Lost the output file after two steps with stdout

CWL Questions
1

My workflow(annotateVCF.cwl) has two steps: snpEff and gzip.

First, snpEff outputted its result(ann.vcf) to stdout, which was used by gzip as the input. Then, gzip compressed the ann.vcf and outputted the ann.vcf.gz to stdout.

The problem is: ann.vcf.gz was lost somewhere in the tmp directory and was not moved to the current working directory. Can anybody give me a solution to this problem?

annotateVCF.cwl

#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: Workflow
label: Annotate the VCF file and compress the resulting VCF

############
inputs:
  species:
    type: string
  input_vcf:
    type: string
  output_vcf:
    type: string

############
steps:
  snpEff:
    run: snpEff.cwl
    in:
      species: species
      input_vcf: input_vcf
      output_vcf: output_vcf
    out: [stdout_vcf]

  gzip:
    run:
      class: CommandLineTool
      baseCommand: [gzip, -f, -c]
      inputs:
        fileToCompress:
          type: File
          inputBinding:
            position: 1
      
      stdout: $(inputs.fileToCompress.basename).gz

      outputs: []

    in:
      fileToCompress: 
        source: snpEff/stdout_vcf
    out: []

############
outputs: []

snpEff.cwl

#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: CommandLineTool
label: snpEff

baseCommand: [java, -jar, /home/user1/snpEff.jar]

inputs:
  species:
    type: string
    inputBinding:
      position: 1
  input_vcf:
    type: string
    inputBinding:
      position: 2
  output_vcf:
    type: string
    
stdout: $(inputs.output_vcf)
 
outputs:
  stdout_vcf:
    type: stdout

job.yml

species: GRCm39.105
input_vcf: /data/input.vcf.gz
output_vcf: ann.vcf
2

Hello @ionox0!

CWL is very explicit: if your output section is empty, then no outputs will be preserved.

  gzip:
    run:
      class: CommandLineTool
      baseCommand: [gzip, -f, -c]
      inputs:
        fileToCompress:
          type: File
          inputBinding:
            position: 1
      
      stdout: $(inputs.fileToCompress.basename).gz

      outputs:
        result: stdout

    in:
      fileToCompress: 
        source: snpEff/stdout_vcf
    out: [result]

############
outputs:
 result:
   type: File
   outputSource: gzip/result