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nextflow.config
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nextflow.config
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manifest {
author = 'Georgie Samaha'
name = 'bamQC-nf'
description = 'Pipeline for producing quality control reports of alignment files (bam)'
homePage = 'https://github.com/Sydney-Informatics-Hub/bamQC-nf'
// Mandate a minimum version of nextflow required to run the pipeline
nextflowVersion = '!>=20.07.1'
}
// resume pipeline from last successful process
resume = true
// Set default parameters
// Any parameters provided by the user with a -params-file or
// with --param (i.e. --outDir) command-line arguments will
// override the values defined here
params.stats = false
params.flagstat = false
params.qualimap = false
params.mosdepth = false
params.ref = false
params.outDir = './bamQC_results'
params.cohort = false
params.help = false
// Resource allocation
params.cpus = 8 // all tools capable of multi-threading
// mem_samtoolsStats = '16 GB' // not yet allocated
// mem_qualimapBamqc = '16 GB' // not yet allocated
// Preset use of containers with Singularity
singularity {
enabled = true
autoMounts = true
temp = '~/containers'
}
params.samtools__container = 'docker://quay.io/biocontainers/samtools:1.15.1--h1170115_0'
params.sambamba__container = 'docker://quay.io/biocontainers/sambamba:0.8.2--h98b6b92_2'
params.mosdepth__container = 'docker://quay.io/biocontainers/mosdepth:0.3.1--ha7ba039_0'
params.qualimap__container = 'docker://pegi3s/qualimap:2.2.1'
params.multiqc__container = 'docker://quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0'
// Fail a task if any command returns non-zero exit code
shell = ['/bin/bash', '-euo', 'pipefail']
// Produce a workflow diagram
dag {
enabled = true
file = 'runInfo/dag.svg'
}
report {
enabled = true
file = 'runInfo/report.html'
}
timeline {
enabled = true
file = 'runInfo/timeline.html'
}
trace {
enabled = true
file = 'runInfo/trace.txt'
}