enable a pre-built bowtie2 index for rrna removal - #1892
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Summary (in progress)
Changes made
bowtie2_rrna_indexhas been added tonextflow_schema.jsonwith a brief description and help textValidation logic added in
main.nfandworkflows/rnaseq/main.nfto set a path to the prebuilt index if provided (initialise empty channel if not provided) and to setmake_bowtie2_indexto trueNo changes made to
FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESSorPREPARE_GENOMEas the index building step insubworkflows/nf-core/fastq_remove_rrna/main.nfalready checks ifmake_bowtie2_indexis set to true before buildingTests in development, need to source or build a bowtie index
PR checklist
If necessary, also make a PR on the nf-core/rnaseq branch on the nf-core/test-datasets repository.nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).