From 332ba0dadb93b0813ac36c9b937c4d8b24fc0b48 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Wed, 7 Aug 2019 11:10:48 +0200 Subject: [PATCH 1/6] fix: update and rearrange munin configuration file and docs --- conf/munin.config | 20 +++++++++++--------- docs/munin.md | 6 ++++-- 2 files changed, 15 insertions(+), 11 deletions(-) diff --git a/conf/munin.config b/conf/munin.config index bca56f7..58e10f7 100644 --- a/conf/munin.config +++ b/conf/munin.config @@ -1,20 +1,22 @@ //Profile config names for nf-core/configs params { - config_profile_description = 'Big iron cluster profile provided by nf-core/configs.' + config_profile_description = 'Munin profile provided by nf-core/configs.' config_profile_contact = 'Szilveszter Juhos (@szilva)' config_profile_url = '' } process { executor = 'local' + maxForks = 48 } +// To use docker, use nextflow run -profile munin,singularity singularity { enabled = true autoMounts = true } -// To use docker instead of singularity, use nextflow run -profile munin,docker +// To use docker, use nextflow run -profile munin,docker docker { enabled = false mountFlags = 'z' @@ -22,11 +24,11 @@ docker { } params { - saveReference = true - - max_memory = 128.GB - max_cpus = 16 + // general params + max_memory = 754.GB + max_cpus = 48 max_time = 72.h - // illumina iGenomes reference file paths on UPPMAX - igenomes_base = '/data1/references/igenomes/' -} + + // AWS iGenomes reference file paths on munin + igenome_base = '/data1/references/igenomes/' +} \ No newline at end of file diff --git a/docs/munin.md b/docs/munin.md index 17233bb..7f164ce 100644 --- a/docs/munin.md +++ b/docs/munin.md @@ -1,8 +1,10 @@ # nf-core/configs: MUNIN Configuration -All nf-core pipelines have been successfully configured for use on the MUNIN cluster aka big iron. +All nf-core pipelines have been successfully configured for use on the MUNIN cluster. -To use, run the pipeline with `-profile munin`. This will download and launch the [`munin.config`](../conf/munin.config) which has been pre-configured with a setup suitable for the MUNIN cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. +To use, run the pipeline with `-profile munin`. +This will download and launch the [`munin.config`](../conf/munin.config) which has been pre-configured with a setup suitable for the MUNIN cluster. +Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. Example: `nextflow run -profile munin` From 12fb2a60c57e85b066d10c18e006759773fe773d Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Wed, 7 Aug 2019 11:47:41 +0200 Subject: [PATCH 2/6] Update conf/munin.config Co-Authored-By: Harshil Patel --- conf/munin.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/munin.config b/conf/munin.config index 58e10f7..d837b08 100644 --- a/conf/munin.config +++ b/conf/munin.config @@ -10,7 +10,7 @@ process { maxForks = 48 } -// To use docker, use nextflow run -profile munin,singularity +// To use singularity, use nextflow run -profile munin,singularity singularity { enabled = true autoMounts = true @@ -31,4 +31,4 @@ params { // AWS iGenomes reference file paths on munin igenome_base = '/data1/references/igenomes/' -} \ No newline at end of file +} From d6a763214cc8dfa09893a1ea1079b6bad8216f9b Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Wed, 7 Aug 2019 11:47:47 +0200 Subject: [PATCH 3/6] Update conf/munin.config Co-Authored-By: Harshil Patel --- conf/munin.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/munin.config b/conf/munin.config index d837b08..24b5dac 100644 --- a/conf/munin.config +++ b/conf/munin.config @@ -29,6 +29,6 @@ params { max_cpus = 48 max_time = 72.h - // AWS iGenomes reference file paths on munin + // Local AWS iGenomes reference file paths on munin igenome_base = '/data1/references/igenomes/' } From 0bd19517b30a1a79b27db1d1163293d38f04ef41 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Wed, 7 Aug 2019 11:55:56 +0200 Subject: [PATCH 4/6] fix: typos --- conf/munin.config | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/conf/munin.config b/conf/munin.config index 58e10f7..b1e4628 100644 --- a/conf/munin.config +++ b/conf/munin.config @@ -1,6 +1,6 @@ //Profile config names for nf-core/configs params { - config_profile_description = 'Munin profile provided by nf-core/configs.' + config_profile_description = 'MUNIN profile provided by nf-core/configs.' config_profile_contact = 'Szilveszter Juhos (@szilva)' config_profile_url = '' } @@ -10,10 +10,9 @@ process { maxForks = 48 } -// To use docker, use nextflow run -profile munin,singularity +// To use singularity, use nextflow run -profile munin,singularity singularity { enabled = true - autoMounts = true } // To use docker, use nextflow run -profile munin,docker @@ -29,6 +28,6 @@ params { max_cpus = 48 max_time = 72.h - // AWS iGenomes reference file paths on munin + // Local AWS iGenomes reference file paths igenome_base = '/data1/references/igenomes/' } \ No newline at end of file From f69524d59a3afdfcb86ddb405f954f27833f3608 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Wed, 7 Aug 2019 11:56:10 +0200 Subject: [PATCH 5/6] feat: update docs --- docs/munin.md | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/docs/munin.md b/docs/munin.md index 7f164ce..167ff9b 100644 --- a/docs/munin.md +++ b/docs/munin.md @@ -2,16 +2,30 @@ All nf-core pipelines have been successfully configured for use on the MUNIN cluster. +## Usage + To use, run the pipeline with `-profile munin`. + This will download and launch the [`munin.config`](../conf/munin.config) which has been pre-configured with a setup suitable for the MUNIN cluster. -Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. Example: `nextflow run -profile munin` -## Docker +### Singularity + +This is the default behavior of this configuration profile. + +Using this profile, if no singularity image are available, one will be downloaded from dockerhub, and converted to a Singularity image before execution of the pipeline. + +It is also possible to specify the singularity profile: + +Example: `nextflow run -profile munin,singularity` + +### Docker It is also possible to execute the pipeline using Docker. +Using this profile, if no docker image are available, one will be downloaded from dockerhub before execution of the pipeline. + Example: `nextflow run -profile munin,docker` ## Below are non-mandatory information on iGenomes specific configuration From 4183090379a031e2c5031ab45aa62f1035f88691 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Wed, 7 Aug 2019 12:26:51 +0200 Subject: [PATCH 6/6] fix: reduce cpu and mem usage --- conf/munin.config | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/munin.config b/conf/munin.config index 9076e38..52062e5 100644 --- a/conf/munin.config +++ b/conf/munin.config @@ -7,7 +7,7 @@ params { process { executor = 'local' - maxForks = 48 + maxForks = 46 } // To use singularity, use nextflow run -profile munin,singularity @@ -24,8 +24,8 @@ docker { params { // general params - max_memory = 754.GB - max_cpus = 48 + max_memory = 752.GB + max_cpus = 46 max_time = 72.h // Local AWS iGenomes reference file paths on munin