name: ultra_pipeline description: uLTRA aligner - A wrapper around minimap2 to improve small exon detection keywords: - uLTRA - minimap2 tools: - ultra: description: Splice aligner of long transcriptomic reads to genome. homepage: https://github.com/ksahlin/uLTRA documentation: https://github.com/ksahlin/uLTRA tool_dev_url: https://github.com/ksahlin/uLTRA doi: "10.1093/bioinformatics/btab540" licence: ['GNU GPLV3'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: type: file description: A fasta or fastq file of reads to align pattern: "*.{fasta,fastq}" - genome: type: file description: fasta file of reference genome pattern: "*.fasta" - gtf: type: file description: A annotation of use the genome pattern: "*.gtf" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - sam: type: file description: The aligned reads in sam format pattern: "*.sam" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@sguizard" - "@lassefolkersen" - "@ksahlin"