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Add and fix ECLint in pipeline #629

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May 12, 2021
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Actually fix files in conf/
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drpatelh committed May 11, 2021
commit 98a8b825622c5bc95e32c20cdab4c1141dbb91d8
87 changes: 43 additions & 44 deletions conf/base.config
Original file line number Diff line number Diff line change
@@ -1,51 +1,50 @@
/*
* -------------------------------------------------
* nf-core/rnaseq Nextflow base config file
* -------------------------------------------------
* A 'blank slate' config file, appropriate for general
* use on most high performace compute environments.
* Assumes that all software is installed and available
* on the PATH. Runs in `local` mode - all jobs will be
* run on the logged in environment.
*/
========================================================================================
nf-core/rnaseq Nextflow base config file
========================================================================================
A 'blank slate' config file, appropriate for general use on most high performance
compute environments. Assumes that all software is installed and available on
the PATH. Runs in `local` mode - all jobs will be run on the logged in environment.
----------------------------------------------------------------------------------------
*/

process {

cpus = { check_max( 1 * task.attempt, 'cpus' ) }
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
time = { check_max( 4.h * task.attempt, 'time' ) }
cpus = { check_max( 1 * task.attempt, 'cpus' ) }
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
time = { check_max( 4.h * task.attempt, 'time' ) }

errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
maxRetries = 1
maxErrors = '-1'
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
maxRetries = 1
maxErrors = '-1'

// Process-specific resource requirements
withLabel:process_low {
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { check_max( 4.h * task.attempt, 'time' ) }
}
withLabel:process_medium {
cpus = { check_max( 6 * task.attempt, 'cpus' ) }
memory = { check_max( 36.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}
withLabel:process_high {
cpus = { check_max( 12 * task.attempt, 'cpus' ) }
memory = { check_max( 72.GB * task.attempt, 'memory' ) }
time = { check_max( 16.h * task.attempt, 'time' ) }
}
withLabel:process_long {
time = { check_max( 20.h * task.attempt, 'time' ) }
}
withLabel:process_high_memory {
memory = { check_max( 200.GB * task.attempt, 'memory' ) }
}
withLabel:error_ignore {
errorStrategy = 'ignore'
}
withLabel:error_retry {
errorStrategy = 'retry'
maxRetries = 2
}
// Process-specific resource requirements
withLabel:process_low {
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { check_max( 4.h * task.attempt, 'time' ) }
}
withLabel:process_medium {
cpus = { check_max( 6 * task.attempt, 'cpus' ) }
memory = { check_max( 36.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}
withLabel:process_high {
cpus = { check_max( 12 * task.attempt, 'cpus' ) }
memory = { check_max( 72.GB * task.attempt, 'memory' ) }
time = { check_max( 16.h * task.attempt, 'time' ) }
}
withLabel:process_long {
time = { check_max( 20.h * task.attempt, 'time' ) }
}
withLabel:process_high_memory {
memory = { check_max( 200.GB * task.attempt, 'memory' ) }
}
withLabel:error_ignore {
errorStrategy = 'ignore'
}
withLabel:error_retry {
errorStrategy = 'retry'
maxRetries = 2
}
}
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