Re build rnaseq

runs/kallisto_quant-pe/run.cwl

+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+
+hints:
+  DockerRequirement:
+    dockerPull: quay.io/biocontainers/kallisto:0.43.0--hdf51.8.17_2
+
+inputs:
+- id: sh_script
+  type: File
+  inputBinding:
+    position: 0
+- id: out_folder
+  type: string
+  inputBinding:
+    position: 1
+- id: in_kallisto_index
+  type: File
+  inputBinding:
+    position: 2
+- id: in_fastq_dir
+  type: Directory
+  inputBinding:
+    position: 3
+- id: kallisto_bootstrap
+  type: int
+  inputBinding:
+    position: 4
+- id: kallisto_threads
+  type: int
+  inputBinding:
+    position: 5
+
+outputs:
+- id: outdir
+  type:
+    type: array
+    items: Directory
+  outputBinding:
+    glob: $(runtime.outdir)/$(inputs.out_folder)
+
+baseCommand:
+- bash