From bb35d8e5d18f7d99b16f6f209b0e0ba589b6842a Mon Sep 17 00:00:00 2001 From: Gwenna Breton Date: Thu, 30 Jun 2022 11:42:36 +0200 Subject: [PATCH 01/21] Added conf file for medair --- conf/medair.config | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 conf/medair.config diff --git a/conf/medair.config b/conf/medair.config new file mode 100644 index 0000000..6cce6f9 --- /dev/null +++ b/conf/medair.config @@ -0,0 +1,39 @@ +//Profile config names for nf-core/configs +params { + config_profile_description = 'Cluster profile for medair (local cluster of Clinical Genomics Gothenburg)' + config_profile_contact = 'Clinical Genomics, Gothenburg' + config_profile_url = 'https://www.scilifelab.se/units/clinical-genomics-goteborg/' +} + +//Nextflow parameters +singularity { + enabled = true +} + +profiles { + + wgs { + process { + queue = 'wgs.q' + executor = 'sge' + penv = 'mpi' + process.clusterOptions = '-l excl=1' + params.max_cpus = 40 + params.max_time = 48.h + params.max_memory = 128.GB + } + } + + production { + process { + queue = 'production.q' + executor = 'sge' + penv = 'mpi' + process.clusterOptions = '-l excl=1' + params.max_cpus = 40 + params.max_time = 480.h + params.max_memory = 128.GB + } + } +} + From f718025e79a0e204c6339ce05a7c1915fcb2e66e Mon Sep 17 00:00:00 2001 From: Gwenna Breton Date: Thu, 30 Jun 2022 11:43:04 +0200 Subject: [PATCH 02/21] Added doc file for medair --- docs/medair.md | 43 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 docs/medair.md diff --git a/docs/medair.md b/docs/medair.md new file mode 100644 index 0000000..3edcfc4 --- /dev/null +++ b/docs/medair.md @@ -0,0 +1,43 @@ +# nf-core/configs: Medair Configuration + +All nf-core pipelines have been successfully configured for use on the medair cluster at Clinical Genomics Gothenburg. + +To use, run the pipeline with `-profile medair`. This will download and launch the [`medair.config`](../conf/medair.config) which has been pre-configured with a setup suitable for the medair cluster. +It will enable Nextflow to manage the pipeline jobs via the `SGE` job scheduler. +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. + +## Modules to load + +Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on medair. You can do this by issuing the commands below: + +```bash +## Load Nextflow and Singularity environment modules +module purge +module load nextflow/21.10.5.5658 +module load singularity/v3.4.0 +``` + +>Should we link to Confluence page about new modules? See something about updating modules? etc. +>Is this a good location to mention the nf-core conda environment? module load miniconda; source activate nf-core + +## Storage of Singularity images + +When downloading a new nf-core pipeline for the first time (or a specific version of a pipeline), you can choose to store the Singularity image for future use. A central location for these images is: `/apps/bio/dependencies/nf-core/singularities` + +Cached Singularity images can be accessed by running (or adding to your `.bashrc`) the following line: `export NXF_SINGULARITY_CACHEDIR="/apps/bio/dependencies/nf-core/singularities"` #is that correct?? + +## Different profiles depending on what you are running + +Depending on what you are running, you can choose between the `clinic`, `research`, `byss` and `qd_rnaseq` profiles. This specify for example which queue will be used. + +>NB: say more about the different queues? + +## iGenomes specific configuration + +>TODO modify this part. Do we want to have the iGenomes somewhere? + +A local copy of the iGenomes resource has been made available on PROFILE CLUSTER so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. +You can do this by simply using the `--genome ` parameter. + +>NB: You will need an account to use the HPC cluster on PROFILE CLUSTER in order to run the pipeline. If in doubt contact IT. +>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT. From 77017e877af4c1de90bb0d37ff52586dcb0f739b Mon Sep 17 00:00:00 2001 From: Gwenna Breton Date: Thu, 30 Jun 2022 11:48:34 +0200 Subject: [PATCH 03/21] Added medair configuration docs to the list --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index d86461c..94ce55c 100644 --- a/README.md +++ b/README.md @@ -120,6 +120,7 @@ Currently documentation is available for the following systems: - [LUGH](docs/lugh.md) - [MAESTRO](docs/maestro.md) - [MARVIN](docs/marvin.md) +- [MEDAIR](docs/medair.md) - [MJOLNIR_GLOBE](docs/mjolnir_globe.md) - [MPCDF](docs/mpcdf.md) - [MUNIN](docs/munin.md) From abccece8a38b8b18daebae8d6b8a82e21be5cc4d Mon Sep 17 00:00:00 2001 From: Gwenna Breton Date: Thu, 30 Jun 2022 11:49:47 +0200 Subject: [PATCH 04/21] Added medair config file to the list --- nfcore_custom.