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Peter Amstutz
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Merge branch 'recursive_directory' of https://github.com/gijzelaerr/common-workflow-language 
2 parents c50c150 + d736a0e commit 71efb7b

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‎v1.0/conformance_test_v1.0.yaml

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@@ -995,4 +995,58 @@
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args: [-A,'2',-B,baz,-C,'10','9','8','7','6','5','4','3','2','1']
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job: v1.0/empty.json
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tool: v1.0/inline-js.cwl
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doc: Test InlineJavascriptRequirement with multiple expressions in the same tool
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doc: Test InlineJavascriptRequirement with multiple expressions in the same tool
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- job: v1.0/recursive-input-directory.yml
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output:
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output_dir: {
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"basename": "work_dir",
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"class": "Directory",
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"listing": [
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{
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"basename": "a",
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"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
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"class": "File",
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"location": "work_dir/a",
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"size": 0
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},
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{
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"basename": "b",
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"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
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"class": "File",
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"location": "work_dir/b",
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"size": 0
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},
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{
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"basename": "c",
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"class": "Directory",
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"listing": [
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{
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"basename": "d",
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"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
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"class": "File",
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"location": "work_dir/c/d",
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"size": 0
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}
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],
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"location": "work_dir/c",
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},
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{
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"basename": "e",
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"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
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"class": "File",
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"location": "work_dir/e",
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"size": 0
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},
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],
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"location": "work_dir",
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}
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test_result: {
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"basename": "output.txt",
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"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
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"class": "File",
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"location": "output.txt",
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"size": 0
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}
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tool: v1.0/recursive-input-directory.cwl
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doc: Test if a writable input directory is recursivly copied and writable

‎v1.0/v1.0/recursive-input-directory.cwl

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cwlVersion: v1.0
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class: CommandLineTool
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requirements:
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- class: InlineJavascriptRequirement
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- class: InitialWorkDirRequirement
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listing:
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- entry: $(inputs.input_dir)
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entryname: work_dir
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writable: true
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- class: ShellCommandRequirement
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stdout: output.txt
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arguments:
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- shellQuote: false
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valueFrom: |
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touch work_dir/e;
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if [ ! -w work_dir ]; then echo work_dir not writable; fi;
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if [ -L work_dir ]; then echo work_dir is a symlink; fi;
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if [ ! -w work_dir/a ]; then echo work_dir/a not writable; fi;
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if [ -L work_dir/a ]; then echo work_dir/a is a symlink; fi;
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if [ ! -w work_dir/c ]; then echo work_dir/c not writable; fi;
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if [ -L work_dir/c ]; then echo work_dir/c is a symlink; fi;
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if [ ! -w work_dir/c/d ]; then echo work_dir/c/d not writable; fi;
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if [ -L work_dir/c/d ]; then echo work_dir/c/d is a symlink; fi;
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if [ ! -w work_dir/e ]; then echo work_dir/e not writable; fi;
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if [ -L work_dir/e ]; then echo work_dir/e is a symlink ; fi;
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inputs:
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input_dir: Directory
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outputs:
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output_dir:
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type: Directory
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outputBinding:
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glob: work_dir
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test_result:
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type: stdout

‎v1.0/v1.0/recursive-input-directory.yml

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input_dir:
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class: Directory
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location: testdir

‎v1.1.0-dev1/conformance_test_v1.1.0-dev1.yaml

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@@ -1001,3 +1001,57 @@
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job: v1.1.0-dev1/default_path_job.yml
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tool: v1.1.0-dev1/default_path.cwl
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doc: Test warning instead of error when default path is not found
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- job: v1.1.0-dev1/recursive-input-directory.yml
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output:
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output_dir: {
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"basename": "work_dir",
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"class": "Directory",
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"listing": [
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{
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"basename": "a",
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"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
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"class": "File",
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"location": "work_dir/a",
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"size": 0
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},
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{
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"basename": "b",
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"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
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"class": "File",
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"location": "work_dir/b",
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"size": 0
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},
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{
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"basename": "c",
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"class": "Directory",
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"listing": [
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{
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"basename": "d",
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"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
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"class": "File",
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"location": "work_dir/c/d",
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"size": 0
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}
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],
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"location": "work_dir/c",
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},
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{
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"basename": "e",
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"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
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"class": "File",
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"location": "work_dir/e",
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"size": 0
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},
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],
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"location": "work_dir",
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}
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test_result: {
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"basename": "output.txt",
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"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
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"class": "File",
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"location": "output.txt",
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"size": 0
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}
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tool: v1.1.0-dev1/recursive-input-directory.cwl
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doc: Test if a writable input directory is recursivly copied and writable

‎v1.1.0-dev1/v1.1.0-dev1/recursive-input-directory.cwl

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cwlVersion: v1.1.0-dev1
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class: CommandLineTool
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requirements:
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- class: InlineJavascriptRequirement
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- class: InitialWorkDirRequirement
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listing:
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- entry: $(inputs.input_dir)
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entryname: work_dir
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writable: true
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- class: ShellCommandRequirement
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stdout: output.txt
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arguments:
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- shellQuote: false
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valueFrom: |
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touch work_dir/e;
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if [ ! -w work_dir ]; then echo work_dir not writable; fi;
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if [ -L work_dir ]; then echo work_dir is a symlink; fi;
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if [ ! -w work_dir/a ]; then echo work_dir/a not writable; fi;
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if [ -L work_dir/a ]; then echo work_dir/a is a symlink; fi;
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if [ ! -w work_dir/c ]; then echo work_dir/c not writable; fi;
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if [ -L work_dir/c ]; then echo work_dir/c is a symlink; fi;
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if [ ! -w work_dir/c/d ]; then echo work_dir/c/d not writable; fi;
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if [ -L work_dir/c/d ]; then echo work_dir/c/d is a symlink; fi;
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if [ ! -w work_dir/e ]; then echo work_dir/e not writable; fi;
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if [ -L work_dir/e ]; then echo work_dir/e is a symlink ; fi;
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inputs:
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input_dir: Directory
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outputs:
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output_dir:
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type: Directory
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outputBinding:
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glob: work_dir
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test_result:
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type: stdout

‎v1.1.0-dev1/v1.1.0-dev1/recursive-input-directory.yml

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input_dir:
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class: Directory
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location: testdir

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