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Gwenna Breton 2022-08-01 16:46:55 +02:00 committed by GitHub
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6 changed files with 51 additions and 61 deletions
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2
conf/mpcdf.config
View file

@ -61,7 +61,7 @@ profiles {
params {
config_profile_description = 'MPCDF raven profile (unofficially) provided by nf-core/configs.'
memory = 2000000.MB
max_memory = 2000000.MB
max_cpus = 72
max_time = 24.h
}

38
conf/pipeline/eager/eva.config
View file

@ -6,11 +6,15 @@ params {
config_profile_description = 'nf-core/eager EVA profile provided by nf-core/configs'
}
env {
_JAVA_OPTIONS = "-XX:ParallelGCThreads=1"
OPENBLAS_NUM_THREADS = 1
OMP_NUM_THREADS = 1
}
// Specific nf-core/eager process configuration
process {
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'
maxRetries = 2
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
@ -69,17 +73,17 @@ process {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: fastqc_after_clipping {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: adapter_removal {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: bwa {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
}
@ -188,26 +192,18 @@ process {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName:get_software_versions {
cache = false
clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" }
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega())}M" }
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 8)}M" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName:eigenstrat_snp_coverage {
beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
}
withName:kraken_merge {
beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
}
withName:multiqc {
beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1;'
clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga() * 2}G" }
}
}
profiles {
@ -226,8 +222,6 @@ profiles {
process {
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'
maxRetries = 2
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
@ -279,7 +273,7 @@ profiles {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: fastqc_after_clipping {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
@ -404,8 +398,6 @@ profiles {
process {
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'
maxRetries = 2
// Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
@ -457,7 +449,7 @@ profiles {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: fastqc_after_clipping {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }

8
conf/pipeline/viralrecon/genomes.config
View file

@ -13,18 +13,18 @@ params {
// Please use 'MN908947.3' if possible because all primer sets are available / have been pre-prepared relative to that assembly
fasta = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
gff = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.gff.gz'
nextclade_dataset = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/nextclade_sars-cov-2_MN908947_2022-01-18T12_00_00Z.tar.gz'
nextclade_dataset = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/nextclade_sars-cov-2_MN908947_2022-06-14T12_00_00Z.tar.gz'
nextclade_dataset_name = 'sars-cov-2'
nextclade_dataset_reference = 'MN908947'
nextclade_dataset_tag = '2022-01-18T12:00:00Z'
nextclade_dataset_tag = '2022-06-14T12:00:00Z'
}
'MN908947.3' {
fasta = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz'
gff = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
nextclade_dataset = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/nextclade_sars-cov-2_MN908947_2022-01-18T12_00_00Z.tar.gz'
nextclade_dataset = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/nextclade_sars-cov-2_MN908947_2022-06-14T12_00_00Z.tar.gz'
nextclade_dataset_name = 'sars-cov-2'
nextclade_dataset_reference = 'MN908947'
nextclade_dataset_tag = '2022-01-18T12:00:00Z'
nextclade_dataset_tag = '2022-06-14T12:00:00Z'
primer_sets {
artic {
'1' {

46
conf/sanger.config
View file

@ -1,35 +1,33 @@
// Profile details
params {
config_profile_description = 'The Wellcome Sanger Institute HPC cluster profile'
config_profile_contact = 'Anthony Underwood (@aunderwo)'
config_profile_url = 'https://www.sanger.ac.uk/group/informatics-support-group/'
}
singularity {
enabled = true
cacheDir = "${baseDir}/singularity"
runOptions = '--bind /lustre --bind /nfs/pathnfs01 --bind /nfs/pathnfs02 --bind /nfs/pathnfs03 --bind /nfs/pathnfs04 --bind /nfs/pathnfs05 --bind /nfs/pathnfs06 --no-home'
config_profile_description = 'The Wellcome Sanger Institute HPC cluster (farm5) profile'
config_profile_contact = 'Priyanka Surana (@priyanka-surana)'
config_profile_url = 'https://www.sanger.ac.uk'
}
// Queue and retry strategy
process{
executor = 'lsf'
queue = 'normal'
errorStrategy = { task.attempt <= 5 ? "retry" : "finish" }
process.maxRetries = 5
withLabel:process_long {
queue = 'long'
}
executor = 'lsf'
queue = { task.time < 12.h ? 'normal' : task.time < 48.h ? 'long' : 'basement' }
errorStrategy = 'retry'
maxRetries = 5
}
// Executor details
executor{
name = 'lsf'
perJobMemLimit = true
poolSize = 4
submitRateLimit = '5 sec'
killBatchSize = 50
name = 'lsf'
perJobMemLimit = true
poolSize = 4
submitRateLimit = '5 sec'
killBatchSize = 50
}
// Max resources
params {
max_memory = 128.GB
max_cpus = 64
max_time = 48.h
max_memory = 683.GB
max_cpus = 256
max_time = 720.h
}
// For singularity
singularity.runOptions = '--bind /lustre --bind /nfs'

2
conf/vsc_ugent.config
View file

@ -9,7 +9,7 @@ workDir = "$scratch_dir/work"
// Reduce the job submit rate to about 5 per second, this way the server won't be bombarded with jobs
executor {
submitRateLimit = '5 sec'
submitRateLimit = '3 sec'
}
// Specify that singularity should be used and where the cache dir will be for the images

16
docs/sanger.md
View file

@ -2,8 +2,6 @@
To use, run the pipeline with `-profile sanger`. This will download and launch the [`sanger.config`](../conf/sanger.config) which has been
pre-configured with a setup suitable for the Wellcome Sanger Institute LSF cluster.
Using this profile, either a docker image containing all of the required software will be downloaded, and converted to a Singularity image or
a Singularity image downloaded directly before execution of the pipeline.
## Running the workflow on the Wellcome Sanger Institute cluster
@ -14,10 +12,12 @@ The latest version of Nextflow is not installed by default on the cluster. You w
A recommended place to move the `nextflow` executable to is `~/bin` so that it's in the `PATH`.
Nextflow manages each process as a separate job that is submitted to the cluster by using the `bsub` command.
Since the Nextflow pipeline will submit individual jobs for each process to the cluster and dependencies will be provided bu Singularity images you shoudl make sure that your account has access to the Singularity binary by adding these lines to your `.bashrc` file
If asking Nextflow to use Singularity to run the individual jobs,
you should make sure that your account has access to the Singularity binary by adding these lines to your `.bashrc` file
```bash
[[ -f /software/pathogen/farm5 ]] && module load ISG/singularity
[[ -f /software/modules/ISG/singularity ]] && module load ISG/singularity
```
Nextflow shouldn't run directly on the submission node but on a compute node.
@ -26,16 +26,16 @@ To do so make a shell script with a similar structure to the following code and
```bash
#!/bin/bash
#BSUB -o /path/to/a/log/dir/%J.o
#BSUB -e /path/to/a/log/dir//%J.e
#BSUB -e /path/to/a/log/dir/%J.e
#BSUB -M 8000
#BSUB -q long
#BSUB -n 4
#BSUB -q oversubscribed
#BSUB -n 2
export HTTP_PROXY='http://wwwcache.sanger.ac.uk:3128'
export HTTPS_PROXY='http://wwwcache.sanger.ac.uk:3128'
export NXF_ANSI_LOG=false
export NXF_OPTS="-Xms8G -Xmx8G -Dnxf.pool.maxThreads=2000"
export NXF_VER=21.04.0-edge
export NXF_VER=22.04.0-5697
nextflow run \