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nfcore_custom.config b/nfcore_custom.config index 4b44d8a..6f0ac6c 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -49,6 +49,7 @@ profiles { lugh { includeConfig "${params.custom_config_base}/conf/lugh.config" } maestro { includeConfig "${params.custom_config_base}/conf/maestro.config" } marvin { includeConfig "${params.custom_config_base}/conf/marvin.config" } + medair { includeConfig "${params.custom_config_base}/conf/medair.config" } mjolnir_globe { includeConfig "${params.custom_config_base}/conf/mjolnir_globe.config" } mpcdf { includeConfig "${params.custom_config_base}/conf/mpcdf.config" } munin { includeConfig "${params.custom_config_base}/conf/munin.config" } From 77dba3256aa4b948dad9bad16036f8a621eff98b Mon Sep 17 00:00:00 2001 From: Gwenna Breton Date: Thu, 30 Jun 2022 11:53:02 +0200 Subject: [PATCH 05/21] Add profile name to test scope --- .github/workflows/main.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index c142eb3..f5ba0d1 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -66,6 +66,7 @@ jobs: - "jax" - "lugh" - "marvin" + - "medair" - "mjolnir_globe" - "maestro" - "mpcdf" From 22f73b06f9da47ebc1c96bf14dabecc4918be938 Mon Sep 17 00:00:00 2001 From: Gwenna Breton Date: Thu, 30 Jun 2022 12:00:05 +0200 Subject: [PATCH 06/21] Updated info about the different profiles --- docs/medair.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/docs/medair.md b/docs/medair.md index 3edcfc4..834ac1d 100644 --- a/docs/medair.md +++ b/docs/medair.md @@ -28,9 +28,7 @@ Cached Singularity images can be accessed by running (or adding to your `.bashrc ## Different profiles depending on what you are running -Depending on what you are running, you can choose between the `clinic`, `research`, `byss` and `qd_rnaseq` profiles. This specify for example which queue will be used. - ->NB: say more about the different queues? +Depending on what you are running, you can choose between the `wgs` and `production` profiles. Jobs running with the `wgs` profile run on a queue with higher priority. Jobs running with the `production` profile can last longer (max time: 20 times, versus 2 days for the `wgs` profile). ## iGenomes specific configuration From 2398110ea54f5f07ddecf5c6b08c52a1f308d3c6 Mon Sep 17 00:00:00 2001 From: Gwenna Breton Date: Thu, 30 Jun 2022 14:24:17 +0200 Subject: [PATCH 07/21] Added info on dowloading pipelines --- docs/medair.md | 49 +++++++++++++++++++++++++++++++++++++++---------- 1 file changed, 39 insertions(+), 10 deletions(-) diff --git a/docs/medair.md b/docs/medair.md index 834ac1d..9f2b51f 100644 --- a/docs/medair.md +++ b/docs/medair.md @@ -6,9 +6,43 @@ To use, run the pipeline with `-profile medair`. This will download and launch t It will enable Nextflow to manage the pipeline jobs via the `SGE` job scheduler. 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. -## Modules to load +## Download nf-core pipelines -Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on medair. You can do this by issuing the commands below: +### Set-up + +First you need to load relevant softwares: Nextflow and nf-core tools. You can do it as follow: + +```bash +## Load Nextflow +module load nextflow/21.10.5.5658 +## Load nf-core tools +module load miniconda +source activate nf-core +``` + +### Download a pipeline + +We have started to download pipelines in the following location: `/apps/bio/repos/nf-core/` + +Use the `nf-core download --singularity-cache-only` command to start a downlonad. It will open an interactive menu. Choose `singularity` and `none` for the compression level. + +### Storage of Singularity images + +When downloading a new nf-core pipeline for the first time (or a specific version of a pipeline), you can choose to store the Singularity image for future use. A central location for these images is: `/apps/bio/dependencies/nf-core/singularities` + +Cached Singularity images can be accessed by running (or adding to your `.bashrc`) the following: + +``` +export NXF_SINGULARITY_CACHEDIR="/apps/bio/dependencies/nf-core/singularities" +``` + +This was also added to cronuser. + +## Run nf-core pipelines + +### Set-up + +Before running a pipeline you will need to load Nextflow and Singularity using the environment module system on medair. You can do this by issuing the commands below: ```bash ## Load Nextflow and Singularity environment modules @@ -18,18 +52,13 @@ module load singularity/v3.4.0 ``` >Should we link to Confluence page about new modules? See something