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when secondaryFiles is in an array, pass to each item #91

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when secondaryFiles is in an array, pass to each item #91

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4fa4157
when secondaryFiles is in an array, pass to each item
jeremiahsavage Jun 2, 2016
2fd8bf3
Merge pull request #1 from common-workflow-language/master
jeremiahsavage Jul 6, 2016
0cb0b7b
Merge pull request #2 from common-workflow-language/master
jeremiahsavage Jul 7, 2016
b86020b
Merge pull request #3 from common-workflow-language/master
jeremiahsavage Jul 10, 2016
a7a5595
Merge pull request #4 from common-workflow-language/master
jeremiahsavage Jul 14, 2016
cdcb9ab
Merge pull request #5 from common-workflow-language/master
jeremiahsavage Jul 18, 2016
5838899
stage files to outdir when using docker
jeremiahsavage Jul 19, 2016
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9 changes: 7 additions & 2 deletions cwltool/builder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -96,8 +96,13 @@ def bind_input(self, schema, datum, lead_pos=[], tail_pos=[]):
if binding:
b2 = copy.deepcopy(binding)
b2["valueFrom"] = item
bindings.extend(self.bind_input({"type": schema["items"], "inputBinding": b2},
item, lead_pos=n, tail_pos=tail_pos))
if "secondaryFiles" in schema:
bindings.extend(self.bind_input({"type": schema["items"], "inputBinding": b2,
"secondaryFiles" : schema["secondaryFiles"]},
item, lead_pos=n, tail_pos=tail_pos))
else:
bindings.extend(self.bind_input({"type": schema["items"], "inputBinding": b2},
item, lead_pos=n, tail_pos=tail_pos))
binding = None

if schema["type"] == "File":
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2 changes: 1 addition & 1 deletion cwltool/job.py
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Expand Up @@ -183,7 +183,7 @@ def linkoutdir(src, tgt):
# the container)
for _, item in self.pathmapper.items():
if src == item.resolved:
os.symlink(item.target, tgt)
os.symlink(src, tgt)
break
stageFiles(generatemapper, linkoutdir)

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2 changes: 1 addition & 1 deletion cwltool/process.py
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Expand Up @@ -420,7 +420,7 @@ def _init_job(self, joborder, **kwargs):
raise WorkflowException("Document has DockerRequirement under 'requirements' but use_container is false. DockerRequirement must be under 'hints' or use_container must be true.")

if dockerReq and kwargs.get("use_container"):
builder.outdir = kwargs.get("docker_outdir") or "/var/spool/cwl"
builder.outdir = kwargs.get("outdir") or "/var/spool/cwl"
builder.tmpdir = kwargs.get("docker_tmpdir") or "/tmp"
builder.stagedir = kwargs.get("docker_stagedir") or "/var/lib/cwl"
else:
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