mirror of
https://github.com/MillironX/nf-configs.git
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Merge pull request #414 from sheffield-bioinformatics-core/sbc_sharc
Added global institutional and pipeline configs for sbc_sharc
This commit is contained in:
commit
3fcf708134
17 changed files with 520 additions and 0 deletions
1
.github/workflows/main.yml
vendored
1
.github/workflows/main.yml
vendored
|
@ -83,6 +83,7 @@ jobs:
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- "sage"
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- "sahmri"
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- "sanger"
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- "sbc_sharc"
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- "seg_globe"
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- "uct_hpc"
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- "unibe_ibu"
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|
|
|
@ -137,6 +137,7 @@ Currently documentation is available for the following systems:
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- [ROSALIND](docs/rosalind.md)
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- [SAGE BIONETWORKS](docs/sage.md)
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- [SANGER](docs/sanger.md)
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- [SBC_SHARC](docs/sbc_sharc.md)
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- [SEG_GLOBE](docs/seg_globe.md)
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- [UCT_HPC](docs/uct_hpc.md)
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- [UNIBE_IBU](docs/unibe_ibu.md)
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|
@ -197,6 +198,10 @@ Currently documentation is available for the following pipelines within specific
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- ampliseq
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- [BINAC](docs/pipeline/ampliseq/binac.md)
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- [UPPMAX](docs/pipeline/ampliseq/uppmax.md)
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- atacseq
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- [SBC_SHARC](docs/pipeline/atacseq/sbc_sharc.md)
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- chipseq
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- [SBC_SHARC](docs/pipeline/chipseq/sbc_sharc.md)
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- eager
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- [EVA](docs/pipeline/eager/eva.md)
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- mag
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@ -204,11 +209,14 @@ Currently documentation is available for the following pipelines within specific
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- rnafusion
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- [HASTA](docs/pipeline/rnafusion/hasta.md)
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- [MUNIN](docs/pipeline/rnafusion/munin.md)
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- rnaseq
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- [SBC_SHARC](docs/pipeline/rnaseq/sbc_sharc.md)
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- rnavar
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- [MUNIN](docs/pipeline/rnavar/munin.md)
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- sarek
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- [Cancer Research UK Manchester Institute](docs/pipeline/sarek/crukmi.md)
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- [MUNIN](docs/pipeline/sarek/munin.md)
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- [SBC_SHARC](docs/pipeline/sarek/sbc_sharc.md)
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- [UPPMAX](docs/pipeline/sarek/uppmax.md)
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- taxprofiler
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- [EVA](docs/pipeline/taxprofiler/eva.md)
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|
74
conf/pipeline/atacseq/sbc_sharc.config
Normal file
74
conf/pipeline/atacseq/sbc_sharc.config
Normal file
|
@ -0,0 +1,74 @@
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Sheffield Bioinformatics Core Configuration Profile - ShARC
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Custom Pipeline Resource Config for nf-core/atacseq
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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// process-specific resource requirements - reduced specification from those in atacseq/conf/base.config
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process {
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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( 4.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 = { check_max( 4 * task.attempt, 'cpus' ) }
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memory = { check_max( 8.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 = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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time = { check_max( 8.h * task.attempt, 'time' ) }
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}
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withLabel:process_long {
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time = { check_max( 12.h * task.attempt, 'time' ) }
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}
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}
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// function 'check_max()' to ensure that resource requirements don't go beyond maximum limit
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def check_max(obj, type) {
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if (type == 'memory') {
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try {
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if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
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return params.max_memory as nextflow.util.MemoryUnit
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else
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return obj
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} catch (all) {
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println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
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return obj
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}
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} else if (type == 'time') {
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try {
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if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
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return params.max_time as nextflow.util.Duration
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else
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return obj
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} catch (all) {
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println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
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return obj
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}
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} else if (type == 'cpus') {
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try {
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return Math.min(obj, params.max_cpus as int)
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} catch (all) {
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println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
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return obj
