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nextflow.config
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nextflow.config
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manifest {
homePage = 'https://github.com/iarcbioinfo/mutect-nf'
description = 'Parallel mutect pipeline with nextflow'
mainScript = 'mutect.nf'
}
profiles {
conda {
process.conda = "$baseDir/environment.yml"
conda.createTimeout = "200 min"
}
conda_gatk3 {
process.conda = "$baseDir/environment_gatk3.yml"
conda.createTimeout = "200 min"
}
conda_gatk2 {
process.conda = "$baseDir/environment_gatk2.yml"
conda.createTimeout = "200 min"
}
docker {
docker.enabled = true
process.container = 'iarcbioinfo/mutect-nf:v2.3'
}
docker_gatk3 {
docker.enabled = true
process.container = 'iarcbioinfo/mutect-nf:v2.3_gatk3'
}
docker_gatk2 {
docker.enabled = true
process.container = 'iarcbioinfo/mutect-nf:v2.3_gatk2'
}
singularity {
singularity.enabled = true
process.container = 'iarcbioinfo/mutect-nf:v2.3'
pullTimeout = "200 min"
}
singularity_gatk3 {
singularity.enabled = true
process.container = 'iarcbioinfo/mutect-nf:v2.3_gatk3'
pullTimeout = "200 min"
}
singularity_gatk2 {
singularity.enabled = true
process.container = 'iarcbioinfo/mutect-nf:v2.3_gatk2'
pullTimeout = "200 min"
}
}
params.output_folder="."
timeline {
enabled = true
file = "${params.output_folder}/nf-pipeline_info/mutect-nf_timeline.html"
}
report {
enabled = true
file = "${params.output_folder}/nf-pipeline_info/mutect-nf_report.html"
}
trace {
enabled = true
file = "${params.output_folder}/nf-pipeline_info/mutect-nf_trace.txt"
}
dag {
enabled = true
file = "${params.output_folder}/nf-pipeline_info/mutect-nf_dag.html"
}