From 482e7cf8de1da4bd6dc678dd7d3612303a656d3c Mon Sep 17 00:00:00 2001 From: pierrespc Date: Thu, 16 Sep 2021 12:40:56 +0200 Subject: [PATCH 01/16] 2 config files for Maestro HPC at Pasteur Institute, Paris --- conf/pasteurMaestroLong.config | 26 ++++++++++++++++++++++++++ conf/pasteurMaestroNormnal.config | 26 ++++++++++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 conf/pasteurMaestroLong.config create mode 100644 conf/pasteurMaestroNormnal.config diff --git a/conf/pasteurMaestroLong.config b/conf/pasteurMaestroLong.config new file mode 100644 index 0000000..f2b8841 --- /dev/null +++ b/conf/pasteurMaestroLong.config @@ -0,0 +1,26 @@ +params { + config_profile_description = 'Institut Pasteur Maestro cluster profile' + config_profile_contact = 'Pierre Luisi (@pierrespc)' +} + +singularity { + enabled = true + autoMounts = true + runOptions = '--home $HOME:/home/$USER --bind /pasteur' +} + +process { + executor = 'slurm' + scratch=false + queue = "common" + clusterOptions = "--qos=long" + +} + +params { + igenomes_ignore = true + igenomesIgnore = true + max_memory = 100.GB + max_cpus = 5 + max_time = 8760.h +} diff --git a/conf/pasteurMaestroNormnal.config b/conf/pasteurMaestroNormnal.config new file mode 100644 index 0000000..9b40262 --- /dev/null +++ b/conf/pasteurMaestroNormnal.config @@ -0,0 +1,26 @@ +params { + config_profile_description = 'Institut Pasteur Maestro cluster profile' + config_profile_contact = 'Pierre Luisi (@pierrespc)' +} + +singularity { + enabled = true + autoMounts = true + runOptions = '--home $HOME:/home/$USER --bind /pasteur' +} + +process { + executor = 'slurm' + scratch=false + queue = "common" + clusterOptions = "--qos=normal" + +} + +params { + igenomes_ignore = true + igenomesIgnore = true + max_memory = 300.GB + max_cpus = 200 + max_time = 24.h +} From b9682bbc91a2492ccb538fbc33d97994b0e7f548 Mon Sep 17 00:00:00 2001 From: pierrespc Date: Thu, 16 Sep 2021 12:53:17 +0200 Subject: [PATCH 02/16] requires files edited --- .github/workflows/main.yml | 2 ++ README.md | 2 ++ docs/pasteurMaestroLong.md | 8 ++++++++ docs/pasteurMaestroNormal.md | 8 ++++++++ nfcore_custom.config | 2 ++ 5 files changed, 22 insertions(+) create mode 100644 docs/pasteurMaestroLong.md create mode 100644 docs/pasteurMaestroNormal.md diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index f6b86ab..b983f44 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -52,6 +52,8 @@ jobs: - 'nu_genomics' - 'oist' - 'pasteur' + - 'pasteurNorm' + - 'pasteurLong' - 'phoenix' - 'prince' - 'sanger' diff --git a/README.md b/README.md index 7a40140..2452442 100644 --- a/README.md +++ b/README.md @@ -121,6 +121,8 @@ Currently documentation is available for the following systems: * [NU_GENOMICS](docs/nu_genomics.md) * [OIST](docs/oist.md) * [PASTEUR](docs/pasteur.md) +* [PASTEURNORM](docs/pasteurMaestroNormal.md) +* [PASTEURLONG](docs/pasteurMaestroLong.md) * [PHOENIX](docs/phoenix.md) * [PRINCE](docs/prince.md) * [SANGER](docs/sanger.md) diff --git a/docs/pasteurMaestroLong.md b/docs/pasteurMaestroLong.md new file mode 100644 index 0000000..22b1bce --- /dev/null +++ b/docs/pasteurMaestroLong.md @@ -0,0 +1,8 @@ +# nf-core/configs: Institut Pasteur Configuration on Maestro + +This is an intent for configuration of nf-core in Maestro cluster on the long qos + +I am not expert of nf-core so pelase refer to docs/pasteur.md for installing and running nf-core + +Run the pipeline with `-profile pasteurLong` + diff --git a/docs/pasteurMaestroNormal.md b/docs/pasteurMaestroNormal.md new file mode 100644 index 0000000..91d2f45 --- /dev/null +++ b/docs/pasteurMaestroNormal.md @@ -0,0 +1,8 @@ +# nf-core/configs: Institut Pasteur Configuration on Maestro + +This is an intent for configuration of nf-core in Maestro cluster on the normal qos + +I am not expert of nf-core so pelase refer to docs/pasteur.md for installing and running nf-core + +Run the pipeline with `-profile pasteurNorm` + diff --git a/nfcore_custom.config b/nfcore_custom.config index da46831..3e41ce8 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -46,6 +46,8 @@ profiles { nu_genomics { includeConfig "${params.custom_config_base}/conf/nu_genomics.config" } oist { includeConfig "${params.custom_config_base}/conf/oist.config" } pasteur { includeConfig "${params.custom_config_base}/conf/pasteur.config" } + pasteurNorm { includeConfig "${params.custom_config_base}/conf/pasteurMaestroNormal.config" } + pasteurLong { includeConfig "${params.custom_config_base}/conf/pasteurMaestroLong.config" } phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } prince { includeConfig "${params.custom_config_base}/conf/prince.config" } sanger { includeConfig "${params.custom_config_base}/conf/sanger.config"} From de2a745fdea845b285869f8d6934ba547f189a5e Mon Sep 17 00:00:00 2001 From: pierrespc Date: Thu, 16 Sep 2021 16:48:26 +0200 Subject: [PATCH 03/16] change type in Normal name --- ...pasteurMaestroNormnal.config => pasteurMaestroNormal.config} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename conf/{pasteurMaestroNormnal.config => pasteurMaestroNormal.config} (96%) diff --git a/conf/pasteurMaestroNormnal.config b/conf/pasteurMaestroNormal.config similarity index 96% rename from conf/pasteurMaestroNormnal.config rename to conf/pasteurMaestroNormal.config index 9b40262..2e6f3e9 100644 --- a/conf/pasteurMaestroNormnal.config +++ b/conf/pasteurMaestroNormal.config @@ -21,6 +21,6 @@ params { igenomes_ignore = true igenomesIgnore = true max_memory = 300.GB - max_cpus = 200 + max_cpus = 96 max_time = 24.h } From 4614ff6f455d5fb75383ca648f4f3c3ef67addfa Mon Sep 17 00:00:00 2001 From: pierrespc Date: Thu, 16 Sep 2021 16:50:45 +0200 Subject: [PATCH 04/16] change max mem in Normal --- conf/pasteurMaestroNormal.