.md

0b8ee5b

olgabot approved these changes Jun 3, 2020

View reviewed changes

apeltzer requested changes Jun 3, 2020

View reviewed changes

pranathivemuri added 2 commits June 3, 2020 14:06

correct assets

b37660e

Merge branch 'master' of https://github.com/pranathivemuri/rnaseq

c30942d

pranathivemuri added 2 commits June 7, 2020 20:38

Merge branch 'dev' into master

32597c4

Update CHANGELOG.md

e54f12e

lint changelog

61ebdcf

apeltzer approved these changes Jun 8, 2020

View reviewed changes

pranathivemuri merged commit c29d0c2 into nf-core:dev Jun 8, 2020

apeltzer mentioned this pull request Jun 17, 2020

No channel created for ch_fasta_for_rsem_reference #432

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add changes from additional fasta PR #419

add changes from additional fasta PR #419

pranathivemuri commented May 22, 2020

pranathivemuri May 22, 2020

pranathivemuri commented May 26, 2020

pranathivemuri commented Jun 3, 2020

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		@@ -0,0 +1 @@
		vm.nr_hugepages=128

add changes from additional fasta PR #419

add changes from additional fasta PR #419

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pranathivemuri commented May 22, 2020

PR checklist

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