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 params: - outdir: type: string description: | The pipeline's output directory. By default, the module will output files into `$params.outdir/` - publish_dir_mode: type: string description: | Value for the Nextflow `publishDir` mode parameter. Available: symlink, rellink, link, copy, copyNoFollow, move. - enable_conda: type: boolean description: | Run the module with Conda using the software specified via the `conda` directive - singularity_pull_docker_container: type: boolean description: | Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead. input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: type: file description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - index: type: directory description: Folder containing the star index files - gtf: type: file description: GTF of the reference transcriptome - transcriptome_fasta: type: file description: Fasta file of the reference transcriptome - alignment_mode: type: boolean description: whether to run salmon in alignment mode output: - sample_output: type: directory description: Folder containing the quantification results for a specific sample pattern: "${prefix}" - version: type: file description: File containing software version pattern: "*.{version.txt}" authors: - "@kevinmenden" - "@drpatelh"