about updating modules? etc. ->Is this a good location to mention the nf-core conda environment? module load miniconda; source activate nf-core -## Storage of Singularity images - -When downloading a new nf-core pipeline for the first time (or a specific version of a pipeline), you can choose to store the Singularity image for future use. A central location for these images is: `/apps/bio/dependencies/nf-core/singularities` - -Cached Singularity images can be accessed by running (or adding to your `.bashrc`) the following line: `export NXF_SINGULARITY_CACHEDIR="/apps/bio/dependencies/nf-core/singularities"` #is that correct?? - -## Different profiles depending on what you are running +### Choose a profile Depending on what you are running, you can choose between the `wgs` and `production` profiles. Jobs running with the `wgs` profile run on a queue with higher priority. Jobs running with the `production` profile can last longer (max time: 20 times, versus 2 days for the `wgs` profile). +>Usage: -profile medair,wgs ?? (Check) + ## iGenomes specific configuration >TODO modify this part. Do we want to have the iGenomes somewhere? From 84174043e4437338c1e11b218b71763de396bcd5 Mon Sep 17 00:00:00 2001 From: Gwenna Breton Date: Thu, 30 Jun 2022 16:41:50 +0200 Subject: [PATCH 08/21] Added details for nf-core pipelines download --- docs/medair.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/medair.md b/docs/medair.md index 9f2b51f..727becb 100644 --- a/docs/medair.md +++ b/docs/medair.md @@ -24,7 +24,7 @@ source activate nf-core We have started to download pipelines in the following location: `/apps/bio/repos/nf-core/` -Use the `nf-core download --singularity-cache-only` command to start a downlonad. It will open an interactive menu. Choose `singularity` and `none` for the compression level. +Use the `nf-core download --singularity-cache-only` command to start a download. It will open an interactive menu. Choose `singularity` for the software container image, and `none` for the compression type. ### Storage of Singularity images From b202ad70ac95bfecd72256e809ac8e734df4debd Mon Sep 17 00:00:00 2001 From: Gwenna Breton Date: Wed, 6 Jul 2022 11:16:38 +0200 Subject: [PATCH 09/21] Removed mention of specific module versions --- docs/medair.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/medair.md b/docs/medair.md index 727becb..7be38e6 100644 --- a/docs/medair.md +++ b/docs/medair.md @@ -14,7 +14,7 @@ First you need to load relevant softwares: Nextflow and nf-core tools. You can d ```bash ## Load Nextflow -module load nextflow/21.10.5.5658 +module load nextflow ## Load nf-core tools module load miniconda source activate nf-core @@ -47,8 +47,8 @@ Before running a pipeline you will need to load Nextflow and Singularity using t ```bash ## Load Nextflow and Singularity environment modules module purge -module load nextflow/21.10.5.5658 -module load singularity/v3.4.0 +module load nextflow +module load singularity ``` >Should we link to Confluence page about new modules? See something about updating modules? etc. From 1d7a34b11f3a657e3db0bc1f2f95a330ee7165a3 Mon Sep 17 00:00:00 2001 From: Gwenna Breton Date: Wed, 6 Jul 2022 11:17:58 +0200 Subject: [PATCH 10/21] Removed comment about internal doc --- docs/medair.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/medair.md b/docs/medair.md index 7be38e6..dd2b9aa 100644 --- a/docs/medair.md +++ b/docs/medair.md @@ -51,8 +51,6 @@ module load nextflow module load singularity ``` ->Should we link to Confluence page about new modules? See something about updating modules? etc. - ### Choose a profile Depending on what you are running, you can choose between the `wgs` and `production` profiles. Jobs running with the `wgs` profile run on a queue with higher priority. Jobs running with the `production` profile can last longer (max time: 20 times, versus 2 days for the `wgs` profile). From 235097e58e545c182bd9d02b00a5e424f150b7bf Mon Sep 17 00:00:00 2001 From: Gwenna Breton Date: Wed, 6 Jul 2022 11:20:59 +0200 Subject: [PATCH 11/21] Addressed review comments - removed mention of iGenomes - clarified whom to contact for support --- docs/medair.md | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/docs/medair.md b/docs/medair.md index dd2b9aa..0c54c81 100644 --- a/docs/medair.md +++ b/docs/medair.md @@ -57,12 +57,5 @@ Depending on what you are running, you can choose between the `wgs` and `product >Usage: -profile medair,wgs ?? (Check) -## iGenomes specific configuration - ->TODO modify this part. Do we want to have the iGenomes somewhere? - -A local copy of the iGenomes resource has been made