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/pasteurMaestroNormal.config b/conf/pasteurMaestroNormal.config index 2e6f3e9..049acd0 100644 --- a/conf/pasteurMaestroNormal.config +++ b/conf/pasteurMaestroNormal.config @@ -20,7 +20,7 @@ process { params { igenomes_ignore = true igenomesIgnore = true - max_memory = 300.GB + max_memory = 400.GB max_cpus = 96 max_time = 24.h } From 3b593d46ecd6390fa9e484dcaa3cb9eda6d1d6d7 Mon Sep 17 00:00:00 2001 From: pierrespc Date: Mon, 20 Sep 2021 15:14:50 +0200 Subject: [PATCH 05/16] merged two pasteur config files for maestro --- .github/workflows/main.yml | 3 +-- README.md | 3 +-- conf/maestro.config | 26 ++++++++++++++++++++++++++ conf/pasteurMaestroLong.config | 26 -------------------------- conf/pasteurMaestroNormal.config | 26 -------------------------- docs/maestro.md | 10 ++++++++++ docs/pasteurMaestroLong.md | 8 -------- docs/pasteurMaestroNormal.md | 8 -------- 8 files changed, 38 insertions(+), 72 deletions(-) create mode 100644 conf/maestro.config delete mode 100644 conf/pasteurMaestroLong.config delete mode 100644 conf/pasteurMaestroNormal.config create mode 100644 docs/maestro.md delete mode 100644 docs/pasteurMaestroLong.md delete mode 100644 docs/pasteurMaestroNormal.md diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index b983f44..a8b6b91 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -47,13 +47,12 @@ jobs: - 'imperial_mb' - 'jax' - 'lugh' + - 'maestro' - 'mpcdf' - 'munin' - 'nu_genomics' - 'oist' - 'pasteur' - - 'pasteurNorm' - - 'pasteurLong' - 'phoenix' - 'prince' - 'sanger' diff --git a/README.md b/README.md index 2452442..e629e4a 100644 --- a/README.md +++ b/README.md @@ -116,13 +116,12 @@ Currently documentation is available for the following systems: * [ICR_DAVROS](docs/icr_davros.md) * [JAX](docs/jax.md) * [LUGH](docs/lugh.md) +* [MAESTRO](docs/maestro.md) * [MPCDF](docs/mpcdf.md) * [MUNIN](docs/munin.md) * [NU_GENOMICS](docs/nu_genomics.md) * [OIST](docs/oist.md) * [PASTEUR](docs/pasteur.md) -* [PASTEURNORM](docs/pasteurMaestroNormal.md) -* [PASTEURLONG](docs/pasteurMaestroLong.md) * [PHOENIX](docs/phoenix.md) * [PRINCE](docs/prince.md) * [SANGER](docs/sanger.md) diff --git a/conf/maestro.config b/conf/maestro.config new file mode 100644 index 0000000..42ba030 --- /dev/null +++ b/conf/maestro.config @@ -0,0 +1,26 @@ +params { + config_profile_description = 'Institut Pasteur Maestro cluster profile' + config_profile_url = 'https://confluence.pasteur.fr/spaces/viewspace.action?key=FAQA' + config_profile_contact = 'Pierre Luisi (@pierrespc)' +} + +singularity { + enabled = true + autoMounts = true + runOptions = '--home $HOME:/home/$USER --bind /pasteur' +} + +process { + executor = 'slurm' + scratch = false + queue = 'common' + clusterOptions = {task.time < 24.h ? '--qos=normal' : '--qos=long'} +} + +params { + igenomes_ignore = true + igenomesIgnore = true + max_memory = {task.time < 24.h ? 400.GB : 100.GB } + max_cpus = {task.time < 24.h ? 96 : 5 } + max_time = {task.time < 24.h ? 24.h : 8760.h } +} diff --git a/conf/pasteurMaestroLong.config b/conf/pasteurMaestroLong.config deleted file mode 100644 index f2b8841..0000000 --- a/conf/pasteurMaestroLong.config +++ /dev/null @@ -1,26 +0,0 @@ -params { - config_profile_description = 'Institut Pasteur Maestro cluster profile' - config_profile_contact = 'Pierre Luisi (@pierrespc)' -} - -singularity { - enabled = true - autoMounts = true - runOptions = '--home $HOME:/home/$USER --bind /pasteur' -} - -process { - executor = 'slurm' - scratch=false - queue = "common" - clusterOptions = "--qos=long" - -} - -params { - igenomes_ignore = true - igenomesIgnore = true - max_memory = 100.GB - max_cpus = 5 - max_time = 8760.h -} diff --git a/conf/pasteurMaestroNormal.config b/conf/pasteurMaestroNormal.config deleted file mode 100644 index 049acd0..0000000 --- a/conf/pasteurMaestroNormal.config +++ /dev/null @@ -1,26 +0,0 @@ -params { - config_profile_description = 'Institut Pasteur Maestro cluster profile' - config_profile_contact = 'Pierre Luisi (@pierrespc)' -} - -singularity { - enabled = true - autoMounts = true - runOptions = '--home $HOME:/home/$USER --bind /pasteur' -} - -process { - executor = 'slurm' - scratch=false - queue = "common" - clusterOptions = "--qos=normal" - -} - -params { - igenomes_ignore = true - igenomesIgnore = true - max_memory = 400.GB - max_cpus = 96 - max_time = 24.h -} diff --git a/docs/maestro.md b/docs/maestro.md new file mode 100644 index 0000000..c931a05 --- /dev/null +++ b/docs/maestro.md @@ -0,0 +1,10 @@ +# nf-core/configs: Institut Pasteur Configuration on Maestro. + +If you are using TARS cluster, please refer to pasteur profile. + +This is an intent for configuration of nf-core in Maestro cluster on the normal or long qos depending on the ressources required + +I am not expert of nf-core so pelase refer to docs/pasteur.md for installing and running nf-core + +Run the pipeline with `-profile pasteur_maestro` + diff --git a/docs/pasteurMaestroLong.md b/docs/pasteurMaestroLong.md deleted file mode 100644 index 22b1bce..0000000 --- a/docs/pasteurMaestroLong.md +++ /dev/null @@ -1,8 +0,0 @@ -# nf-core/configs: Institut Pasteur Configuration on Maestro - -This is an intent for configuration of nf-core in Maestro cluster on the long qos - -I am not