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main.nf
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main.nf
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process TEST_SUCCESS {
/*
This process should automatically succeed
*/
output:
stdout
script:
"""
exit 0
"""
}
process TEST_CREATE_FILE {
/*
Creates a file on the worker node which is uploaded to the working directory.
*/
output:
path("*.txt"), emit: outfile
"""
echo "test" > test.txt
"""
}
process TEST_CREATE_EMPTY_FILE {
/*
Creates an empty file on the worker node which is uploaded to the working directory.
*/
output:
path("*.txt"), emit: outfile
"""
touch test.txt
"""
}
process TEST_CREATE_FOLDER {
/*
Creates a file on the worker node which is uploaded to the working directory.
*/
output:
path("test"), type: 'dir', emit: outfolder
"""
mkdir -p test
echo "test1" > test/test1.txt
echo "test2" > test/test2.txt
"""
}
process TEST_INPUT {
/*
Stages a file from the working directory to the worker node.
*/
input:
path input
output:
stdout
"""
cat $input
"""
}
process TEST_BIN_SCRIPT {
/*
Runs a script from the bin/ directory
*/
output:
path("*.txt")
"""
bash run.sh
"""
}
process TEST_STAGE_REMOTE {
/*
Stages a file from a remote file to the worker node.
*/
input:
path input
output:
stdout
"""
cat $input
"""
}
process TEST_PASS_FILE {
/*
Stages a file from the working directory to the worker node, copies it and stages it back to the working directory.
*/
input:
path input
output:
path "out.txt", emit: outfile
"""
cp "$input" "out.txt"
"""
}
process TEST_PASS_FOLDER {
/*
Stages a folder from the working directory to the worker node, copies it and stages it back to the working directory.
*/
input:
path input
output:
path "out", type: 'dir', emit: outfolder
"""
cp -rL $input out
"""
}
process TEST_PUBLISH_FILE {
/*
Creates a file on the worker node and uploads to the publish directory.
*/
publishDir { params.outdir ?: file(workflow.workDir).resolve("outputs").toUriString() }, mode: 'copy'
output:
path("*.txt")
"""
touch test.txt
"""
}
process TEST_PUBLISH_FOLDER {
/*
Creates a file on the worker node and uploads to the publish directory.
*/
publishDir { params.outdir ?: file(workflow.workDir).resolve("outputs").toUriString() }, mode: 'copy'
output:
path("test", type: 'dir')
"""
mkdir -p test
touch test/test1.txt
touch test/test2.txt
"""
}
process TEST_IGNORED_FAIL {
/*
This process should automatically fail but be ignored.
*/
errorStrategy 'ignore'
output:
stdout
"""
exit 1
"""
}
process TEST_MV_FILE {
/*
This process moves a file within a working directory.
*/
output:
path "output.txt"
"""
touch test.txt
mv test.txt output.txt
"""
}
process TEST_MV_FOLDER_CONTENTS {
/*
Moves the contents of a folder from within a folder
*/
output:
path "out", type: 'dir', emit: outfolder
"""
mkdir -p test
touch test/test.txt
mkdir -p out/
mv test/* out/
"""
}
process TEST_STDOUT {
/*
This process should create and capture STDOUT
*/
output:
stdout
script:
"""
"""
}
process TEST_VAL_INPUT {
/*
This process should read in val and echo to STDOUT
*/
input:
val input
output:
stdout
script:
"""
echo $input
"""
}
workflow NF_CANARY {
main:
// Create test file on head node
Channel
.of("alpha", "beta", "gamma")
.collectFile(name: 'sample.txt', newLine: true)
.set { test_file }
remote_file = params.remoteFile ? Channel.fromPath(params.remoteFile) : Channel.empty()
// Run tests
TEST_SUCCESS()
TEST_CREATE_FILE()
TEST_CREATE_EMPTY_FILE()
TEST_CREATE_FOLDER()
TEST_INPUT(test_file)
TEST_BIN_SCRIPT()
TEST_STAGE_REMOTE(remote_file)
TEST_PASS_FILE(TEST_CREATE_FILE.out.outfile)
TEST_PASS_FOLDER(TEST_CREATE_FOLDER.out.outfolder)
TEST_PUBLISH_FILE()
TEST_PUBLISH_FOLDER()
TEST_IGNORED_FAIL()
TEST_MV_FILE()
TEST_MV_FOLDER_CONTENTS()
TEST_VAL_INPUT("Hello World")
// POC of emitting the channel
Channel.empty()
.mix(
TEST_SUCCESS.out,
TEST_CREATE_FILE.out,
TEST_CREATE_EMPTY_FILE.out,
TEST_CREATE_FOLDER.out,
TEST_INPUT.out,
TEST_BIN_SCRIPT.out,
TEST_STAGE_REMOTE.out,
TEST_PASS_FILE.out,
TEST_PASS_FOLDER.out,
TEST_PUBLISH_FILE.out,
TEST_PUBLISH_FOLDER.out,
TEST_IGNORED_FAIL.out,
TEST_MV_FILE.out,
TEST_MV_FOLDER_CONTENTS.out
)
.set { ch_out }
emit:
out = ch_out
}
workflow {
NF_CANARY()
}