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nextflow-docker.config
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nextflow-docker.config
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/* Additonal configuration for the Bovine TB pipeline, using docker defined in the profile
This configuration will be appended to main config: nextflow.config , when use as following:
nextflow run btb-docker.nf -c nextflow-docker.config --kraken2db krakendb/minikraken2_v1_8GB -profile docker -resume
*/
process.scratch = true
process.echo = true
profiles {
standard {
singularity {
enabled = true
}
process{
withLabel: btb {
container = '/data/images/apha-btb-v0.5.4.img'
}
errorStrategy = 'ignore'
}
env {
TOOLS_PATH = "/biotools"
FASTUNIQ = "$TOOLS_PATH/FastUniq-1.1"
TRIM = "$TOOLS_PATH/Trimmomatic-0.38"
BWA = "$TOOLS_PATH/bwa-0.7.17"
SAMTOOLS = "$TOOLS_PATH/samtools-1.9"
BCFTOOLS = "$TOOLS_PATH/bcftools-1.9"
BLAST = "$TOOLS_PATH/ncbi-blast-2.9.0+/bin"
KRAKEN2 = "$TOOLS_PATH/Kraken2"
}
}
docker {
docker {
enabled = true
}
process{
withLabel: btb {
container = 'apha-btb:latest'
}
}
env {
TOOLS_PATH = "/biotools"
FASTUNIQ = "$TOOLS_PATH/FastUniq-1.1"
TRIM = "$TOOLS_PATH/Trimmomatic-0.38"
BWA = "$TOOLS_PATH/bwa-0.7.17"
SAMTOOLS = "$TOOLS_PATH/samtools-1.9"
BCFTOOLS = "$TOOLS_PATH/bcftools-1.9"
BLAST = "$TOOLS_PATH/ncbi-blast-2.9.0+/bin"
KRAKEN2 = "$TOOLS_PATH/Kraken2"
}
}
}