Commit 07c77a7f authored by Jerome Mariette's avatar Jerome Mariette
Browse files

new version of jflow article

parent a6756ef5
......@@ -112,10 +112,9 @@ data type compliance for each parameter. Job submission, status
checking and error handling, rely on Makeflow (Albrecht et al., 2012) and
weaver (Bui et al., 2012). Therefore Jflow manages error recovery and supports
most distributed resource management systems (Condor, SGE, Work Queue or a
single multicore machine, \ldots). Changing Makeflow by an other jobs submiter
can be done by implementing a new \textit{Engine} subclass. This one is in
charge to create, in the right format, and execute the workflow directed acyclic
graph (DAG).
single multicore machine, \ldots). Replacing Makeflow by an other job submiter
requires to implement a new \textit{Engine} subclass. This class creates and
execute the workflow directed acyclic graph (DAG).
\section{Example}
......@@ -136,16 +135,15 @@ form using the \textit{wfform} plugin. Considering the parameter type, Jflow
adapts its display. For example, a date is displayed as a calendar and a boolean
as a checkbox.
One of a common analysis performed by NG6 is to check the contamination of
experimental samples. This can be done by aligning the samples sequences against
a reference genome. Biological samples are often composed of read files and
metadata such as sample name, tissue, developpement stage. To help biologists to enter
such information, Jflow uses structured data inputs. Such parameter sets are
displayed within the \textit{wfform} plugin as a spreadsheet, allowing to copy
and paste multiple lines. The reference genome is a single file represented in
the form by a standard text input with a button allowing to browse and upload
local files. At execution, Jflow will iterate on the table content to align
each samples against the reference genome.
Biologists use NG6 to check sequencing reads quality, including experimental
samples contamination measure (quantification/search). The first input of this
analysis is the contaminant reference genome fasta file, displayed as a file
selector. The second input is a parameter set describing the biological samples.
It includes the read files and metadata such as sample name, tissue and
developpement stage. To help biologists populate it, Jflow uses a structured
data input rendered by the \textit{wfform} plugin as a spreadsheet. It allows to
copy and paste multiple lines. Jflow iterates then on the table content to
launch each sample processing.
\begin{figure}[ht]
\centering
......
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