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https://github.com/MillironX/nf-configs.git
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Merge pull request #339 from jfy133/rnaseq_mpcdf
Add RNASEQ specific config for MPCDF
This commit is contained in:
Alexander Peltzer
GitHub
commit
d0d86bfb2a
6 changed files with 185 additions and 63 deletions
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@ -32,7 +32,7 @@ profiles {
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params {
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config_profile_description = 'MPCDF cobra profile (unofficially) provided by nf-core/configs.'
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max_memory = 725.GB
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max_cpus = 80
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max_cpus = 40
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max_time = 24.h
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}
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}
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@ -47,7 +47,7 @@ profiles {
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}
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executor {
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queueSize = 8
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queueSize = 30
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pollInterval = '1 min'
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queueStatInterval = '5 min'
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}
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@ -61,7 +61,7 @@ profiles {
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params {
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config_profile_description = 'MPCDF raven profile (unofficially) provided by nf-core/configs.'
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max_memory = 368.GB
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memory = 2000000.MB
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max_cpus = 72
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max_time = 24.h
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}
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@ -1,64 +1,121 @@
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// Profile config names for nf-core/configs
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params {
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// Specific nf-core/configs params
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config_profile_contact = 'James Fellows Yates (@jfy133)'
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config_profile_description = 'nf-core/eager MPCDF profile provided by nf-core/configs'
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}
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profile {
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cobra {
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// Specific nf-core/eager process configuration
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process {
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cobra {
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params {
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// Specific nf-core/configs params
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config_profile_contact = 'James Fellows Yates (@jfy133)'
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config_profile_description = 'nf-core/eager MPCDF cobra profile provided by nf-core/configs'
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}
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process {
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withName: malt {
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maxRetries = 1
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memory = 725.GB
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cpus = 40
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time = 24.h
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}
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withLabel:'sc_tiny'{
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 1.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withName: malt {
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maxRetries = 1
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memory = 725.GB
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cpus = 40
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time = 24.h
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}
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withLabel:'sc_tiny'{
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 1.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withLabel:'sc_small'{
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withLabel:'sc_small'{
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withLabel:'sc_medium'{
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withLabel:'sc_medium'{
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withLabel:'mc_small'{
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cpus = { check_max( 2 * task.attempt, 'cpus' ) }
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withLabel:'mc_small'{
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cpus = { check_max( 2 * task.attempt, 'cpus' ) }
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withLabel:'mc_medium' {
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withLabel:'mc_medium' {
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withLabel:'mc_large'{
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withLabel:'mc_large'{
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withLabel:'mc_huge'{
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cpus = { check_max( 32 * task.attempt, 'cpus' ) }
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memory = { check_max( 256.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withLabel:'mc_huge'{
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cpus = { check_max( 32 * task.attempt, 'cpus' ) }
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memory = { check_max( 256.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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}
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}
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raven {
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// Specific nf-core/eager process configuration
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params {
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// Specific nf-core/configs params
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config_profile_contact = 'James Fellows Yates (@jfy133)'
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config_profile_description = 'nf-core/eager MPCDF raven profile provided by nf-core/configs'
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}
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process {
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withName: malt {
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maxRetries = 1
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memory = 2000000.MB
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cpus = 72
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time = 24.h
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}
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withLabel:'sc_tiny'{
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 1.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withLabel:'sc_small'{
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withLabel:'sc_medium'{
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cpus = { check_max( 1, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withLabel:'mc_small'{
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cpus = { check_max( 2 * task.attempt, 'cpus' ) }
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withLabel:'mc_medium' {
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withLabel:'mc_large'{
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withLabel:'mc_huge'{
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cpus = { check_max( 72, 'cpus' ) }
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memory = { check_max( 240.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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}
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}
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}
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50
conf/pipeline/rnaseq/mpcdf.config
Normal file
50
conf/pipeline/rnaseq/mpcdf.config
Normal file
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@ -0,0 +1,50 @@
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// Profile config names for nf-core/configs
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profiles {
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cobra {
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params {
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// Specific nf-core/configs params
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config_profile_contact = 'James Fellows Yates (@jfy133)'
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config_profile_description = 'nf-core/rnaseq MPCDF cobra profile provided by nf-core/configs'
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}
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process {
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cpus = { check_max( 1 * task.attempt, 'cpus' ) }
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memory = { check_max( 6.GB * task.attempt, 'memory' ) }
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time = { check_max( 4.h * task.attempt, 'time' ) }
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errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
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maxRetries = 1
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maxErrors = '-1'
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// Process-specific resource requirements
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withLabel:process_low {
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cpus = { check_max( 2 * task.attempt, 'cpus' ) }
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memory = { check_max( 12.GB * task.attempt, 'memory' ) }
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time = { check_max( 4.h * task.attempt, 'time' ) }
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}
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withLabel:process_medium {
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cpus = 40
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memory = { check_max( 36.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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withLabel:process_high {
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cpus = 40
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memory = { check_max( 72.GB * task.attempt, 'memory' ) }
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time = { check_max( 10.h * task.attempt, 'time' ) }
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}
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withLabel:process_long {
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time = 24.h
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}
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withLabel:process_high_memory {
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cpus = 40
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memory = { check_max( 200.GB * task.attempt, 'memory' ) }
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}
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withLabel:error_ignore {
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errorStrategy = 'ignore'
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}
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withName:CUSTOM_DUMPSOFTWAREVERSIONS {
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cache = false
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}
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}
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}
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}
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@ -12,24 +12,38 @@ All profiles use `singularity` as the corresponding containerEngine. To prevent
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>NB: Nextflow will need to submit the jobs via SLURM to the clusters and as such the commands above will have to be executed on one of the head nodes. Check the [MPCDF documentation](https://www.mpcdf.mpg.de/services/computing).
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## cobra
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## Global Profiles
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To use: `-profile cobra,mpcdf`
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### cobra
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To use: `-profile mpcdf,cobra`
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Sets the following parameters:
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- Maximum parallel running jobs: 8
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- Max. memory: 750.GB
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- Max. CPUs: 80
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- Max. memory: 725.GB
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- Max. CPUs: 40
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- Max. walltime: 24.h
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## raven
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### raven
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To use: `-profile raven,mpcdf`
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To use: `-profile mpcdf,raven`
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Sets the following parameters:
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- Maximum parallel running jobs: 8
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- Max. memory: 368.GB
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- Max. CPUs: 192
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- Max. memory: 2000000.MB (2.TB)
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- Max. CPUs: 72
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- Max. walltime: 24.h
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## Pipeline Profiles
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### nf-core/eager
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We offer a pipeline specific profile optimised for [nf-core/eager](https://nf-co.re/eager)
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- Maximum parallel running jobs: 30
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### nf-core/rnaseq
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We offer a pipeline specific profile optimised for [nf-core/rnaseq](https://nf-co.re/rnaseq)
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@ -9,7 +9,7 @@
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*/
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profiles {
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mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/eager/mpcdf.config" }
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eva { includeConfig "${params.custom_config_base}/conf/pipeline/eager/eva.config" }
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maestro { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestro.config" }
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mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/eager/mpcdf.config" }
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}
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@ -10,5 +10,6 @@
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profiles {
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eddie { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/eddie.config" }
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mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/mpcdf.config" }
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utd_sysbio { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/utd_sysbio.config" }
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}
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