Invalid process input definition
gary...@gmail.com
Hi all, I'm now to nextflow and I'm wondering if this is the right way to generate data for each group size and then run inference for each dateset generated? I'm wondering if there's syntax error in generateData and runInference, since it's giving me ERROR ~ Invalid process input definition. It's really difficult for me to code since there are only very few examples.
deliverableDir = 'deliverables/' + workflow.scriptName.replace('.nf','')
nGroups = 2
minGroupSize = 10
maxGroupSize = 20
process build {
cache false
output:
file 'jars_hash' into jars_hash
file 'classpath' into classpath
"""
set -e
current_dir=`pwd`
cd ../../../..
./gradlew build
./gradlew printClasspath | grep CLASSPATH-ENTRY | sort | sed 's/CLASSPATH[-]ENTRY //' > \$current_dir/temp_classpath
for file in `ls build/libs/*jar`
do
echo `pwd`/\$file >> \$current_dir/temp_classpath
done
cd -
touch jars_hash
for jar_file in `cat temp_classpath`
do
shasum \$jar_file >> jars_hash
done
cat temp_classpath | paste -sd ":" - > classpath
"""
}
jars_hash.into {
jars_hash1
jars_hash2
}
classpath.into {
classpath1
classpath2
}
process generateData {
cache 'deep'
input:
each i from minGroupSize..maxGroupSize
file classpath1
file jars_hash1
output:
file 'generated$i' into data
"""
set -e
java -cp `cat classpath` -Xmx2g matchings.PermutedClustering \
--experimentConfigs.managedExecutionFolder false \
--experimentConfigs.saveStandardStreams false \
--experimentConfigs.recordExecutionInfo false \
--experimentConfigs.recordGitInfo false \
--model.nGroups $nGroups \
--model.groupSize $i \
--engine Forward
mv samples generated$i
"""
}
process runInference {
cache 'deep'
input:
each i from minGroupSize..maxGroupSize
file data.collect()
file classpath2
file jars_hash2
output:
file 'samples' into samples
"""
set -e
tail -n +2 generated${i}/observations.csv | awk -F "," '{print \$2, ",", \$3, ",", \$4}' | sed 's/ //g' > data.csv
java -cp `cat classpath` -Xmx2g matchings.PermutedClustering \
--initRandom 123 \
--experimentConfigs.managedExecutionFolder false \
--experimentConfigs.saveStandardStreams false \
--experimentConfigs.recordExecutionInfo false \
--experimentConfigs.recordGitInfo false \
--model.nGroups $nGroups \
--model.groupSize $i \
--model.observations.file data.csv \
--engine PT \
--engine.nScans 2_000 \
--engine.nThreads MAX \
--engine.nChains 8
done
mv samples generated$i
"""
}
Paolo Di Tommaso
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