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input schema generation tests: use local files, not remote
1 parent 7af7522 commit ebf39cc

14 files changed

+404
-43
lines changed

‎testdata/bwa-mem-job.json

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{
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"reference": {
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"class": "File",
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"location": "chr20.fa",
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"size": 123,
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"checksum": "sha1$hash"
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},
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"reads": [
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{
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"class": "File",
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"location": "example_human_Illumina.pe_1.fastq"
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},
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{
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"class": "File",
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"location": "example_human_Illumina.pe_2.fastq"
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}
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],
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"min_std_max_min": [
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1,
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2,
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3,
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4
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],
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"minimum_seed_length": 3
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}

‎testdata/bwa-mem-tool.cwl

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#!/usr/bin/env cwl-runner
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cwlVersion: v1.2
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class: CommandLineTool
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hints:
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- class: ResourceRequirement
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coresMin: 2
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- class: DockerRequirement
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dockerPull: docker.io/python:3-slim
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inputs:
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- id: reference
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type: File
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inputBinding: { position: 2 }
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- id: reads
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type:
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type: array
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items: File
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inputBinding: { position: 3 }
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- id: minimum_seed_length
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type: int
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inputBinding: { position: 1, prefix: -m }
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- id: min_std_max_min
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type: { type: array, items: int }
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inputBinding:
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position: 1
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prefix: -I
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itemSeparator: ","
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- id: args.py
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type: File
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default:
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class: File
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location: args.py
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inputBinding:
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position: -1
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outputs:
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- id: sam
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type: ["null", File]
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outputBinding: { glob: output.sam }
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- id: args
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type:
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type: array
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items: string
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baseCommand: python
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arguments:
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- bwa
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- mem
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- valueFrom: $(runtime.cores)
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position: 1
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prefix: -t
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stdout: output.sam

‎testdata/dir-job.yml

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indir:
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class: Directory
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location: testdir

‎testdata/dir.cwl

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class: CommandLineTool
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cwlVersion: v1.2
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requirements:
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- class: ShellCommandRequirement
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inputs:
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indir: Directory
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outputs:
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outlist:
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type: File
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outputBinding:
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glob: output.txt
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arguments: ["cd", "$(inputs.indir.path)",
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{shellQuote: false, valueFrom: "&&"},
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"find", ".",
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{shellQuote: false, valueFrom: "|"},
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"sort"]
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stdout: output.txt

‎testdata/env-job.json

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{
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"in": "hello test env"
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}

‎testdata/env-tool1.cwl

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class: CommandLineTool
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cwlVersion: v1.2
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inputs:
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in: string
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outputs:
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out:
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type: File
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outputBinding:
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glob: out
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requirements:
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EnvVarRequirement:
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envDef:
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TEST_ENV: $(inputs.in)
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baseCommand: ["/bin/sh", "-c", "echo $TEST_ENV"]
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stdout: out

‎testdata/rename-inputs.cwl

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#!/usr/bin/env cwl-runner
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id: InputSecondaryFileConformanceTest
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class: CommandLineTool
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cwlVersion: v1.2
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doc: |
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Simple test to confirm the implementation of expressions returning a File within a CommandInputParameter.secondaryFile field.
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Use GREP to filter the result from ls to ensure we only get the secondary files in there.
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Related links:
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- Issue: https://github.com/common-workflow-language/cwltool/issues/1232
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- PR: https://github.com/common-workflow-language/cwltool/pull/1233
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- Discourse: https://cwl.discourse.group/t/ask-cwl-to-rename-a-secondary-file/72
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inputs:
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- id: inputWithSecondary
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type: File
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doc: |
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This input will with a secondary file `.accessory`. You could create these files (and its accessory) with:
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```bash
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touch secondary_file_test.txt
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touch secondary_file_test.txt.accessory
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```
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secondaryFiles:
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- |
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${
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function resolveSecondary(base, secPattern) {
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if (secPattern[0] == '^') {
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var spl = base.split('.');
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var endIndex = spl.length > 1 ? spl.length - 1 : 1;
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return resolveSecondary(spl.slice(undefined, endIndex).join("."), secPattern.slice(1));
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}
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return base + secPattern;
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}
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return [{
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"class": "File",
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"location": inputs.accessory.location,
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"basename": resolveSecondary(self.basename, '^.accessory')
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}];
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}
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- id: accessory
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type: File
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arguments:
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- "ls"
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- $(inputs.inputWithSecondary.dirname)
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- valueFrom: "|"
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shellQuote: false
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- "grep"
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- "secondary"
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outputs:
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- id: output_file
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type: stdout
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stdout: result
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requirements:
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InlineJavascriptRequirement: {}
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ShellCommandRequirement: {}

‎testdata/rename-inputs.yml

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inputWithSecondary:
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class: File
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location: secondary_file_test.txt
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accessory:
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class: File
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location: secondary_file_test.txt.accessory

‎testdata/revsort-job.json

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{
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"input": {
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"class": "File",
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"location": "whale.txt"
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}
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}

‎testdata/revsort-packed.cwl

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{
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"cwlVersion": "v1.2",
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"$graph": [
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{
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"class": "Workflow",
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"doc": "Reverse the lines in a document, then sort those lines.",
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"hints": [
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{
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"class": "DockerRequirement",
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"dockerPull": "docker.io/debian:stable-slim"
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}
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],
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"inputs": [
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{
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"type": "File",
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"doc": "The input file to be processed.",
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"id": "#main/input"
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},
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{
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"type": "boolean",
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"default": true,
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"doc": "If true, reverse (descending) sort",
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"id": "#main/reverse_sort"
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}
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],
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"outputs": [
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{
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"type": "File",
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"outputSource": "#main/sorted/output",
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"doc": "The output with the lines reversed and sorted.",
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"id": "#main/output"
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}
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],
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"steps": [
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{
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"in": [
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{
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"source": "#main/input",
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"id": "#main/rev/input"
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}
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],
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"out": [
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"#main/rev/output"
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],
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"run": "#revtool.cwl",
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"id": "#main/rev"
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},
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{
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"in": [
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{
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"source": "#main/rev/output",
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"id": "#main/sorted/input"
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},
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{
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"source": "#main/reverse_sort",
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"id": "#main/sorted/reverse"
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}
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],
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"out": [
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"#main/sorted/output"
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],
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"run": "#sorttool.cwl",
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"id": "#main/sorted"
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}
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],
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"id": "#main"
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},
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{
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"class": "CommandLineTool",
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"doc": "Reverse each line using the `rev` command",
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"inputs": [
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{
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"type": "File",
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"inputBinding": {},
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"id": "#revtool.cwl/input"
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}
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],
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"outputs": [
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{
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"type": "File",
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"outputBinding": {
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"glob": "output.txt"
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},
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"id": "#revtool.cwl/output"
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}
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],
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"baseCommand": "rev",
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"stdout": "output.txt",
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"id": "#revtool.cwl"
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},
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{
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"class": "CommandLineTool",
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"doc": "Sort lines using the `sort` command",
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"inputs": [
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{
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"id": "#sorttool.cwl/reverse",
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"type": "boolean",
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"inputBinding": {
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"position": 1,
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"prefix": "-r"
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}
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},
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{
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"id": "#sorttool.cwl/input",
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"type": "File",
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"inputBinding": {
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"position": 2
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}
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}
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],
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"outputs": [
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{
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"id": "#sorttool.cwl/output",
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"type": "File",
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"outputBinding": {
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"glob": "output.txt"
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}
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}
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],
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"baseCommand": "sort",
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"stdout": "output.txt",
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"id": "#sorttool.cwl"
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}
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]
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}

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