expert of nf-core so pelase refer to docs/pasteur.md for installing and running nf-core - -Run the pipeline with `-profile pasteurLong` - diff --git a/docs/pasteurMaestroNormal.md b/docs/pasteurMaestroNormal.md deleted file mode 100644 index 91d2f45..0000000 --- a/docs/pasteurMaestroNormal.md +++ /dev/null @@ -1,8 +0,0 @@ -# nf-core/configs: Institut Pasteur Configuration on Maestro - -This is an intent for configuration of nf-core in Maestro cluster on the normal qos - -I am not expert of nf-core so pelase refer to docs/pasteur.md for installing and running nf-core - -Run the pipeline with `-profile pasteurNorm` - From 3e22b85b0260465eb3e526e1f97face1c75282d2 Mon Sep 17 00:00:00 2001 From: pierrespc Date: Wed, 22 Sep 2021 10:13:46 +0200 Subject: [PATCH 06/16] maestro only for normal qos --- conf/maestro.config | 8 ++++---- nfcore_custom.config | 3 +-- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/conf/maestro.config b/conf/maestro.config index 42ba030..a3fb7b5 100644 --- a/conf/maestro.config +++ b/conf/maestro.config @@ -14,13 +14,13 @@ process { executor = 'slurm' scratch = false queue = 'common' - clusterOptions = {task.time < 24.h ? '--qos=normal' : '--qos=long'} + clusterOptions = '--qos=normal' } params { igenomes_ignore = true igenomesIgnore = true - max_memory = {task.time < 24.h ? 400.GB : 100.GB } - max_cpus = {task.time < 24.h ? 96 : 5 } - max_time = {task.time < 24.h ? 24.h : 8760.h } + max_memory = 400.GB + max_cpus = 96 + max_time = 24.h } diff --git a/nfcore_custom.config b/nfcore_custom.config index 3e41ce8..c7dcbf4 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -41,13 +41,12 @@ profiles { imperial_mb { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" } jax { includeConfig "${params.custom_config_base}/conf/jax.config" } lugh { includeConfig "${params.custom_config_base}/conf/lugh.config" } + maestro { includeConfig "${params.custom_config_base}/conf/maestro.config" } mpcdf { includeConfig "${params.custom_config_base}/conf/mpcdf.config" } munin { includeConfig "${params.custom_config_base}/conf/munin.config" } nu_genomics { includeConfig "${params.custom_config_base}/conf/nu_genomics.config" } oist { includeConfig "${params.custom_config_base}/conf/oist.config" } pasteur { includeConfig "${params.custom_config_base}/conf/pasteur.config" } - pasteurNorm { includeConfig "${params.custom_config_base}/conf/pasteurMaestroNormal.config" } - pasteurLong { includeConfig "${params.custom_config_base}/conf/pasteurMaestroLong.config" } phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } prince { includeConfig "${params.custom_config_base}/conf/prince.config" } sanger { includeConfig "${params.custom_config_base}/conf/sanger.config"} From 9ea3e2096af742f2449447954b9ca9d75295046f Mon Sep 17 00:00:00 2001 From: pierrespc Date: Wed, 29 Sep 2021 13:11:14 +0200 Subject: [PATCH 07/16] long and normal qos profiles defined now in an unique maestro config file. maestro.config also defined in pipeline/eager for ressources assignation to specific processes --- conf/maestro.config | 47 +++++++++++++++++------ conf/pipeline/eager/maestro.config | 60 ++++++++++++++++++++++++++++++ pipeline/eager.config | 1 + 3 files changed, 96 insertions(+), 12 deletions(-) create mode 100644 conf/pipeline/eager/maestro.config diff --git a/conf/maestro.config b/conf/maestro.config index a3fb7b5..bf48c23 100644 --- a/conf/maestro.config +++ b/conf/maestro.config @@ -10,17 +10,40 @@ singularity { runOptions = '--home $HOME:/home/$USER --bind /pasteur' } -process { - executor = 'slurm' - scratch = false - queue = 'common' - clusterOptions = '--qos=normal' -} +profiles { + + normal { + process { + executor = 'slurm' + scratch = false + queue = 'common' + clusterOptions = '--qos=normal' + } + + params { + igenomes_ignore = true + igenomesIgnore = true + max_memory = 400.GB + max_cpus = 96 + max_time = 24.h + } + } + + long { + process { + executor = 'slurm' + scratch = false + queue = 'common' + clusterOptions = '--qos=long' + } + + params { + igenomes_ignore = true + igenomesIgnore = true + max_memory = 400.GB + max_cpus = 5 + max_time = 8760.h + } + } -params { - igenomes_ignore = true - igenomesIgnore = true - max_memory = 400.GB - max_cpus = 96 - max_time = 24.h } diff --git a/conf/pipeline/eager/maestro.config b/conf/pipeline/eager/maestro.config new file mode 100644 index 0000000..8046c80 --- /dev/null +++ b/conf/pipeline/eager/maestro.config @@ -0,0 +1,60 @@ +/* + * ------------------------------------------------- + * Nextflow config file for running tests + * ------------------------------------------------- + * Defines bundled input files and everything required + * to run a fast and simple test. Use as follows: + * nextflow run nf-core/eager -profile test, docker (or singularity, or conda) + */ + +params { + + config_profile_name = 'nf-core/eager nucleaer - human profile' + + config_profile_description = "A simple profile for human nuclear genomes" + + email = 'pluisi@pasteur.fr' +} + + +process { + errorStrategy = 'retry' + maxRetries = 2 + + withName:'makeBWAIndex'{ + cpus = { check_max( 8 * task.attempt, 'cpus' ) } + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = { check_max( 12.h * task.attempt, 'time' ) } + } + withName:'adapter_removal'{ + cpus = { check_max( 8 * task.attempt, 'cpus' ) } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } + time = { check_max( 12.h * task.attempt, 'time' ) } + } + withName:'bwa'{ + cpus = { check_max( 15 * task.attempt, 'cpus' ) } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } + time = 24.h + } + withName:'markduplicates'{ + errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } + cpus = { check_max( 8 * task.attempt, 'cpus' ) } + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = { check_max( 6.h * task.attempt, 'time' ) } + } + withName:'damageprofiler'{ + cpus = 1 + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = { check_max( 6.h * task.attempt, 'time' ) } + } + withName:'fastp'{ + cpus = 8 + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = { check_max( 6.h * task.attempt, 'time' ) } + } + withName:'fastqc'{ + cpus = 2 + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = { check_max( 6.h * task.attempt, 'time' ) } + } +} diff --git a/pipeline/eager.config b/pipeline/eager.config index 3e47276..352395b 100644 --- a/pipeline/eager.config +++ b/pipeline/eager.config @@ -11,4 +11,5 @@ profiles { mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/eager/mpcdf.config" } eva { includeConfig "${params.custom_config_base}/conf/pipeline/eager/eva.config" } + maestro { includeConfig "${params.custom_config_base}/conf/maestro.config" } } From b71df6fe571041ca9a6ee8cdc556ba083c6b4caa Mon Sep 17 00:00:00 2001 From: pierrespc Date: Wed, 29 Sep 2021 13:22:07 +0200 Subject: [PATCH 08/16] renamed eager pipeline config file --- conf/pipeline/eager/{maestro.config => maestronuclear.config} | 0 pipeline/eager.config | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) rename conf/pipeline/eager/{maestro.config => maestronuclear.config} (100%) diff --git a/conf/pipeline/eager/maestro.config b/conf/pipeline/eager/maestronuclear.config similarity index 100% rename from conf/pipeline/eager/maestro.config rename to conf/pipeline/eager/maestronuclear.config diff --git a/pipeline/eager.config b/pipeline/eager.config index 352395b..9758f0d 100644 --- a/pipeline/eager.config +++ b/pipeline/eager.config @@ -11,5 +11,5 @@ profiles { mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/eager/mpcdf.config" } eva { includeConfig "${params.custom_config_base}/conf/pipeline/eager/eva.config" } - maestro { includeConfig "${params.custom_config_base}/conf/maestro.config" } + maestronuclear { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestronuclear.config" } } From f6266879d6a94ee3f442cae6a4efaa7c2e85f1ab Mon Sep 17 00:00:00 2001 From: pierrespc Date: Wed, 29 Sep 2021 13:47:35 +0200 Subject: [PATCH 09/16] edited maestronuclear and maestromitocondrial configs. The latter has not been optimized yet --- .../pipeline/eager/maestromitocondrial.config | 58 +++++++++++++++++++ conf/pipeline/eager/maestronuclear.config | 6 +- pipeline/eager.config | 1 + 3 files changed, 61 insertions(+), 4 deletions(-) create mode 100644 conf/pipeline/eager/maestromitocondrial.config diff --git a/conf/pipeline/eager/maestromitocondrial.config b/conf/pipeline/eager/maestromitocondrial.config new file mode 100644 index 0000000..62c6e4e --- /dev/null +++ b/conf/pipeline/eager/maestromitocondrial.config @@ -0,0 +1,58 @@ +/* + * ------------------------------------------------- + * Nextflow config file for running nf-core eager on mitocondrial data (providing reference genome only the reference genome for mitogenomes)_ + * ------------------------------------------------- + * nextflow run nf-core/eager -profile maestro,,maestromitocondrial (where is long or normal) + */ + +params { + + config_profile_name = 'nf-core/eager mitrocondrial - human profile' + + config_profile_description = "A simple profile for human mitogenomes" + + email = 'pluisi@pasteur.fr' +} + + +process { + errorStrategy = 'retry' + maxRetries = 2 + + withName:'makeBWAIndex'{ + cpus = { check_max( 8 * task.attempt, 'cpus' ) } + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = { check_max( 12.h * task.attempt, 'time' ) } + } + withName:'adapter_removal'{ + cpus = { check_max( 8 * task.attempt, 'cpus' ) } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } + time = { check_max( 12.h * task.attempt, 'time' ) } + } + withName:'bwa'{ + cpus = { check_max( 5 * task.attempt, 'cpus' ) } + memory = { check_max( 5.GB * task.attempt, 'memory' ) } + time = 24.h + } + withName:'markduplicates'{ + errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } + cpus = { check_max( 5 * task.attempt, 'cpus' ) } + memory = { check_max( 5.GB * task.attempt, 'memory' ) } + time = { check_max( 6.h * task.attempt, 'time' ) } + } + withName:'damageprofiler'{ + cpus = 1 + memory = { check_max( 5.GB * task.attempt, 'memory' ) } + time = { check_max( 3.h * task.attempt, 'time' ) } + } + withName:'fastp'{ + cpus = 8 + memory = { check_max( 5.GB * task.attempt, 'memory' ) } + time = { check_max( 3.h * task.attempt, 'time' ) } + } + withName:'fastqc'{ + cpus = 2 + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = { check_max( 6.h * task.attempt, 'time' ) } + } +} diff --git a/conf/pipeline/eager/maestronuclear.config b/conf/pipeline/eager/maestronuclear.config index 8046c80..7ec6a9c 100644 --- a/conf/pipeline/eager/maestronuclear.config +++ b/conf/pipeline/eager/maestronuclear.config @@ -1,10 +1,8 @@ /* * ------------------------------------------------- - * Nextflow config file for running tests + * Nextflow config file for running nf-core eager on whole genome data * ------------------------------------------------- - * Defines bundled input files and everything required - * to run a fast and simple test. Use as follows: - * nextflow run nf-core/eager -profile test, docker (or singularity, or conda) + * nextflow run nf-core/eager -profile maestro,,maestronuclear (where is long or normal) */ params { diff --git a/pipeline/eager.config b/pipeline/eager.config index 9758f0d..5825bab 100644 --- a/pipeline/eager.config +++ b/pipeline/eager.config @@ -12,4 +12,5 @@ profiles { mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/eager/mpcdf.config" } eva { includeConfig "${params.custom_config_base}/conf/pipeline/eager/eva.config" } maestronuclear { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestronuclear.config" } + maestromitocondrial { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestromitocondrial.config" } } From 136fd44e0c37c01786df8c4179818bbccf39ea8d Mon Sep 17 00:00:00 2001 From: pierrespc Date: Wed, 29 Sep 2021 13:50:56 +0200 Subject: [PATCH 10/16] corrected docs/maestro.config --- docs/maestro.