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Templating for multiple envs/containers

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This commit is contained in:
Chris Wright 2021-02-04 14:26:27 +00:00
parent ed2a961f9b
commit d57326dbff
2 changed files with 9 additions and 9 deletions
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14
nextflow.config
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@ -9,13 +9,6 @@
// //
// for further help editing this file. // for further help editing this file.
process {
withLabel:containerCPU {
container = 'workflow-template:latest'
}
}
profiles { profiles {
// the "standard" profile is used implicitely by nextflow // the "standard" profile is used implicitely by nextflow
// if no other profile is given on the CLI // if no other profile is given on the CLI
@ -26,6 +19,11 @@ profiles {
// also adds host user to the within-container group // also adds host user to the within-container group
runOptions = "--user \$(id -u):\$(id -g) --group-add 100" runOptions = "--user \$(id -u):\$(id -g) --group-add 100"
} }
process {
withLabel:default {
container = 'workflow-template:latest'
}
}
} }
// profile using conda environments rather than docker // profile using conda environments rather than docker
@ -35,8 +33,10 @@ profiles {
enabled = false enabled = false
} }
process { process {
withLabel:default {
conda = "environment.yaml" conda = "environment.yaml"
} }
}
conda { conda {
cacheDir = "" cacheDir = ""
} }

2
workflow.nf
View File

@ -32,7 +32,7 @@ if(params.help) {
process readSeqs { process readSeqs {
// Just write a file with sequence lengths // Just write a file with sequence lengths
label "containerCPU" label "default"
input: input:
file reads file reads
output: output: