Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
primary["secondaryFiles"] = secondaryspec
for i, sf in enumerate(aslist(secondaryspec)):
if builder.cwlVersion == "v1.0":
primary["secondaryFiles"] = secondaryspec
for i, sf in enumerate(aslist(secondaryspec)):
if builder.cwlVersion == "v1.0":
- pattern = builder.do_eval(sf, context=primary)
- pattern = builder.do_eval(sf["pattern"], context=primary)
+ pattern = sf["pattern"]
if pattern is None:
continue
if isinstance(pattern, list):
if pattern is None:
continue
if isinstance(pattern, list):
"Expression must return list, object, string or null")
if pattern is not None:
"Expression must return list, object, string or null")
if pattern is not None:
- sfpath = substitute(primary["location"], pattern)
+ if "${" in pattern or "$(" in pattern:
+ sfname = builder.do_eval(pattern, context=primary)
+ else:
+ sfname = substitute(primary["basename"], pattern)
+
+ if sfname is None:
+ continue
+
+ p_location = primary["location"]
+ if "/" in p_location:
+ sfpath = (
+ p_location[0 : p_location.rindex("/") + 1]
+ + sfname
+ )
required = builder.do_eval(required, context=primary)
required = builder.do_eval(required, context=primary)
cwlVersion: v1.2
class: Workflow
cwlVersion: v1.2
class: Workflow
+
+requirements:
+ InlineJavascriptRequirement: {}
+
inputs:
file1:
type: File?
secondaryFiles:
- pattern: .tbi
required: true
inputs:
file1:
type: File?
secondaryFiles:
- pattern: .tbi
required: true
+ file2:
+ type: File
+ secondaryFiles:
+ - pattern: |
+ ${
+ return self.basename + '.tbi';
+ }
+ required: true
outputs:
out:
type: File
outputSource: cat/out
outputs:
out:
type: File
outputSource: cat/out
+ out2:
+ type: File
+ outputSource: cat2/out
steps:
cat:
in:
inp: file1
run: cat2.cwl
out: [out]
steps:
cat:
in:
inp: file1
run: cat2.cwl
out: [out]
+ cat2:
+ in:
+ inp: file2
+ run: cat2.cwl
+ out: [out]
file1:
class: File
location: 19109-upload-secondary/file1.txt
file1:
class: File
location: 19109-upload-secondary/file1.txt
+file2:
+ class: File
+ location: 19109-upload-secondary/file2.txt
--- /dev/null
+mango
\ No newline at end of file