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}
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}
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}
|
74
conf/pipeline/chipseq/sbc_sharc.config
Normal file
74
conf/pipeline/chipseq/sbc_sharc.config
Normal file
|
@ -0,0 +1,74 @@
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Sheffield Bioinformatics Core Configuration Profile - ShARC
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Custom Pipeline Resource Config for nf-core/chipseq
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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// process-specific resource requirements - reduced specification from those in chipseq/conf/base.config
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process {
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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( 4.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 = { check_max( 4 * task.attempt, 'cpus' ) }
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memory = { check_max( 8.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 = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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time = { check_max( 8.h * task.attempt, 'time' ) }
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}
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withLabel:process_long {
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time = { check_max( 12.h * task.attempt, 'time' ) }
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}
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}
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// function 'check_max()' to ensure that resource requirements don't go beyond maximum limit
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def check_max(obj, type) {
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if (type == 'memory') {
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try {
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if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
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return params.max_memory as nextflow.util.MemoryUnit
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else
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return obj
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} catch (all) {
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println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
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return obj
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}
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} else if (type == 'time') {
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try {
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if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
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return params.max_time as nextflow.util.Duration
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else
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return obj
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} catch (all) {
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println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
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return obj
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}
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} else if (type == 'cpus') {
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try {
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return Math.min(obj, params.max_cpus as int)
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} catch (all) {
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println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
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return obj
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||||
}
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}
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}
|
79
conf/pipeline/rnaseq/sbc_sharc.config
Normal file
79
conf/pipeline/rnaseq/sbc_sharc.config
Normal file
|
@ -0,0 +1,79 @@
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|||
/*
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||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Sheffield Bioinformatics Core Configuration Profile - ShARC
|
||||
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
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Custom Pipeline Resource Config for nf-core/rnaseq
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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// process-specific resource requirements - reduced specification from those in rnaseq/conf/base.config
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process {
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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( 4.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 = { check_max( 4 * task.attempt, 'cpus' ) }
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memory = { check_max( 8.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 = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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time = { check_max( 8.h * task.attempt, 'time' ) }
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}
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withLabel:process_long {
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time = { check_max( 12.h * task.attempt, 'time' ) }
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}
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withLabel:process_high_memory {
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memory = { check_max( 60.GB * task.attempt, 'memory' ) }
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}
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}
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// function 'check_max()' to ensure that resource requirements don't go beyond maximum limit
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def check_max(obj, type) {
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if (type == 'memory') {
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try {
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if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
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return params.max_memory as nextflow.util.MemoryUnit
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else
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return obj
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} catch (all) {
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println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
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return obj
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}
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} else if (type == 'time') {
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try {
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if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
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return params.max_time as nextflow.util.Duration
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else
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return obj
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} catch (all) {
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println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
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return obj
