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Gael MILLOT
micmac
Commits
3f684e32
Commit
3f684e32
authored
3 months ago
by
Gael MILLOT
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nextflow.config corrected: now the executor is correctly set
parent
23cb6613
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nextflow.config
+6
-6
6 additions, 6 deletions
nextflow.config
with
6 additions
and
6 deletions
nextflow.config
+
6
−
6
View file @
3f684e32
...
...
@@ -57,6 +57,7 @@ env {
//
see
https
://
confluence
.
pasteur
.
fr
/
pages
/
viewpage
.
action
?
pageId
=
69304504
system_exec
=
'local'
//
single
character
string
of
the
system
that
runs
the
workflow
.
Either
'local'
to
run
on
our
own
computer
or
'slurm'
to
run
on
the
pasteur
cluster
.
Example
:
system_exec
=
'local'
queue
=
'common,dedicated'
//
single
character
string
of
the
-
p
option
of
slurm
.
Example
:
queue
=
'common,dedicated'
.
Example
:
queue
=
'hubbioit'
simult_jobs
=
3000
//
number
of
max
simultaneous
jobs
.
This
is
to
avoid
to
saturated
a
cluster
if
millions
of
jobs
in
parallel
.
Write
0
for
all
the
threads
.
Not
used
if
system_exec
is
'local'
qos
=
'--qos=ultrafast'
//
single
character
string
of
the
--
qos
option
of
slurm
.
Example
:
qos
=
'--qos=fast'
.
Example
:
qos
=
'--qos=ultrafast'
.
Example
:
qos
=
'--qos=hubbioit'
add_options
=
' '
//
single
character
string
of
the
additional
option
of
slurm
.
Example
:
add_options
=
'--exclude=maestro-1101,maestro-1034'
or
add_options
=
' '
,
add_options
=
'--time=70:00:00'
(
acceptable
time
formats
include
"minutes"
,
"minutes:seconds"
,
"hours:minutes:seconds"
,
"days-hours"
,
"days-hours:minutes"
and
"days-hours:minutes:seconds"
).
See
https
://
slurm
.
schedmd
.
com
/
sbatch
.
html
#OPT_time for other options
...
...
@@ -117,14 +118,12 @@ env {
////////
Scopes
//
kind
of
execution
.
Either
'local'
or
'slurm'
//
those
are
closures
.
See
https
://
www
.
nextflow
.
io
/
docs
/
latest
/
script
.
html
#closures
executor
{
name
=
"
${system_exec}"
queueSize
=
2000
executor
{
//
name
=
"
slurm"
//
means
"if name of the executor is slurm, then ${simult_jobs}, i.e., max ${simult_jobs} simultaneous jobs"
.
Inactivated
because
applied
to
all
kinds
of
executors
queueSize
=
"${simult_jobs}"
//
can
only
be
written
here
and
not
below
because
queueSize
is
a
method
of
executor
{}
}
//
create
a
report
folder
and
print
a
html
report
file
.
If
no
absolute
path
,
will
be
where
the
run
is
executed
...
...
@@ -187,7 +186,8 @@ process {
//
directives
for
all
the
processes
cpus
=
1
memory
=
'3G'
executor
=
"${system_exec}"
//
end
directives
for
all
the
processes
if
(
system_exec
==
'slurm'
){
queue
=
"$queue"
clusterOptions
=
"$qos $add_options"
...
...
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