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cutandrun_runner
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nf-core
cutandrun_runner
Commits
7432e93c
Commit
7432e93c
authored
2 years ago
by
Peng Lian
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Optimized trace
parent
469dcd80
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master
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cutandrun_runner.sh
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7432e93c
...
...
@@ -497,6 +497,7 @@ update_trace() {
if
[[
-f
$from_trace
]]
&&
[[
-f
$to_trace
]]
;
then
# from to_trace
grep
-v
"CUTANDRUN:"
$to_trace
>
./.trace.tmp
echo
-e
"
\n\n
"
>>
./.trace.tmp
# from from_trace
grep
"CUTANDRUN:"
$from_trace
|
awk
-F
"
\t
"
'BEGIN {OFS="\t"}; {if ($19) print $1,$2,$3,$4,$5,$6,$7,$10,$11,$15,$16,$17,$18,$19}'
|
sort
-un
|
sed
s
"/NFCORE_CUTANDRUN://g"
>>
./.trace.tmp
# update to_trace
...
...
@@ -519,9 +520,10 @@ while sleep 2; do
# workflow finished
if
grep
"Completed at:"
.nextflow.cutandrun.log &> /dev/null
;
then
kill
-9
$nextflowPID
&> /dev/null
sleep
2
sleep
5
# update the trace file before leaving
update_trace
$from_trace
$to_trace
sleep
5
exit
0
# nextflow is NOT running
elif
!
ps
-p
$nextflowPID
&> /dev/null
;
then
...
...
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