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/maestro.md b/docs/maestro.md index c931a05..cda14f7 100644 --- a/docs/maestro.md +++ b/docs/maestro.md @@ -6,5 +6,5 @@ This is an intent for configuration of nf-core in Maestro cluster on the normal I am not expert of nf-core so pelase refer to docs/pasteur.md for installing and running nf-core -Run the pipeline with `-profile pasteur_maestro` +Run the pipeline with `-profile maestro,` where qos is long or normal From e5d4a357c5cddedd35a29dafee5c9c986cf291be Mon Sep 17 00:00:00 2001 From: pierrespc Date: Mon, 4 Oct 2021 15:08:01 +0200 Subject: [PATCH 11/16] clean doc --- conf/maestro.config | 2 +- conf/pipeline/eager/maestro.config | 107 ++++++++++++++++++ .../pipeline/eager/maestromitocondrial.config | 58 ---------- conf/pipeline/eager/maestronuclear.config | 58 ---------- docs/maestro.md | 4 +- pipeline/eager.config | 3 +- 6 files changed, 111 insertions(+), 121 deletions(-) create mode 100644 conf/pipeline/eager/maestro.config delete mode 100644 conf/pipeline/eager/maestromitocondrial.config delete mode 100644 conf/pipeline/eager/maestronuclear.config diff --git a/conf/maestro.config b/conf/maestro.config index bf48c23..8815932 100644 --- a/conf/maestro.config +++ b/conf/maestro.config @@ -1,6 +1,6 @@ params { config_profile_description = 'Institut Pasteur Maestro cluster profile' - config_profile_url = 'https://confluence.pasteur.fr/spaces/viewspace.action?key=FAQA' + config_profile_url = 'https://research.pasteur.fr/en/equipment/maestro-compute-cluster/' config_profile_contact = 'Pierre Luisi (@pierrespc)' } diff --git a/conf/pipeline/eager/maestro.config b/conf/pipeline/eager/maestro.config new file mode 100644 index 0000000..473eec3 --- /dev/null +++ b/conf/pipeline/eager/maestro.config @@ -0,0 +1,107 @@ +/* + * ------------------------------------------------- + * Nextflow config file for running nf-core eager on whole genome data or mitogenomes + * ------------------------------------------------- + * nextflow run nf-core/eager -profile maestro,,maestro, (where is long or normal and is nuclear or mitocondrial) + */ + +params { + + config_profile_name = 'nf-core/eager nuclear/mitocondrial - human profiles' + + config_profile_description = "Simple profiles for human nuclear or mito genomes" + + email = 'pluisi@pasteur.fr' +} + + +profiles { + + nuclear { + process { + errorStrategy = 'retry' + maxRetries = 2 + + withName:'makeBWAIndex'{ + cpus = { check_max( 8 * task.attempt, 'cpus' ) } + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = { check_max( 12.h * task.attempt, 'time' ) } + } + withName:'adapter_removal'{ + cpus = { check_max( 8 * task.attempt, 'cpus' ) } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } + time = { check_max( 12.h * task.attempt, 'time' ) } + } + withName:'bwa'{ + cpus = { check_max( 30 * task.attempt, 'cpus' ) } + memory = { check_max( 40.GB * task.attempt, 'memory' ) } + time = 24.h + } + withName:'markduplicates'{ + errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } + cpus = { check_max( 8 * task.attempt, 'cpus' ) } + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = { check_max( 6.h * task.attempt, 'time' ) } + } + withName:'damageprofiler'{ + cpus = 1 + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = { check_max( 6.h * task.attempt, 'time' ) } + } + withName:'fastp'{ + cpus = 8 + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = { check_max( 6.h * task.attempt, 'time' ) } + } + withName:'fastqc'{ + cpus = 2 + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = { check_max( 6.h * task.attempt, 'time' ) } + } + } + } + + mitocondrial { + process { + errorStrategy = 'retry' + maxRetries = 2 + + withName:'makeBWAIndex'{ + cpus = { check_max( 8 * task.attempt, 'cpus' ) } + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = { check_max( 12.h * task.attempt, 'time' ) } + } + withName:'adapter_removal'{ + cpus = { check_max( 8 * task.attempt, 'cpus' ) } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } + time = { check_max( 12.h * task.attempt, 'time' ) } + } + withName:'bwa'{ + cpus = { check_max( 5 * task.attempt, 'cpus' ) } + memory = { check_max( 5.GB * task.attempt, 'memory' ) } + time = 24.h + } + withName:'markduplicates'{ + errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } + cpus = { check_max( 5 * task.attempt, 'cpus' ) } + memory = { check_max( 5.GB * task.attempt, 'memory' ) } + time = { check_max( 6.h * task.attempt, 'time' ) } + } + withName:'damageprofiler'{ + cpus = 1 + memory = { check_max( 5.GB * task.attempt, 'memory' ) } + time = { check_max( 3.h * task.attempt, 'time' ) } + } + withName:'fastp'{ + cpus = 8 + memory = { check_max( 5.GB * task.attempt, 'memory' ) } + time = { check_max( 3.h * task.attempt, 'time' ) } + } + withName:'fastqc'{ + cpus = 2 + memory = { check_max( 8.GB * task.attempt, 'memory' ) } + time = { check_max( 6.h * task.attempt, 'time' ) } + } + } + } +} diff --git a/conf/pipeline/eager/maestromitocondrial.config b/conf/pipeline/eager/maestromitocondrial.config deleted file mode 100644 index 62c6e4e..0000000 --- a/conf/pipeline/eager/maestromitocondrial.config +++ /dev/null @@ -1,58 +0,0 @@ -/* - * ------------------------------------------------- - * Nextflow config file for running nf-core eager on mitocondrial data (providing reference genome only the reference genome for mitogenomes)_ - * ------------------------------------------------- - * nextflow run nf-core/eager -profile maestro,,maestromitocondrial (where is long or normal) - */ - -params { - - config_profile_name = 'nf-core/eager mitrocondrial - human profile' - - config_profile_description = "A simple profile for human mitogenomes" - - email = 'pluisi@pasteur.fr' -} - - -process { - errorStrategy = 'retry' - maxRetries = 2 - - withName:'makeBWAIndex'{ - cpus = { check_max( 8 * task.attempt, 'cpus' ) } - memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = { check_max( 12.h * task.attempt, 'time' ) } - } - withName:'adapter_removal'{ - cpus = { check_max( 8 * task.attempt, 'cpus' ) } - memory = { check_max( 16.GB * task.attempt, 'memory' ) } - time = { check_max( 12.h * task.attempt, 'time' ) } - } - withName:'bwa'{ - cpus = { check_max( 5 * task.attempt, 'cpus' ) } - memory = { check_max( 5.GB * task.attempt, 'memory' ) } - time = 24.h - } - withName:'markduplicates'{ - errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } - cpus = { check_max( 5 * task.attempt, 'cpus' ) } - memory = { check_max( 5.GB * task.attempt, 'memory' ) } - time = { check_max( 6.h * task.attempt, 'time' ) } - } - withName:'damageprofiler'{ - cpus = 1 - memory = { check_max( 5.GB * task.attempt, 'memory' ) } - time = { check_max( 3.h * task.attempt, 'time' ) } - } - withName:'fastp'{ - cpus = 8 - memory = { check_max( 5.GB * task.attempt, 'memory' ) } - time = { check_max( 3.h * task.attempt, 'time' ) } - } - withName:'fastqc'{ - cpus = 2 - memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = { check_max( 6.h * task.attempt, 'time' ) } - } -} diff --git a/conf/pipeline/eager/maestronuclear.config b/conf/pipeline/eager/maestronuclear.config deleted file mode 100644 index 7ec6a9c..0000000 --- a/conf/pipeline/eager/maestronuclear.config +++ /dev/null @@ -1,58 +0,0 @@ -/* - * ------------------------------------------------- - * Nextflow config file for running nf-core eager on whole genome data - * ------------------------------------------------- - * nextflow run nf-core/eager -profile maestro,,maestronuclear (where is long or normal) - */ - -params { - - config_profile_name = 'nf-core/eager nucleaer - human profile' - - config_profile_description = "A simple profile for human nuclear genomes" - - email = 'pluisi@pasteur.fr' -} - - -process { - errorStrategy = 'retry' - maxRetries = 2 - - withName:'makeBWAIndex'{ - cpus = { check_max( 8 * task.attempt, 'cpus' ) } - memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = { check_max( 12.h * task.attempt, 'time' ) } - } - withName:'adapter_removal'{ - cpus = { check_max( 8 * task.attempt, 'cpus' ) } - memory = { check_max( 16.GB * task.attempt, 'memory' ) } - time = { check_max( 12.h * task.attempt, 'time' ) } - } - withName:'bwa'{ - cpus = { check_max( 15 * task.attempt, 'cpus' ) } - memory = { check_max( 16.GB * task.attempt, 'memory' ) } - time = 24.h - } - withName:'markduplicates'{ - errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } - cpus = { check_max( 8 * task.attempt, 'cpus' ) } - memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = { check_max( 6.h * task.attempt, 'time' ) } - } - withName:'damageprofiler'{ - cpus = 1 - memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = { check_max( 6.h * task.attempt, 'time' ) } - } - withName:'fastp'{ - cpus = 8 - memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = { check_max( 6.h * task.attempt, 'time' ) } - } - withName:'fastqc'{ - cpus = 2 - memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = { check_max( 6.h * task.attempt, 'time' ) } - } -} diff --git a/docs/maestro.md b/docs/maestro.md index cda14f7..59daa80 100644 --- a/docs/maestro.md +++ b/docs/maestro.md @@ -4,7 +4,7 @@ If you are using TARS cluster, please refer to pasteur profile. This is an intent for configuration of nf-core in Maestro cluster on the normal or long qos depending on the ressources required -I am not expert of nf-core so pelase refer to docs/pasteur.md for installing and running nf-core +Please refer to docs/pasteur.md for installing and running nf-core instructions. -Run the pipeline with `-profile maestro,` where qos is long or normal +Run the pipeline with -profile maestro, where qos is long or normal. diff --git a/pipeline/eager.config b/pipeline/eager.config index 5825bab..10dd990 100644 --- a/pipeline/eager.config +++ b/pipeline/eager.config @@ -11,6 +11,5 @@ profiles { mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/eager/mpcdf.config" } eva { includeConfig "${params.custom_config_base}/conf/pipeline/eager/eva.config" } - maestronuclear { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestronuclear.config" } - maestromitocondrial { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestromitocondrial.config" } + maestro { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestro.config" } } From 162158555823bcc57388888b2c59b5e1f3698e6a