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Merged
apeltzer merged 5 commits into from
Sep 14, 2020
Merged

Timelimit mods #548

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8f175fd
Move short time limits to test profiles, and bump base run times to 24h
jfy133 Sep 10, 2020
102a62f
Update changelog
jfy133 Sep 10, 2020
32dfeb0
Merge pull request #550 from nf-core/dev
jfy133 Sep 11, 2020
8897be8
Update base.config
jfy133 Sep 14, 2020
92e7b1a
Update CHANGELOG.md
jfy133 Sep 14, 2020
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -33,6 +33,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
* Added a `.dockstore.yml` config file for automatic workflow registration with [dockstore.org](https://dockstore.org/)
* Updated template to nf-core/tools 1.10.2
* [#544](https://github.com/nf-core/eager/pull/544) Add script to perform bam filtering on fragment length
* [#456](https://github.com/nf-core/eager/pull/546) Bumps the base (default) runtime of all processes to 24 hours, and set shorter timelimits for test profiles (1 hour)

### `Fixed`

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24 changes: 12 additions & 12 deletions conf/base.config
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Expand Up @@ -12,7 +12,7 @@
process {
cpus = { check_max( 1 * task.attempt, 'cpus' ) }
memory = { check_max( 7.GB * task.attempt, 'memory' ) }
time = { check_max( 4.h * task.attempt, 'time' ) }
time = { check_max( 24.h * task.attempt, 'time' ) }

errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
maxRetries = 3
Expand All @@ -23,43 +23,43 @@ process {
withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
time = { check_max( 2.h * task.attempt, 'time' ) }
time = { check_max( 24.h * task.attempt, 'time' ) }
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@apeltzer apeltzer Sep 11, 2020

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Shouldn't tiny jobs not also be less than 24hours? e.g. lets say 3 for tiny, 6 for small, 8 for medium and 16 for large?

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@apeltzer apeltzer Sep 11, 2020

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My fear here is that some clusters actually send you to the end of the queue if you ask for more hours than you actually need - so it shouldn't be set to too much more than the initial process will most likely need.

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@jfy133 jfy133 Sep 11, 2020 •
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Tiny is actually referring to the resources rather than time (at least in the eager concept).

Hmm ok. That's tricky then. I originally honestly felt 2.h was enough but #545 made me realise this could occur when people run their own data. Maybe 4.h for everything? Half a day I think would be pretty solid for testing with your own data... (run at 8, check again at lunch?).

}

withLabel:'sc_small'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = { check_max( 2.h * task.attempt, 'time' ) }
time = { check_max( 24.h * task.attempt, 'time' ) }
}

withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 2.h * task.attempt, 'time' ) }
time = { check_max( 24.h * task.attempt, 'time' ) }
}

withLabel:'mc_small'{
cpus = { check_max( 2, 'cpus' ) }
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = { check_max( 2.h * task.attempt, 'time' ) }
time = { check_max( 24.h * task.attempt, 'time' ) }
}

withLabel:'mc_medium' {
cpus = { check_max( 4, 'cpus' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 2.h * task.attempt, 'time' ) }
time = { check_max( 24.h * task.attempt, 'time' ) }
}

withLabel:'mc_large'{
cpus = { check_max( 8, 'cpus' ) }
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 2.h * task.attempt, 'time' ) }
time = { check_max( 24.h * task.attempt, 'time' ) }
}

withLabel:'mc_huge'{
cpus = { check_max( 32, 'cpus' ) }
cpus = { check_max( 32 * task.attempt, 'cpus' ) }
memory = { check_max( 256.GB * task.attempt, 'memory' ) }
time = { check_max( 2.h * task.attempt, 'time' ) }
time = { check_max( 24.h * task.attempt, 'time' ) }
}

// Process-specific resource requirements (others leave at default, e.g. Fastqc)
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5 changes: 2 additions & 3 deletions conf/benchmarking_pathogenscreening.config
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Expand Up @@ -8,9 +8,8 @@
*/

params {
config_profile_name = 'AWS Megatest Pathogen Screening profile'
config_profile_description = "An AWS 'megatest' for testing complex sequencing aDNA data for human genome mapping and pathogen screening"
name = "nf-core_eager_awsmegatest_pathogenscreening"
config_profile_name = 'nf-core/eager benchmarking - pathogen screening profile'
config_profile_description = "A 'fullsized' benchmarking profile for deep screening pathogen aDNA data"

//Input data
input = 'https://github.com/nf-core/test-datasets/raw/eager/testdata/Benchmarking/benchmarking_pathogenscreening.tsv'
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46 changes: 46 additions & 0 deletions conf/test.config
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Expand Up @@ -20,3 +20,49 @@ params {
// Genome references
fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
}

process {

withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

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

withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_small'{
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_medium' {
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_large'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_huge'{
cpus = { check_max( 32 * task.attempt, 'cpus' ) }
memory = { check_max( 256.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

}
1 change: 1 addition & 0 deletions conf/test_full.config
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Expand Up @@ -31,6 +31,7 @@ params {
}

process {

withName:'adapter_removal'{
cpus = { check_max( 8, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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46 changes: 46 additions & 0 deletions conf/test_tsv.config
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Expand Up @@ -20,3 +20,49 @@ params {
// Genome references
fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
}

process {

withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

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

withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_small'{
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_medium' {
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_large'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_huge'{
cpus = { check_max( 32 * task.attempt, 'cpus' ) }
memory = { check_max( 256.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

}
46 changes: 46 additions & 0 deletions conf/test_tsv_bam.config
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Expand Up @@ -19,4 +19,50 @@ params {
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/mammoth_design_bam.tsv'
// Genome references
fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
}

process {

withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

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

withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_small'{
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_medium' {
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_large'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_huge'{
cpus = { check_max( 32 * task.attempt, 'cpus' ) }
memory = { check_max( 256.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

}
46 changes: 46 additions & 0 deletions conf/test_tsv_complex.config
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Expand Up @@ -20,3 +20,49 @@ params {
// Genome references
fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
}

process {

withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

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

withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_small'{
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_medium' {
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_large'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_huge'{
cpus = { check_max( 32 * task.attempt, 'cpus' ) }
memory = { check_max( 256.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

}
46 changes: 46 additions & 0 deletions conf/test_tsv_fna.config
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Expand Up @@ -19,4 +19,50 @@ params {
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/mammoth_design_fastq.tsv'
// Genome references
fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fna'
}

process {

withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

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

withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_small'{
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_medium' {
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_large'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_huge'{
cpus = { check_max( 32 * task.attempt, 'cpus' ) }
memory = { check_max( 256.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

}
46 changes: 46 additions & 0 deletions conf/test_tsv_humanbam.config
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Expand Up @@ -24,3 +24,49 @@ params {
pileupcaller_bedfile = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz'
pileupcaller_snpfile = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Human/1240K_covered_in_JK2067_downsampled_s0.1.numeric_chromosomes.snp'
}

process {

withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

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

withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_small'{
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_medium' {
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_large'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

withLabel:'mc_huge'{
cpus = { check_max( 32 * task.attempt, 'cpus' ) }
memory = { check_max( 256.GB * task.attempt, 'memory' ) }
time = { check_max( 1.h * task.attempt, 'time' ) }
}

}
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