From df0429ce9d72ae02c0a319d4e14325707cc7b517 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 3 Jun 2022 14:20:39 +0200 Subject: [PATCH 01/17] Replace oracle specific _JAVA_OPTIONS to portable JAVA_TOOLS_OPTIONS --- conf/pipeline/eager/eva.config | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index f35f1ed..f633bae 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -9,7 +9,7 @@ params { // Specific nf-core/eager process configuration process { - beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"' + beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"' maxRetries = 2 @@ -69,17 +69,17 @@ 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)" } } @@ -188,19 +188,19 @@ process { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } - + withName:get_software_versions { cache = false clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" } - beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1' + beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1' clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega())}M" } 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' } @@ -226,7 +226,7 @@ profiles { process { - beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"' + beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"' maxRetries = 2 @@ -279,7 +279,7 @@ 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' } @@ -404,7 +404,7 @@ profiles { process { - beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"' + beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"' maxRetries = 2 @@ -457,7 +457,7 @@ 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' } From c40ebb9acfa5f46b98654d3adeae5c8057d01a96 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 3 Jun 2022 14:21:41 +0200 Subject: [PATCH 02/17] Add overhead for get_software_versions --- conf/pipeline/eager/eva.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index f633bae..92ce500 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -192,8 +192,8 @@ process { withName:get_software_versions { cache = false clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" } - beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1' - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega())}M" } + beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1' + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 2)}M" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } From 9ef52af084fd8b9fa21d047022bf993ffe55b55f Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 3 Jun 2022 14:24:27 +0200 Subject: [PATCH 03/17] Increase overhead --- conf/pipeline/eager/eva.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 92ce500..55b254c 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -193,7 +193,7 @@ process { cache = false clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" } beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1' - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 2)}M" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 4)}M" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } From 05cc8a08f133c66ff724b4032a3810d5549fe59b Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 3 Jun 2022 21:08:19 +0200 Subject: [PATCH 04/17] Update eva.config --- conf/pipeline/eager/eva.config | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 55b254c..fa045b1 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -193,7 +193,7 @@ process { cache = false clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" } beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1' - clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 4)}M" } + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 8)}M" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } @@ -207,6 +207,7 @@ process { 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=${task.memory.toGiga()}G" } } } From 46fba9c5970ca4ff7a235dfe3c9943ec58bd09d6 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 3 Jun 2022 21:10:48 +0200 Subject: [PATCH 05/17] Update eva.config --- conf/pipeline/eager/eva.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index fa045b1..a50c969 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -207,7 +207,7 @@ process { withName:multiqc { beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1;' - clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" } + clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga() * 2}G" } } } From 58dd9d49c7532ca114ce7dba2b8d6182806a4419 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Wed, 15 Jun 2022 15:21:20 +0200 Subject: [PATCH 06/17] Move beforeScript exports to env scope --- conf/pipeline/eager/eva.config | 24 ++++++------------------ 1 file changed, 6 insertions(+), 18 deletions(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 55b254c..a82257a 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -6,11 +6,15 @@ params { config_profile_description = 'nf-core/eager EVA profile provided by nf-core/configs' } +env { + JAVA_TOOL_OPTIONS = "-XX:ParallelGCThreads=1" + OPENBLAS_NUM_THREADS = 1 + OMP_NUM_THREADS = 1 +} + // Specific nf-core/eager process configuration process { - beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"' - maxRetries = 2 // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion @@ -192,22 +196,10 @@ process { withName:get_software_versions { cache = false clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" } - beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1' clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega() * 4)}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;' - } } profiles { @@ -226,8 +218,6 @@ profiles { process { - beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"' - maxRetries = 2 // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion @@ -404,8 +394,6 @@ profiles { process { - beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"' - maxRetries = 2 // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion From acabcbd9e8779305bf7470e22c935900085615ce Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Wed, 15 Jun 2022 15:27:40 +0200 Subject: [PATCH 07/17] Use _JAVA_OPTIONS instead --- conf/pipeline/eager/eva.