name: salmon_quant description: gene/transcript quantification with Salmon keywords: - index - fasta - genome - reference tools: - salmon: description: | Salmon is a tool for wicked-fast transcript quantification from RNA-seq data homepage: https://salmon.readthedocs.io/en/latest/salmon.html manual: https://salmon.readthedocs.io/en/latest/salmon.html doi: 10.1038/nmeth.4197 licence: ['GPL-3.0-or-later'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: type: file description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - index: type: directory description: Folder containing the star index files - gtf: type: file description: GTF of the reference transcriptome - transcriptome_fasta: type: file description: Fasta file of the reference transcriptome - alignment_mode: type: boolean description: whether to run salmon in alignment mode - lib_type: type: string description: | Override library type inferred based on strandedness defined in meta object output: - sample_output: type: directory description: Folder containing the quantification results for a specific sample pattern: "${prefix}" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh"