Allowing to use a genome not in igenomes

[sdjebali]

Description of changes

• correct gunzip action and variable assignment of hairpin and mature fasta files in bowtie_indices step
• remove file 'genome.fa' into fasta from the bowtie_indices outputs
• replace fasta by reference_genome in file refgenome from fasta of mirdeep2 inputs
• replace Y nt by N in hairpin.fa

Adding tests

Tested with the following commands:

module load bioinfo/Nextflow-v20.10.0
module load system/singularity-3.6.4
export SINGULARITY_PULLFOLDER=/work/project/fragencode/workspace/geneswitch/code/containers/singularity
nextflow run <codedir>/smrnaseq \
  --input <datadir>/sus_scrofa/*.fastq.gz \
  --fasta <datadir>/sus_scrofa/Sscrofa11.1.101/sus_scrofa_nowhitespace.fa \
  --mirtrace_species ssc \
  -profile singularity \
  --protocol nextflex \
  --outdir <outdir> \
  --max_memory '16.GB' \
  --max_cpus 2 \
  --email <myemail> \
  --skip_mirdeep \
  -resume \
  > nextflow.out 2> nextflow.err

(edited by @ewels to split arguments onto their own lines)

Minimal inputs for this pipeline can be found at http://genoweb.toulouse.inra.fr/~sdjebali/nf-core/smrnaseq/

However I am still getting an error:

No such variable: reference_genome
 -- Check script '/work2/project/fragencode/workspace/sdjebali/geneswitch/pipelines/srnaseq/smrnaseq/main.nf' at line: 830 or see '.nextflow.log' file for more details

Ensure the test suite passes

I have tried it
but
nextflow run . -profile test,docker
returns
Cannot enable more than one container engine -- Choose either one of: docker, singularity

Make sure your code lints

do not know where to find nf-core executable sorry

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

• 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/smrnaseq 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

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

[lpantano]

I put some changes to make this work with the skip_mirdeep option. It is working for me.

[lpantano]

the line below should be:
sed '/^[^>]/s/[^ATGCatgc]/N/g' $refgenome > genome.fa

[lpantano]

and update below to bowtie-build genome.fa genome

[ewels]

Made a couple of these "suggested changes" so that they can be applied easily. Can't do all of them sadly.

[lpantano]

this PR was addressed in #65, should we close this? or there is another feature/bug here? Thanks!

[sdjebali]

yes this can be closed thanks a lot Lorena

On 2/26/21 12:02 AM, Lorena Pantano wrote: this PR was addressed in #65 <#65>, should we close this? or there is another feature/bug here? Thanks! — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#63 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AATLUALSKKV3PHDSKMQOYSDTA3JITANCNFSM4V5W2PZA>.

-- Sarah Djebali - PhD - CR INSERM Iron metabolism genetics and regulation IRSD INSERM U1220 - Bat B - CHU Purpan Place du Docteur Baylac - CS 60039 31024 Toulouse Cedex 3 +33 5 62 74 45 08 sarah dot djebali at inserm dot fr