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 9f1853f..8376719 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -7,7 +7,7 @@ params { } env { - JAVA_TOOL_OPTIONS = "-XX:ParallelGCThreads=1" + _JAVA_OPTIONS = "-XX:ParallelGCThreads=1" OPENBLAS_NUM_THREADS = 1 OMP_NUM_THREADS = 1 } From 2ab126fa4d2f235ad9dc949d2dfae6d1146cd468 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 11 Jul 2022 18:28:41 +0100 Subject: [PATCH 08/17] Update default Nextclade dataset to 2022-06-14T12:00:00Z --- conf/pipeline/viralrecon/genomes.config | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/conf/pipeline/viralrecon/genomes.config b/conf/pipeline/viralrecon/genomes.config index baad834..0d5e754 100644 --- a/conf/pipeline/viralrecon/genomes.config +++ b/conf/pipeline/viralrecon/genomes.config @@ -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' { From f40825ac142f3c13a8b1b01605193100f752a49d Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 14 Jul 2022 15:50:50 +0200 Subject: [PATCH 09/17] lower submission rate for vsc_ugent --- conf/vsc_ugent.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/vsc_ugent.config b/conf/vsc_ugent.config index e1e9418..0bc6ffd 100644 --- a/conf/vsc_ugent.config +++ b/conf/vsc_ugent.config @@ -9,7 +9,7 @@ workDir = "$scratch_dir/work" // Reduce the job submit rate to about 5 per second, this way the server won't be bombarded with jobs executor { - submitRateLimit = '5 sec' + submitRateLimit = '3 sec' } // Specify that singularity should be used and where the cache dir will be for the images From 58508c4fbc27bd71c82a16f6ec2bee277bc53aea Mon Sep 17 00:00:00 2001 From: Priyanka Surana Date: Wed, 20 Jul 2022 13:14:42 +0100 Subject: [PATCH 10/17] Sanger profile update --- conf/sanger.config | 46 ++++++++++++++++++++++------------------------ 1 file changed, 22 insertions(+), 24 deletions(-) diff --git a/conf/sanger.config b/conf/sanger.config index 1955ca9..df2dee7 100644 --- a/conf/sanger.config +++ b/conf/sanger.config @@ -1,35 +1,33 @@ +// Profile details params { - config_profile_description = 'The Wellcome Sanger Institute HPC cluster profile' - config_profile_contact = 'Anthony Underwood (@aunderwo)' - config_profile_url = 'https://www.sanger.ac.uk/group/informatics-support-group/' -} - -singularity { - enabled = true - cacheDir = "${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' From fd87fbcb9dadd51ed8dff1804f465132f1cc72e3 Mon Sep 17 00:00:00 2001 From: Priyanka Surana Date: Wed, 20 Jul 2022 13:22:51 +0100 Subject: [PATCH 11/17] Sanger profile update --- docs/sanger.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/sanger.md b/docs/sanger.md index ee75755..3fa7ae3 100644 --- a/docs/sanger.md +++ b/docs/sanger.md @@ -14,7 +14,7 @@ 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 +Since the Nextflow pipeline will submit individual jobs for each process to the cluster and dependencies will be provided by Singularity images 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 @@ -26,7 +26,7 @@ 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 From 2aad355fbfbb694a88727eaf0884d76ee40ffce2 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Wed, 20 Jul 2022 14:32:43 +0100 Subject: [PATCH 12/17] The config doesn't mandate Singularity any more (Conda is fine too) --- docs/sanger.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/sanger.md b/docs/sanger.md index 3fa7ae3..f4c490c 100644 --- a/docs/sanger.md +++ b/docs/sanger.md @@ -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 @@ -14,7 +12,9 @@ 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 by Singularity images you should 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 From 1f1a9ac5f0fe13401d857adc5472bb7d8da21975 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Wed, 20 Jul 2022 14:34:25 +0100 Subject: [PATCH 13/17] ISG provide the module, not the pathogen informatics team --- docs/sanger.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/sanger.md b/docs/sanger.md index f4c490c..a44acf3 100644 --- a/docs/sanger.md +++ b/docs/sanger.md @@ -17,7 +17,7 @@ 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. From 60dc451569971795c7f20b4c8ad7bc6517b53b7b Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Wed, 20 Jul 2022 14:34:59 +0100 Subject: [PATCH 14/17] The oversubscribed queue is recommended for workflow managers --- docs/sanger.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/sanger.md b/docs/sanger.md index a44acf3..caf74bb 100644 --- a/docs/sanger.md +++ b/docs/sanger.md @@ -28,7 +28,7 @@ To do so make a shell script with a similar structure to the following code and #BSUB -o /path/to/a/log/dir/%J.o #BSUB -e /path/to/a/log/dir/%J.e #BSUB -M 8000 -#BSUB -q long +#BSUB -q oversubscribed #BSUB -n 4 export HTTP_PROXY='http://wwwcache.sanger.ac.uk:3128' From 1ee20f0bb0d018f341067a27c9e05b66ae1b6ce4 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Wed, 20 Jul 2022 14:35:22 +0100 Subject: [PATCH 15/17] 2 cores should be enough for the nextflow manager itself --- docs/sanger.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/sanger.md b/docs/sanger.md index caf74bb..a3b590f 100644 --- a/docs/sanger.md +++ b/docs/sanger.md @@ -29,7 +29,7 @@ To do so make a shell script with a similar structure to the following code and #BSUB -e /path/to/a/log/dir/%J.e #BSUB -M 8000 #BSUB -q oversubscribed -#BSUB -n 4 +#BSUB -n 2 export HTTP_PROXY='http://wwwcache.sanger.ac.uk:3128' export HTTPS_PROXY='http://wwwcache.sanger.ac.uk:3128' From dda1d810b1a772ea3947561a69de59299a677728 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Wed, 20 Jul 2022 14:35:39 +0100 Subject: [PATCH 16/17] Latest stable version (rather than an edge one) --- docs/sanger.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/sanger.md b/docs/sanger.md index a3b590f..ac6df4d 100644 --- a/docs/sanger.md +++ b/docs/sanger.md @@ -35,7 +35,7 @@ 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 \ From 0b47849532ec03528fef5d551804a5fb330d4e8f Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 27 Jul 2022 14:23:29 +0200 Subject: [PATCH 17/17] Update mpcdf.config --- conf/mpcdf.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/mpcdf.config b/conf/mpcdf.config index ee33913..93e2924 100644 --- a/conf/mpcdf.config +++ b/conf/mpcdf.config @@ -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 }