Move process "convertGFFtoGTF" before "makeSTARindex"

[silviamorins]

Running the command:

nextflow run nf-core/rnaseq -r 1.3 -profile cfc --fasta 'Streptomyces_coelicolor_a3_2_.ASM20383v1.dna_rm.toplevel.fa' --gff 'Streptomyces_coelicolor_a3_2_.ASM20383v1.43.chromosome.Chromosome.gff' --reads '[...]*_{R1,R2}.fastq.gz' -resume --skip_preseq --reverse_stranded --skip_genebody_coverage

I get the following error:
ERROR ~ No such variable: gtf_makeSTARindex

As suggested by @lpantano here I tried moving the process convertGFFtoGTF before makeSTARindex, so that as this last one starts, the necessary input file ${gff.baseName}.gtf (coming from convertGFFtoGTF) exists; the error doesn't show up anymore.

PR checklist

• This comment contains a description of changes (with reason)
• Make sure your code lints (nf-core lint .).
• CHANGELOG.md is updated

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

[drpatelh]

Nice! Great debugging @lpantano ! Thanks @silviamorins 👍

[drpatelh]

Did you change environment.yml @silviamorins . There seems to be something funky going on with the PR. The featureCounts commit isnt showing up either...

[silviamorins]

I took away a change I had previously pushed to my fork (I had added a -M flag) in the featureCounts command, and updated my environment.yml so that is is the dame to the file in the dev branch of nf-core/rnaseq - I tend to miss up with git, I am sorry, can I do something to solve this?

[drpatelh]

Git gets me sometimes too 👍 There may be a more cleverer way to do this but for a small change like this I would just re-download all 3 original files you have amended and then make the changes again. Git should work out the differences based on that. e.g.

wget -L https://raw.githubusercontent.com/nf-core/rnaseq/dev/environment.yml
wget -L https://raw.githubusercontent.com/nf-core/rnaseq/dev/main.nf
wget -L https://raw.githubusercontent.com/nf-core/rnaseq/dev/CHANGELOG.md

[silviamorins]

I should have fixed it .. ?

[apeltzer]

environment.yml missing - that should be required too 👍

[silviamorins]

But I haven't changed it, is the same as in https://raw.githubusercontent.com/nf-core/rnaseq/dev/environment.yml

[apeltzer]

Hmm, the PR says you did ;-)

https://github.com/nf-core/rnaseq/pull/248/files

[silviamorins]

I removed it and then downloaded it again with wget -L https://raw.githubusercontent.com/nf-core/rnaseq/dev/environment.yml. So it's the same as in the dev branch now.

[drpatelh]

When did you fork the pipeline? Im wondering if its because you havent updated your local branch to contain the current code on dev..

[drpatelh]

Can you try running these commands:
git remote add upstream https://github.com/nf-core/rnaseq.git
git pull upstream dev
git push

[silviamorins]

I did as you said, had a conflict on the CHANGELOG, solved it and pushed. It still doesn't look alright to me ..

[drpatelh]

Looks fine now 👍 Only the files you amended are showing up now with only the changes you made.

[silviamorins]

Great, thanks! sorry for the loss of time. Will try not to mess it up next time.

[drpatelh]

No worries. The trick is to make sure you update the code on your fork every time you want to add new commits because this will factor in new changes to dev since your last changes.