Skip to content

enable a pre-built bowtie2 index for rrna removal - #1892

Draft
emmanuel-tan wants to merge 2 commits into
nf-core:devfrom
emmanuel-tan:enhancement/rrna-bt-index
Draft

enable a pre-built bowtie2 index for rrna removal#1892
emmanuel-tan wants to merge 2 commits into
nf-core:devfrom
emmanuel-tan:enhancement/rrna-bt-index

Conversation

@emmanuel-tan

Copy link
Copy Markdown

Summary (in progress)

Changes made

  • bowtie2_rrna_index has been added to nextflow_schema.json with a brief description and help text

  • Validation logic added in main.nf and workflows/rnaseq/main.nf to set a path to the prebuilt index if provided (initialise empty channel if not provided) and to set make_bowtie2_index to true

  • No changes made to FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS or PREPARE_GENOME as the index building step in subworkflows/nf-core/fastq_remove_rrna/main.nf already checks if make_bowtie2_index is set to true before building

  • Tests in development, need to source or build a bowtie index

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! (In progress)
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/rnaseq branch on the nf-core/test-datasets repository.
  • 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).

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant