This question may be best asked on Galaxy support page: https://help.galaxyproject.org/

That said. Are you pointing MultiQC to FastQC results file(s)? Here is what the multiQC help says:

The FastQC MultiQC module looks for files called fastqc_data.txt or ending in _fastqc.zip. If the zip files are found, they are read in memory and fastqc_data.txt parsed.

Any workaround to this?, I am trying the same....

Basically, want to translate the following script's lines to CWL:

$ fastqc *.fastq.gz -o ${WORKDIR}/fastqc_analysis
$ cd ${WORKDIR}/fastqc_analysis
$ multiqc .

For that, i have written 2 tools (fastqc.cwl and multiqc.cwl) and got a workflow that uses that tools, the problem here is "fastqc tool", this tool read all files inside a directory and process it using scatter, and output a list of files.

How can I link the directory that contains all outputs to the next step (multiqc)?, I have tried adding the "working dir" (outputBinding: {glob: "."}) in the fastqc tool but since it is a scatter method it returns an array of directories and not a single dir.

There exists another way to run fastqc over a group of files that doesn't involve scatter?.

fatqc.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
label: fastqc tool

requirements:
  - class: DockerRequirement
    dockerPull: fastqc:0.11.8

baseCommand: [fastqc, --outdir, .]

inputs:
  fastqcFile:
    type: File
    inputBinding:
      position: 3
  threads:
    type: int
    inputBinding:
      position: 4
      prefix: "-t"
      separate: true

outputs:
    resultFiles:
      type:
        type: array
        items: File
      outputBinding:
        glob: "*"

    resultDir:
      type: Directory
      outputBinding:
        glob: "."

multiqc.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
label: fastqc tool

requirements:
  - class: DockerRequirement
    dockerPull: ewels/multiqc:1.7

baseCommand: multiqc

inputs:
  multiqcInputDir:
    type: Directory
    inputBinding:
      position: 1

outputs:
  report:
    type: File
    outputBinding:
      glob: "multiqc_report.html"
  metadata:
    type: Directory
    outputBinding:
      glob: "multiqc_data"

workflow.cwl This is not finished, just draft.

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: Workflow

requirements:
  - class: InlineJavascriptRequirement
  - class: ScatterFeatureRequirement
  - class: StepInputExpressionRequirement

inputs:
  fastqcSourceDir: Directory
  fastqcThreads: int

outputs:
  report:
    type: File
    outputSource: [multiqc/report]
  metadata:
    type: Directory
    outputSource: [multiqc/metadata]

steps:
  readDir:
    run: readDirFiles.cwl
    in:
      dir: fastqcSourceDir
    out: [files]
  fastqc:
    run: fastqc.cwl
    scatter: fastqcFile
    in:
      fastqcFile: readDir/files
      threads: fastqcThreads
    out: [resultFiles, resultDir]
  multiqc:
    run: multiqc.cwl
    in:
      multiqcInputDir: fastqc/resultDir
    out: [report, metadata]