Fix/run only proteomics#79
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…E_REFERENCE module runs for files without RNA predicted proteome input
…_PROTEOME_REFERENCE to use pipeline-wide protein FASTA if available instead of direct download
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PR checklist
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).