Poly a

[karlaarz]

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 you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[karlaarz]

Hi @matbonfanti and @leandrotiburske! I made several changes and additions to the pipeline (it wasn't intended, but all these changes ended up being correlated, so I couldn't make different PRs). The main addition was the new polyA module, available only for direct RNA data.

Overall, the main changes include:

• new tests/pipeline_direct_rna.nf.test: 2-sample (HEK293T-WT + METTL3-KO) end-to-end run. Self-contained via config "../conf/test_direct_rna.config"so it uses the mini-genome/direct_rna params
• tests/default.nf.test: 2nd case exercising the direct cDNA branch (direct_rna=false); snapshot refreshed.
• tests/data/directrna: committed mini-genome (drna_genome.fa/drna.gtf), spliced transcriptome (drna_transcriptome.fa), and WT+KO direct-RNA reads (fastq + fast5 to test direct_RNA data).

Pipeline fixes:

• fast5 wiring: emit fast5 dir through NANOPOLISH_INDEX -> POLYA
• drimseq.R / dexseq.R: coerce gene_id/feature_id with as.character
• renamed DIRECT_RNA_QC -> CDNA_QC to easily detect processes

Please let me know if you have questions or what do you think.

Have a nice weekend!

[matbonfanti]

ciao @karlaarz, it is very nice that you have set up a lightweight test for the workflow... However, it is better to put the input data of the test in the nf code repo itself, to avoid making this repo unnecessarily heavy...

There are several place in which the data could be stored, the easier being the github repo that I have set specifically for this purpose: https://github.com/nfdata-omics/test-datasets

If you are available, we can meet and discuss this!

[leandrotiburske]

Hi @karlaarz,

I like having these test on the pipeline! I agree with @matbonfanti when it comes to storing the files though. By the way, we already have a folder called "nanopore" under the branch "refs": https://github.com/nfdata-omics/test-datasets/tree/refs/nanopore . We could move it to a branch of its own if you'd like it better

[karlaarz]

hi @matbonfanti ! I applied the changes we discussed last time about the test data. The tests pass now but I have one error. do I need to update the template version?