Mon Sep 17 00:00:00 2001 From: pierrespc Date: Mon, 4 Oct 2021 16:08:33 +0200 Subject: [PATCH 12/16] improving documentation --- conf/pipeline/eager/maestro.config | 1 - docs/maestro.md | 19 +++++++++++++++---- docs/pipeline/eager/maestro.md | 29 +++++++++++++++++++++++++++++ 3 files changed, 44 insertions(+), 5 deletions(-) create mode 100644 docs/pipeline/eager/maestro.md diff --git a/conf/pipeline/eager/maestro.config b/conf/pipeline/eager/maestro.config index 473eec3..3705d8c 100644 --- a/conf/pipeline/eager/maestro.config +++ b/conf/pipeline/eager/maestro.config @@ -11,7 +11,6 @@ params { config_profile_description = "Simple profiles for human nuclear or mito genomes" - email = 'pluisi@pasteur.fr' } diff --git a/docs/maestro.md b/docs/maestro.md index 59daa80..fe1b5f1 100644 --- a/docs/maestro.md +++ b/docs/maestro.md @@ -1,10 +1,21 @@ -# nf-core/configs: Institut Pasteur Configuration on Maestro. +# nf-core/configs: Maestro (at Pateur Institute, Paris) Configuration. +To use, run the pipeline with -profile maestro, (with qos being long or normal). This will download and launch the maestro.config which has been pre-configured with a setup suitable for the Maestro cluster on either the long or normal qos. +Using one of these profiles, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline + + +## needed Modules +Please first load java, nextflow and singularity modules +`module load java` +`module load nextflow` +`module load singularity` + +Also, do not forget to run nextflow using tmux or alike. + + +## Other profiles at Pasteur: If you are using TARS cluster, please refer to pasteur profile. -This is an intent for configuration of nf-core in Maestro cluster on the normal or long qos depending on the ressources required - Please refer to docs/pasteur.md for installing and running nf-core instructions. -Run the pipeline with -profile maestro, where qos is long or normal. diff --git a/docs/pipeline/eager/maestro.md b/docs/pipeline/eager/maestro.md new file mode 100644 index 0000000..45a151e --- /dev/null +++ b/docs/pipeline/eager/maestro.md @@ -0,0 +1,29 @@ +# nf-core/configs: maestro eager specific configuration + +Extra specific configuration for eager pipeline for human DNA data processing + +## Usage + +To use, run the pipeline with `-profile maestro,,`, where can be normal or long and can be nuclear or mitochondrial + +This will download and launch the eager specific [`maestro.config`](../../../conf/pipeline/eager/maestro.config) which has been pre-configured with a setup suitable for the Maestro cluster. + +Example: `nextflow run nf-core/eager -profile maestro,normal,nuclear` + +## eager specific configurations for maestro + +Specific configurations for maestro has been made for eager. + +We decided not to provide any Tool parameter here and focus the profile only for ressource management: Maestro profiles runs with default nf-core/eager parameters, but with modifications concerning time (limit to 24h in normal qos so increasing the memnory and CPUs, specially for alignments). + + +## nuclear + +Increases the number of CPUs and the amount of memory for key processes + + +##mitochondrial + +more limited computational ressources + + From 035ab61f616a4aaf5a6472b4d9d35cbf92531e24 Mon Sep 17 00:00:00 2001 From: pierrespc Date: Fri, 8 Oct 2021 09:05:46 +0200 Subject: [PATCH 13/16] added unlimitedtime profile to maestro; changed cache for bwa process --- conf/pipeline/eager/maestro.config | 22 ++++++++++++++++------ docs/pipeline/eager/maestro.md | 9 ++++++--- 2 files changed, 22 insertions(+), 9 deletions(-) diff --git a/conf/pipeline/eager/maestro.config b/conf/pipeline/eager/maestro.config index 3705d8c..4a6a185 100644 --- a/conf/pipeline/eager/maestro.config +++ b/conf/pipeline/eager/maestro.config @@ -2,14 +2,14 @@ * ------------------------------------------------- * Nextflow config file for running nf-core eager on whole genome data or mitogenomes * ------------------------------------------------- - * nextflow run nf-core/eager -profile maestro,,maestro, (where is long or normal and is nuclear or mitocondrial) + * nextflow run nf-core/eager -profile maestro,,maestro, (where is long or normal and is nuclear, mitocondrial or unlimitedtime) */ params { config_profile_name = 'nf-core/eager nuclear/mitocondrial - human profiles' - config_profile_description = "Simple profiles for human nuclear or mito genomes" + config_profile_description = "Simple profiles for assessing computational ressources that fit human nuclear dna, human mitogenomes processing. unlimitedtime is also available " } @@ -32,15 +32,16 @@ profiles { time = { check_max( 12.h * task.attempt, 'time' ) } } withName:'bwa'{ - cpus = { check_max( 30 * task.attempt, 'cpus' ) } + cpus = { check_max( 40 * task.attempt, 'cpus' ) } memory = { check_max( 40.GB * task.attempt, 'memory' ) } time = 24.h + cache = 'deep' } withName:'markduplicates'{ errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } - cpus = { check_max( 8 * task.attempt, 'cpus' ) } - memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = { check_max( 6.h * task.attempt, 'time' ) } + cpus = { check_max( 16 * task.attempt, 'cpus' ) } + memory = { check_max( 16.GB * task.attempt, 'memory' ) } + time = { check_max( 12.h * task.attempt, 'time' ) } } withName:'damageprofiler'{ cpus = 1 @@ -103,4 +104,13 @@ profiles { } } } + unlimitedtime { + process { + errorStrategy = 'finish' + + cpus = 5 + memory = 200.GB + time = 8760.h + + } } diff --git a/docs/pipeline/eager/maestro.md