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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
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genotoul-bioinfo
jflow
Commits
afc3629c
Commit
afc3629c
authored
Feb 25, 2015
by
Philippe Bardou
Browse files
highlight ini !
parent
751c8808
Changes
2
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docs/jflow-core-component.html
View file @
afc3629c
...
...
@@ -127,12 +127,12 @@
├── src/
├── workflows/
│ ├── myWorkflowName/
│ │ ├── components/
**
workflow specific components
**
│ │ │ └── myComponentName.py
**
the component code
**
│ │ ├── components/
[
workflow specific components
]
│ │ │ └── myComponentName.py
[
the component code
]
│ │ └── __init__.py
│ ├── components/
**
general components
**
│ ├── components/
[
general components
]
│ │ ├── __init__.py
│ │ └── myComponentName.py
**
the component code
**
│ │ └── myComponentName.py
[
the component code
]
│ ├── extparsers/
│ ├── __init__.py
│ ├── formats.py
...
...
@@ -791,8 +791,8 @@ self.add_output_file_list("sais", "sai files",
│ ├── components/
│ ├── extparsers/
│ │ ├── __init__.py
│ │ ├── yourParser.py
**
the code for your parser
**
│ │ └── mobyle.py
**
default mobyle component parser
**
│ │ ├── yourParser.py
[
the code for your parser
]
│ │ └── mobyle.py
[
default mobyle component parser
]
│ ├── __init__.py
│ ├── formats.py
│ └── types.py
...
...
docs/jflow-core-workflow.html
View file @
afc3629c
...
...
@@ -94,16 +94,16 @@
<li>
a
<code>
bin
</code>
folder with the binaries used in the workflow.
</li>
</ul>
<pre
class=
"pre-hl "
><code
class=
"
text
"
>
jflow/
<pre
class=
"pre-hl "
><code
class=
"
ini
"
>
jflow/
├── bin/
├── docs/
├── src/
├── workflows/
│ ├── myworkflow/
**
the new workflow package
**
│ │ ├── components/
**
specific components
**
│ │ ├── lib/
**
specific libraries
**
│ │ ├── bin/
**
specific binairies
**
│ │ └── __init__.py
**
the workflow implementation
**
│ ├── myworkflow/
[
the new workflow package
]
│ │ ├── components/
[
specific components
]
│ │ ├── lib/
[
specific libraries
]
│ │ ├── bin/
[
specific binairies
]
│ │ └── __init__.py
[
the workflow implementation
]
│ ├── components/
│ ├── extparsers/
│ ├── __init__.py
...
...
@@ -173,8 +173,7 @@ class MyWorkflow (Workflow):
self.add_parameter("sequencer",
"The sequencer type.",
choices = ["HiSeq2000", "ILLUMINA","SLX","SOLEXA","454","UNKNOWN"],
default="HiSeq2000")
</code></pre>
default="HiSeq2000")
</code></pre>
</div>
<h4>
Options
</h4>
...
...
@@ -423,8 +422,7 @@ class MyWorkflow (Workflow):
self.add_input_file("R1", "Path to R1 file.", required=True, add_to="library")
self.add_input_file("R2", "Path to R2 file.", add_to="library")
self.add_parameter("sequencer", "The sequencer type.", choices=["HiSeq2000",
"ILLUMINA", "UNKNOWN"], default="HiSeq2000", add_to="library")
</code></pre>
"ILLUMINA", "UNKNOWN"], default="HiSeq2000", add_to="library")
</code></pre>
</div>
<h3>
how to populate a multiple parameter
</h3>
...
...
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