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nextflow.config
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nextflow.config
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/*
* -------------------------------------------------
* TRON-Bioinformatics/tronflow-template Nextflow config file
* -------------------------------------------------
*/
profiles {
conda { process.conda = "$baseDir/environment.yml" }
debug { process.beforeScript = 'echo $HOSTNAME' }
test {
params.input_files = "$baseDir/test_data/input_data.txt"
params.cpus = 1
params.memory = "2g"
timeline.enabled = false
report.enabled = false
trace.enabled = false
dag.enabled = false
}
}
// Export this variable to prevent local Python libraries from conflicting with those in the container
env {
PYTHONNOUSERSITE = 1
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
VERSION = '1.0.0'
manifest {
name = 'TRON-Bioinformatics/tronflow-template'
author = 'Pablo Riesgo-Ferreiro'
homePage = 'https://github.com/TRON-Bioinformatics/tronflow-template'
description = 'TronFlow template'
mainScript = 'main.nf'
nextflowVersion = '>=19.10.0'
version = VERSION
}
params.help_message = """
TronFlow template v${VERSION}
Usage:
nextflow run tron-bioinformatics/tronflow-template -profile conda --input_files input_files
Input:
* input_files: the path to a tab-separated values file containing in each row the sample name and a BAM file
The input file does not have header!
Example input file:
name1 bam1
name2 bam2
Optional input:
* output: the folder where to publish output
* memory: the ammount of memory used by each job (default: 16g)
* cpus: the number of CPUs used by each job (default: 2)
Output:
* Output FASTQ and FASTA out of BAM files
"""