b/docs/pipeline/eager/maestro.md index 45a151e..d272757 100644 --- a/docs/pipeline/eager/maestro.md +++ b/docs/pipeline/eager/maestro.md @@ -14,8 +14,7 @@ Example: `nextflow run nf-core/eager -profile maestro,normal,nuclear` Specific configurations for maestro has been made for eager. -We decided not to provide any Tool parameter here and focus the profile only for ressource management: Maestro profiles runs with default nf-core/eager parameters, but with modifications concerning time (limit to 24h in normal qos so increasing the memnory and CPUs, specially for alignments). - +We decided not to provide any tool parameters here, and focus the profile only for resource management: Maestro profiles runs with default nf-core/eager parameters, but with modifications concerning time (limit to 24h in normal qos, so increasing the memory and CPUs, specially for alignments). ## nuclear @@ -24,6 +23,10 @@ Increases the number of CPUs and the amount of memory for key processes ##mitochondrial -more limited computational ressources +More limited computational resources +##unlimitedtime + +Every process has one year time limit. To be used only when some processes can not be completed for time reasons when using mitochondrial or nuclear profiles. +Expect slow processes when using this profile because only 5 CPUs are available at a time. From 2d102eafbc8e5b7036f614f752e507437af52d6f Mon Sep 17 00:00:00 2001 From: pierrespc Date: Fri, 8 Oct 2021 13:46:47 +0200 Subject: [PATCH 14/16] format docs --- docs/maestro.md | 9 ++++----- docs/pipeline/eager/maestro.md | 9 ++++----- 2 files changed, 8 insertions(+), 10 deletions(-) diff --git a/docs/maestro.md b/docs/maestro.md index fe1b5f1..7a17064 100644 --- a/docs/maestro.md +++ b/docs/maestro.md @@ -1,10 +1,10 @@ -# nf-core/configs: Maestro (at Pateur Institute, Paris) Configuration. +# nf-core/configs Maestro (at Pateur Institute, Paris) Configuration -To use, run the pipeline with -profile maestro, (with qos being long or normal). This will download and launch the maestro.config which has been pre-configured with a setup suitable for the Maestro cluster on either the long or normal qos. +To use, run the pipeline with `-profile maestro,` (with qos being long or normal). This will download and launch the maestro.config which has been pre-configured with a setup suitable for the Maestro cluster on either the long or normal qos. Using one of these profiles, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline - ## needed Modules + Please first load java, nextflow and singularity modules `module load java` `module load nextflow` @@ -12,10 +12,9 @@ Please first load java, nextflow and singularity modules Also, do not forget to run nextflow using tmux or alike. +## Other profiles at Pasteur -## Other profiles at Pasteur: If you are using TARS cluster, please refer to pasteur profile. Please refer to docs/pasteur.md for installing and running nf-core instructions. - diff --git a/docs/pipeline/eager/maestro.md b/docs/pipeline/eager/maestro.md index d272757..59af8a3 100644 --- a/docs/pipeline/eager/maestro.md +++ b/docs/pipeline/eager/maestro.md @@ -1,10 +1,10 @@ -# nf-core/configs: maestro eager specific configuration +# nf-core/configs maestro eager specific configuration Extra specific configuration for eager pipeline for human DNA data processing ## Usage -To use, run the pipeline with `-profile maestro,,`, where can be normal or long and can be nuclear or mitochondrial +To use, run the pipeline with `-profile maestro,,`, where qos can be normal or long and type can be nuclear or mitochondrial This will download and launch the eager specific [`maestro.config`](../../../conf/pipeline/eager/maestro.config) which has been pre-configured with a setup suitable for the Maestro cluster. @@ -21,12 +21,11 @@ We decided not to provide any tool parameters here, and focus the profile only f Increases the number of CPUs and the amount of memory for key processes -##mitochondrial +## mitochondrial More limited computational resources -##unlimitedtime +## unlimitedtime Every process has one year time limit. To be used only when some processes can not be completed for time reasons when using mitochondrial or nuclear profiles. Expect slow processes when using this profile because only 5 CPUs are available at a time. - From b26e495e1983bb234a5d7c438928bb5535697a76 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 8 Oct 2021 14:08:51 +0200 Subject: [PATCH 15/16] Apply suggestions from code review --- docs/pipeline/eager/maestro.md | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/pipeline/eager/maestro.md b/docs/pipeline/eager/maestro.md index 59af8a3..8853eef 100644 --- a/docs/pipeline/eager/maestro.md +++ b/docs/pipeline/eager/maestro.md @@ -20,7 +20,6 @@ We decided not to provide any tool parameters here, and focus the profile only f Increases the number of CPUs and the amount of memory for key processes - ## mitochondrial More limited computational resources From 98bbc2b7448b903cfbf0816cc19fdc46d3941e8f Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 8 Oct 2021 14:11:39 +0200 Subject: [PATCH 16/16] Linting --- docs/maestro.md | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/maestro.md b/docs/maestro.md index 7a17064..718342b 100644 --- a/docs/maestro.md +++ b/docs/maestro.md @@ -17,4 +17,3 @@ Also, do not forget to run nextflow using tmux or alike. If you are using TARS cluster, please refer to pasteur profile. Please refer to docs/pasteur.md for installing and running nf-core instructions. -