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}
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} else if (type == 'cpus') {
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try {
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return Math.min(obj, params.max_cpus as int)
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} catch (all) {
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println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
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return obj
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}
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}
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}
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|
114
conf/pipeline/sarek/sbc_sharc.config
Normal file
114
conf/pipeline/sarek/sbc_sharc.config
Normal file
|
@ -0,0 +1,114 @@
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/*
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Sheffield Bioinformatics Core Configuration Profile - ShARC
|
||||
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Custom Pipeline Resource Config for nf-core/sarek
|
||||
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
*/
|
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|
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// process-specific resource requirements - reduced specification from those in sarek/conf/base.config
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||||
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process {
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||||
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// process labels
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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( 4.GB * task.attempt, 'memory' ) }
|
||||
time = { check_max( 4.h * task.attempt, 'time' ) }
|
||||
}
|
||||
|
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withLabel:process_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 = { check_max( 6.h * task.attempt, 'time' ) }
|
||||
}
|
||||
|
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withLabel:process_high {
|
||||
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
|
||||
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
|
||||
time = { check_max( 8.h * task.attempt, 'time' ) }
|
||||
}
|
||||
|
||||
withLabel:process_long {
|
||||
time = { check_max( 12.h * task.attempt, 'time' ) }
|
||||
}
|
||||
|
||||
withLabel:process_high_memory {
|
||||
memory = { check_max( 60.GB * task.attempt, 'memory' ) }
|
||||
}
|
||||
|
||||
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// process name
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||||
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withName:'BWAMEM1_MEM|BWAMEM2_MEM' {
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cpus = { check_max( 12 * task.attempt, 'cpus' ) }
|
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
|
||||
time = { check_max( 8.h * task.attempt, 'time' ) }
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||||
}
|
||||
|
||||
withName:'FASTP' {
|
||||
cpus = { check_max( 12 * task.attempt, 'cpus' ) }
|
||||
}
|
||||
|
||||
withName:'FASTQC|FASTP|MOSDEPTH|SAMTOOLS_CONVERT' {
|
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
|
||||
}
|
||||
|
||||
withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|SAMTOOLS_STATS' {
|
||||
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
|
||||
}
|
||||
|
||||
withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_GATHERBQSRREPORTS' {
|
||||
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
|
||||
}
|
||||
|
||||
withName:'GATK4_MARKDUPLICATES' {
|
||||
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
|
||||
}
|
||||
|
||||
withName:'FREEBAYES|SAMTOOLS_STATS|SAMTOOLS_INDEX|UNZIP' {
|
||||
cpus = { check_max( 1 * task.attempt, 'cpus' ) }
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
// function 'check_max()' to ensure that resource requirements don't go beyond maximum limit
|
||||
|
||||
def check_max(obj, type) {
|
||||
if (type == 'memory') {
|
||||
try {
|
||||
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
|
||||
return params.max_memory as nextflow.util.MemoryUnit
|
||||
else
|
||||
return obj
|
||||
} catch (all) {
|
||||
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
|
||||
return obj
|
||||
}
|
||||
} else if (type == 'time') {
|
||||
try {
|
||||
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
|
||||
return params.max_time as nextflow.util.Duration
|
||||
else
|
||||
return obj
|
||||
} catch (all) {
|
||||
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
|
||||
return obj
|
||||
}
|
||||
} else if (type == 'cpus') {
|
||||
try {
|
||||
return Math.min(obj, params.max_cpus as int)
|
||||
} catch (all) {
|
||||
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
|
||||
return obj
|
||||
}
|
||||
}
|
||||
}
|
57
conf/sbc_sharc.config
Normal file
57
conf/sbc_sharc.config
Normal file
|
@ -0,0 +1,57 @@
|
|||
/*
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Sheffield Bioinformatics Core Configuration Profile - ShARC
|
||||
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
Base Institutional Configuration
|
||||
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
*/
|
||||
|
||||
|
||||
params {
|
||||
|
||||
// nf-core specific parameters displayed in header summary of each run
|
||||
|
||||
config_profile_description = 'Sheffield Bioinformatics Core - ShARC'
|
||||
config_profile_contact = 'Lewis Quayle (l.quayle@sheffield.ac.uk)'
|
||||
config_profile_url = 'https://docs.hpc.shef.ac.uk/en/latest/sharc/index.html'
|
||||
|
||||
// hpc resource limits
|
||||
|
||||
max_cpus = 16
|
||||
max_memory = 64.GB
|
||||
max_time = 96.h
|
||||
|
||||
}
|
||||
|
||||
|
||||
// container engine
|
||||
|
||||
singularity {
|
||||
|
||||
enabled = true
|
||||
autoMounts = true
|
||||
|
||||
}
|
||||
|
||||
|
||||
// hpc configuration specific to ShARC
|
||||
|
||||
process {
|
||||
|
||||
// scheduler
|
||||
|
||||
executor = 'sge'
|
||||
penv = 'smp'
|
||||
queue = { task.time <= 6.h ? 'shortint.q' : 'all.q' }
|
||||
clusterOptions = { "-l rmem=${task.memory.toGiga()}G" }
|
||||
|
||||
// error and retry handling
|
||||
|
||||
errorStrategy = { task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
maxRetries = 2
|
||||
|
||||
}
|
11
docs/pipeline/atacseq/sbc_sharc.md
Normal file
11
docs/pipeline/atacseq/sbc_sharc.md
Normal file
|
@ -0,0 +1,11 @@
|
|||
# nf-core/configs: ATAC-Seq Specific Configuration - Sheffield Bioinformatics Core Facility ShARC
|
||||
|
||||
Specific configuration for [nf-co.re/atacseq](https://nf-co.re/atacseq) pipeline
|
||||
|
||||
## Usage
|
||||
|
||||
To use, run nextflow with the pipeline using `-profile sbc_sharc` (note the single hyphen).
|
||||
|
||||
This will download and launch the atacseq specific [`sbc_sharc.config`](../../../conf/pipeline/atacseq/sbc_sharc.config) which has been pre-configured with a setup suitable for the [University of Sheffield ShARC cluster](https://docs.hpc.shef.ac.uk/en/latest/index.html) and will automatically load the appropriate pipeline-specific configuration file.
|
||||
|
||||
Example: `nextflow run nf-core/atacseq -profile sbc_sharc`
|
11
docs/pipeline/chipseq/sbc_sharc.md
Normal file
11
docs/pipeline/chipseq/sbc_sharc.md
Normal file
|
@ -0,0 +1,11 @@
|
|||
# nf-core/configs: ChIP-Seq Specific Configuration - Sheffield Bioinformatics Core Facility ShARC
|
||||
|
||||
Specific configuration for [nf-co.re/chipseq](https://nf-co.re/chipseq) pipeline
|
||||
|
||||
## Usage
|
||||
|
||||
To use, run nextflow with the pipeline using `-profile sbc_sharc` (note the single hyphen).
|
||||
|
||||
This will download and launch the chipseq specific [`sbc_sharc.config`](../../../conf/pipeline/chipseq/sbc_sharc.config) which has been pre-configured with a setup suitable for the [University of Sheffield ShARC cluster](https://docs.hpc.shef.ac.uk/en/latest/index.html) and will automatically load the appropriate pipeline-specific configuration file.
|
||||
|
||||
Example: `nextflow run nf-core/chipseq -profile sbc_sharc`
|
11
docs/pipeline/rnaseq/sbc_sharc.md
Normal file
11
docs/pipeline/rnaseq/sbc_sharc.md
Normal file
|
@ -0,0 +1,11 @@
|
|||
# nf-core/configs: RNA-Seq Specific Configuration - Sheffield Bioinformatics Core Facility ShARC
|
||||
|
||||
Specific configuration for [nf-co.re/rnaseq](https://nf-co.re/rnaseq) pipeline
|
||||
|
||||
## Usage
|
||||
|
||||
To use, run nextflow with the pipeline using `-profile sbc_sharc` (note the single hyphen).
|
||||
|
||||
This will download and launch the rnaseq specific [`sbc_sharc.config`](../../../conf/pipeline/rnaseq/sbc_sharc.config) which has been pre-configured with a setup suitable for the [University of Sheffield ShARC cluster](https://docs.hpc.shef.ac.uk/en/latest/index.html) and will automatically load the appropriate pipeline-specific configuration file.
|
||||
|
||||
Example: `nextflow run nf-core/rnaseq -profile sbc_sharc`
|
11
docs/pipeline/sarek/sbc_sharc.md
Normal file
11
docs/pipeline/sarek/sbc_sharc.md
Normal file
|
@ -0,0 +1,11 @@
|
|||
# nf-core/configs: Sarek Specific Configuration - Sheffield Bioinformatics Core Facility ShARC
|
||||
|
||||
Specific configuration for [nf-co.re/sarek](https://nf-co.re/sarek) pipeline
|
||||
|
||||
## Usage
|
||||
|
||||
To use, run nextflow with the pipeline using `-profile sbc_sharc` (note the single hyphen).
|
||||
|
||||
This will download and launch the sarek specific [`sbc_sharc.config`](../../../conf/pipeline/sarek/sbc_sharc.config) which has been pre-configured with a setup suitable for the [University of Sheffield ShARC cluster](https://docs.hpc.shef.ac.uk/en/latest/index.html) and will automatically load the appropriate pipeline-specific configuration file.
|
||||
|
||||
Example: `nextflow run nf-core/sarek -profile sbc_sharc`
|
40
docs/sbc_sharc.md
Normal file
40
docs/sbc_sharc.md
Normal file
|
@ -0,0 +1,40 @@
|
|||
# nf-core/configs: Sheffield Bioinformatics Core Facility ShARC Configuration
|
||||
|
||||
## Using the SBC_ShARC Institutional Configuration Profile
|
||||
|
||||
To use [`sbc_sharc.config`](../conf/sbc_sharc.config), run nextflow with an nf-core pipeline using `-profile sbc_sharc` (note the single hyphen).
|
||||
|
||||
This will download and launch [`sbc_sharc.config`](../conf/sbc_sharc.config) which has been pre-configured with a setup suitable for the ShARC cluster and will automatically load the appropriate pipeline-specific configuration file.
|
||||
|
||||
The following nf-core pipelines have been successfully configured for use on the the [University of Sheffield ShARC cluster](https://docs.hpc.shef.ac.uk/en/latest/index.html):
|
||||
|
||||
- [nf-co.re/atacseq](https://nf-co.re/atacseq)
|
||||
- [nf-co.re/chipseq](https://nf-co.re/chipseq)
|
||||
- [nf-co.re/rnaseq](https://nf-co.re/rnaseq)
|
||||
- [nf-co.re/sarek](https://nf-co.re/sarek)
|
||||
|
||||
When using [`sbc_sharc.config`](../conf/sbc_sharc.config) with the pipelines listed above, the appropriate configuration file from the list below will be loaded automatically:
|
||||
|
||||
- [atacseq sbc_sharc.config](../conf/pipeline/atacseq/sbc_sharc.config)
|
||||
- [chipseq sbc_sharc.config](../conf/pipeline/chipseq/sbc_sharc.config)
|
||||
- [rnaseq sbc_sharc.config](../conf/pipeline/rnaseq/sbc_sharc.config)
|
||||
- [sarek sbc_sharc.config](../conf/pipeline/sarek/sbc_sharc.config)
|
||||
|
||||
The [`sbc_sharc.config`](../conf/sbc_sharc.config) configuration file might work with other nf-core pipelines as it stands but we cannot guarantee they will run without issue. We will be continuing to create, test and optimise configurations for new pipelines in the future.
