79 lines
1.8 KiB
Plaintext
79 lines
1.8 KiB
Plaintext
set -e
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export NXF_ANSI_LOG=false
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#
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# create the `hello.sh` executable script
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#
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mkdir -p bin
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echo "echo Hola mundo" > bin/hello.sh
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chmod +x bin/hello.sh
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#
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# create the nextflow config file
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#
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cat << EOF > nextflow.config
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env.FOO = 'HOLA'
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process.container = 'quay.io/nextflow/bash'
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EOF
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#
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# create the nextflow script
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#
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cat << EOF > foo.nf
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process foo {
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debug true
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input:
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env 'BAR'
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script:
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'''
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env | grep -E "^(FOO|BAR)" | sort
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hello.sh
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'''
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}
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workflow {
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channel.value('Hello World!') | foo
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}
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EOF
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#
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# not the testing part
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#
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# NF plain run
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$NXF_CMD run foo.nf | tee stdout
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# run tests
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[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
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[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
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[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
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[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
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# NF run with trace
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$NXF_CMD run foo.nf -with-trace | tee stdout
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# run tests
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[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
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[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
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[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
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[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
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# NF run with docker
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$NXF_CMD run foo.nf -with-docker | tee stdout
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# run tests
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[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
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[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
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[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
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[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
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# NF run with docker and trace
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$NXF_CMD run foo.nf -with-trace -with-docker | tee stdout
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# run tests
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[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
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[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
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[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
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[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
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