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Add EVA and EAGER@EVA

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James Fellows Yates 2021-04-06 17:48:16 +02:00
parent d69af0f287
commit be1d35840d
5 changed files with 24 additions and 21 deletions
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2
.github/workflows/main.yml vendored
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@ -16,7 +16,7 @@ jobs:
needs: test_all_profiles
strategy:
matrix:
profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'imperial', 'imperial_mb', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
steps:
- uses: actions/checkout@v1
- name: Install Nextflow

2
conf/eva.config
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@ -49,4 +49,4 @@ profiles {
debug {
cleanup = false
}
}
}

37
conf/pipeline/eager/eva.config
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@ -9,10 +9,12 @@ params {
// Specific nf-core/eager process configuration
process {
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -XX:+PrintCommandLineFlags"'
maxRetries = 2
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
clusterOptions = { "-S /bin/bash -j y -o output.log -l h_vmem=${task.memory.toMega().toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().toString().replaceAll(/[\sB]/,'')}M" }
clusterOptions = { "-S /bin/bash -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
@ -59,63 +61,64 @@ process {
// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
withName: makeSeqDict {
clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M" }
clusterOptions = { "-S /bin/bash -v JAVA_OPTS='-XX:ParallelGCThreads=1' -l h_vmem=${(task.memory.toGiga() + 3)}G,virtual_free=${(task.memory.toGiga() + 3)}G" }
}
withName: fastqc {
clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M" }
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: adapter_removal {
clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(12000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(12000).toString().replaceAll(/[\sB]/,'')}M" }
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: dedup {
clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M" }
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: markduplicates {
clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(8000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(8000).toString().replaceAll(/[\sB]/,'')}M" }
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
}
withName: malt {
clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: maltextract {
clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: multivcfanalyzer {
clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: mtnucratio {
clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: vcf2genome {
clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: qualimap {
clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(5000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(5000).toString().replaceAll(/[\sB]/,'')}M" }
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
}
withName: damageprofiler {
clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(5000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(5000).toString().replaceAll(/[\sB]/,'')}M" }
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
}
withName: circularmapper {
clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: circulargenerator {
clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
}
withName: preseq {
clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M" }
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
}
}
@ -209,4 +212,4 @@ profiles {
bwaalnl = 16500
}
}
}
}

2
docs/eva.md
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@ -25,4 +25,4 @@ Note the following characteristics of this profile:
### debug
This simple profile just turns off automatic clean up of intermediate files. This can be useful for debugging. Specify e.g. with `-profile eva,archgen`
This simple profile just turns off automatic clean up of intermediate files. This can be useful for debugging. Specify e.g. with `-profile eva,archgen`

2
docs/pipeline/eager/eva.md
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@ -31,4 +31,4 @@ Specific configurations for eva has been made for eager.
#### Pathogen
- `pathogen_loose`: optimised for mapping of human aDNA reads (i.e. bwa aln defaults as `-l 16 -n 0.01`)
- `pathogen_strict`: optimised for mapping of human aDNA reads (i.e. bwa aln defaults as `-l 32, -n 0.1`)
- `pathogen_strict`: optimised for mapping of human aDNA reads (i.e. bwa aln defaults as `-l 32, -n 0.1`)