|
||||
|
||||
## A Note on Singularity Containers
|
||||
|
||||
The [`sbc_sharc.config`](../conf/sbc_sharc.config) configuration file supports running nf-core pipelines with Singularity containers; Singularity images will be downloaded automatically before execution of the pipeline.
|
||||
|
||||
When you run nextflow for the first time, Singularity will create a hidden directory `.singularity` in your `$HOME` directory `/home/$USER` which has very very limited (10GB) space available. It is therefore a good idea to create a directory somewhere else (e.g., `/data/$USER`) with more room and link the locations. To do this, run the following series of commands:
|
||||
|
||||
```shell
|
||||
# change directory to $HOME
|
||||
cd $HOME
|
||||
|
||||
# make the directory that will be linked to
|
||||
mkdir /data/$USER/.singularity
|
||||
|
||||
# link the new directory with the existing one
|
||||
ln -s /data/$USER/.singularity .singularity
|
||||
```
|
|
@ -65,6 +65,7 @@ profiles {
|
|||
sage { includeConfig "${params.custom_config_base}/conf/sage.config" }
|
||||
sahmri { includeConfig "${params.custom_config_base}/conf/sahmri.config" }
|
||||
sanger { includeConfig "${params.custom_config_base}/conf/sanger.config"}
|
||||
sbc_sharc { includeConfig "${params.custom_config_base}/conf/sbc_sharc.config"}
|
||||
seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"}
|
||||
uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }
|
||||
unibe_ibu { includeConfig "${params.custom_config_base}/conf/unibe_ibu.config" }
|
||||
|
|
13
pipeline/atacseq.config
Normal file
13
pipeline/atacseq.config
Normal file
|
@ -0,0 +1,13 @@
|
|||
/*
|
||||
* -------------------------------------------------
|
||||
* nfcore/atacseq custom profile Nextflow config file
|
||||
* -------------------------------------------------
|
||||
* Config options for custom environments.
|
||||
* Cluster-specific config options should be saved
|
||||
* in the conf/pipeline/atacseq folder and imported
|
||||
* under a profile name here.
|
||||
*/
|
||||
|
||||
profiles {
|
||||
sbc_sharc { includeConfig "${params.custom_config_base}/conf/pipeline/atacseq/sbc_sharc.config" }
|
||||
}
|
13
pipeline/chipseq.config
Normal file
13
pipeline/chipseq.config
Normal file
|
@ -0,0 +1,13 @@
|
|||
/*
|
||||
* -------------------------------------------------
|
||||
* nfcore/chipseq custom profile Nextflow config file
|
||||
* -------------------------------------------------
|
||||
* Config options for custom environments.
|
||||
* Cluster-specific config options should be saved
|
||||
* in the conf/pipeline/chipseq folder and imported
|
||||
* under a profile name here.
|
||||
*/
|
||||
|
||||
profiles {
|
||||
sbc_sharc { includeConfig "${params.custom_config_base}/conf/pipeline/chipseq/sbc_sharc.config" }
|
||||
}
|
|
@ -11,5 +11,6 @@
|
|||
profiles {
|
||||
eddie { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/eddie.config" }
|
||||
mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/mpcdf.config" }
|
||||
sbc_sharc { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/sbc_sharc.config" }
|
||||
utd_sysbio { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/utd_sysbio.config" }
|
||||
}
|
||||
|
|
|
@ -15,5 +15,6 @@ profiles {
|
|||
eddie { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/eddie.config" }
|
||||
icr_davros { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/icr_davros.config" }
|
||||
munin { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/munin.config" }
|
||||
sbc_sharc { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/sbc_sharc.config" }
|
||||
uppmax { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/uppmax.config" }
|
||||
}
|
||||
|
|
Loading…
Reference in a new issue