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Fix config

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This commit is contained in:
Chris Wright 2021-02-04 14:40:48 +00:00
parent e2d83e14c9
commit 416b482a01
2 changed files with 6 additions and 5 deletions
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9
nextflow.config
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@ -4,11 +4,12 @@
// The workflow should run without editing this configuration file, // The workflow should run without editing this configuration file,
// however there may be instances in which you wish to edit this // however there may be instances in which you wish to edit this
// file for compute performance or other reasons. Please see: // file for compute performance or other reasons. Please see:
// //
// https://nextflow.io/docs/latest/config.html#configuration // https://nextflow.io/docs/latest/config.html#configuration
// //
// for further help editing this file. // for further help editing this file.
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
@ -20,12 +21,12 @@ profiles {
runOptions = "--user \$(id -u):\$(id -g) --group-add 100" runOptions = "--user \$(id -u):\$(id -g) --group-add 100"
} }
process { process {
withLabel:default { withLabel:pysam {
container = 'workflow-template:latest' container = 'workflow-template:latest'
} }
} }
} }
// profile using conda environments rather than docker // profile using conda environments rather than docker
// containers // containers
conda { conda {
@ -33,7 +34,7 @@ profiles {
enabled = false enabled = false
} }
process { process {
withLabel:default { withLabel:pysam {
conda = "environment.yaml" conda = "environment.yaml"
} }
} }

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 "default" label "pysam"
input: input:
file reads file reads
output: output: