#!/usr/bin/env cwltool ### This is kind of a worthless workflow, ### ### but to keep consistent with the paired-end ### ### pipeline, I'm keeping it here. ### cwlVersion: v1.0 class: Workflow requirements: - class: StepInputExpressionRequirement - class: SubworkflowFeatureRequirement - class: ScatterFeatureRequirement # TODO needed? - class: MultipleInputFeatureRequirement #hints: # - class: ex:ScriptRequirement # scriptlines: # - "#!/bin/bash" inputs: dataset: type: string # randomer_length: # type: string # barcodesfasta: # type: File read: type: type: record fields: read1: type: File # barcodeids: # type: string[] name: type: string outputs: ### DEMUXED FILES ### A_output_demuxed_read1: type: File outputSource: gzip_demux/gzipped read_name: type: string outputSource: AB_demux/name dataset_name: type: string outputSource: AB_demux/output_dataset ### TRIM/CUTADAPT PARAMS ### steps: ########################################################################### # Upstream ########################################################################### AB_demux: run: demux_se.cwl in: reads: read dataset: dataset out: [ demuxedAfwd, output_demuxedsingleend_metrics, output_dataset, name ] ########################################################################### # Downstream ########################################################################### gzip_demux: run: gzip.cwl in: input: AB_demux/demuxedAfwd out: - gzipped doc: | This workflow takes in single-end reads, and performs the following steps in order: demux_se.cwl (does not actually demux for single end, but mirrors the paired-end processing protocol)