available on PROFILE CLUSTER so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. -You can do this by simply using the `--genome ` parameter. - ->NB: You will need an account to use the HPC cluster on PROFILE CLUSTER in order to run the pipeline. If in doubt contact IT. ->NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT. +>NB: You will need an account to use the HPC cluster on PROFILE CLUSTER in order to run the pipeline. If in doubt contact cgg-it. +>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact cgg-it. From 1d13dd9fbce6b3c8a7169e9d4f7be51ac717e49a Mon Sep 17 00:00:00 2001 From: Gwenna Breton Date: Wed, 6 Jul 2022 11:24:03 +0200 Subject: [PATCH 12/21] Changed where cgg-it is mentioned --- docs/medair.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/docs/medair.md b/docs/medair.md index 0c54c81..96c44e3 100644 --- a/docs/medair.md +++ b/docs/medair.md @@ -6,6 +6,8 @@ To use, run the pipeline with `-profile medair`. This will download and launch t It will enable Nextflow to manage the pipeline jobs via the `SGE` job scheduler. 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. +You will need an account to use the Medair cluster in order to download or run pipelines. If in doubt, contact cgg-it. + ## Download nf-core pipelines ### Set-up @@ -40,6 +42,8 @@ This was also added to cronuser. ## Run nf-core pipelines +Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands below will have to be executed on one of the login nodes. If in doubt contact cgg-it. + ### Set-up Before running a pipeline you will need to load Nextflow and Singularity using the environment module system on medair. You can do this by issuing the commands below: @@ -56,6 +60,3 @@ module load singularity Depending on what you are running, you can choose between the `wgs` and `production` profiles. Jobs running with the `wgs` profile run on a queue with higher priority. Jobs running with the `production` profile can last longer (max time: 20 times, versus 2 days for the `wgs` profile). >Usage: -profile medair,wgs ?? (Check) - ->NB: You will need an account to use the HPC cluster on PROFILE CLUSTER in order to run the pipeline. If in doubt contact cgg-it. ->NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact cgg-it. From 96fd2bf217b71c73f07552857c70569dbbcb4c55 Mon Sep 17 00:00:00 2001 From: Gwennid Date: Wed, 6 Jul 2022 11:42:05 +0200 Subject: [PATCH 13/21] Fixed formatting --- docs/medair.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/medair.md b/docs/medair.md index 96c44e3..6185f64 100644 --- a/docs/medair.md +++ b/docs/medair.md @@ -1,8 +1,8 @@ # nf-core/configs: Medair Configuration -All nf-core pipelines have been successfully configured for use on the medair cluster at Clinical Genomics Gothenburg. +All nf-core pipelines have been successfully configured for use on the Medair cluster at Clinical Genomics Gothenburg. -To use, run the pipeline with `-profile medair`. This will download and launch the [`medair.config`](../conf/medair.config) which has been pre-configured with a setup suitable for the medair cluster. +To use, run the pipeline with `-profile medair`. This will download and launch the [`medair.config`](../conf/medair.config) which has been pre-configured with a setup suitable for the Medair cluster. It will enable Nextflow to manage the pipeline jobs via the `SGE` job scheduler. 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. @@ -10,7 +10,7 @@ You will need an account to use the Medair cluster in order to download or run p ## Download nf-core pipelines -### Set-up +### Set-up: load Nextflow and nf-core tools First you need to load relevant softwares: Nextflow and nf-core tools. You can do it as follow: @@ -32,9 +32,9 @@ Use the `nf-core download --singularity-cache-only` command to start a download. When downloading a new nf-core pipeline for the first time (or a specific version of a pipeline), you can choose to store the Singularity image for future use. A central location for these images is: `/apps/bio/dependencies/nf-core/singularities` -Cached Singularity images can be accessed by running (or adding to your `.bashrc`) the following: +Cached Singularity images can be accessed by running (or adding to your `.bashrc`) the following: -``` +```bash export NXF_SINGULARITY_CACHEDIR="/apps/bio/dependencies/nf-core/singularities" ``` @@ -44,9 +44,9 @@ This was also added to cronuser. Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands below will have to be executed on one of the login nodes. If in doubt contact cgg-it. -### Set-up +### Set-up: load Nextflow and Singularity -Before running a pipeline you will need to load Nextflow and Singularity using the environment module system on medair. You can do this by issuing the commands below: +Before running a pipeline you will need to load Nextflow and Singularity using the environment module system on Medair. You can do this by issuing the commands below: ```bash ## Load Nextflow and Singularity environment modules @@ -59,4 +59,4 @@ module load singularity Depending on what you are running, you can choose between the `wgs` and `production` profiles. Jobs running with the `wgs` profile run on a queue with higher priority. Jobs running with the `production` profile can last longer (max time: 20 times, versus 2 days for the `wgs` profile). ->Usage: -profile medair,wgs ?? (Check) +> Usage: -profile medair,wgs ?? (Check) From b6e2d03a02938b2eb6a1aff451140b43bf1835fa Mon Sep 17 00:00:00 2001 From: Gwennid Date: Wed, 6 Jul 2022 13:59:35 +0200 Subject: [PATCH 14/21] Added Singularity cache dir --- conf/medair.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/medair.config b/conf/medair.config index 6cce6f9..183d4f6 100644 --- a/conf/medair.config +++ b/conf/medair.config @@ -8,6 +8,7 @@ params { //Nextflow parameters singularity { enabled = true + cacheDir = "/apps/bio/dependencies/nf-core/singularities" } profiles { From 746db14d4745ad3369d12d09b3b056db55c787f9 Mon Sep 17 00:00:00 2001 From: Gwenna Breton Date: Thu, 7 Jul 2022 11:42:46 +0200 Subject: [PATCH 15/21] Update medair.md - updated text about storing singularity images - updated text about using profiles --- docs/medair.md | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/docs/medair.md b/docs/medair.md index 6185f64..5eb1c46 100644 --- a/docs/medair.md +++ b/docs/medair.md @@ -22,23 +22,23 @@ module load miniconda source activate nf-core ``` -### Download a pipeline - -We have started to download pipelines in the following location: `/apps/bio/repos/nf-core/` - -Use the `nf-core download --singularity-cache-only` command to start a download. It will open an interactive menu. Choose `singularity` for the software container image, and `none` for the compression type. - ### Storage of Singularity images -When downloading a new nf-core pipeline for the first time (or a specific version of a pipeline), you can choose to store the Singularity image for future use. A central location for these images is: `/apps/bio/dependencies/nf-core/singularities` +When downloading a nf-core pipeline for the first time (or a specific version of a pipeline), you can choose to store the Singularity image for future use. A central location for these images is: `/apps/bio/dependencies/nf-core/singularities`. -Cached Singularity images can be accessed by running (or adding to your `.bashrc`) the following: +If you run or add the following to your `.bashrc`, Nexflow will know where to store the images: ```bash export NXF_SINGULARITY_CACHEDIR="/apps/bio/dependencies/nf-core/singularities" ``` -This was also added to cronuser. +> Comment: This was also added to cronuser. + +### Download a pipeline + +We have started to download pipelines in the following location: `/apps/bio/repos/nf-core/` + +Use the `nf-core download --singularity-cache-only` command to start a download. It will open an interactive menu. Choose `singularity` for the software container image, and `none` for the compression type. ## Run nf-core pipelines @@ -59,4 +59,8 @@ module load singularity Depending on what you are running, you can choose between the `wgs` and `production` profiles. Jobs running with the `wgs` profile run on a queue with higher priority. Jobs running with the `production` profile can last longer (max time: 20 times, versus 2 days for the `wgs` profile). -> Usage: -profile medair,wgs ?? (Check) +For example, the following job would run with the `wgs` profile: + +```bash +run nextflow nf-core/raredisease -profile medair,wgs +``` From 4538e8aa36d71b06cbf46a68f82596f513b1c506 Mon Sep 17 00:00:00 2001 From: Gwenna Breton Date: Thu, 7 Jul 2022 13:41:42 +0200 Subject: [PATCH 16/21] Update medair.config - added path to singularity image for Sentieon - harmonized alignment --- conf/medair.config | 36 +++++++++++++++++++++--------------- 1 file changed, 21 insertions(+), 15 deletions(-) diff --git a/conf/medair.config b/conf/medair.config index 183d4f6..eeda705 100644 --- a/conf/medair.config +++ b/conf/medair.config @@ -1,13 +1,13 @@ //Profile config names for nf-core/configs params { config_profile_description = 'Cluster profile for medair (local cluster of Clinical Genomics Gothenburg)' - config_profile_contact = 'Clinical Genomics, Gothenburg' - config_profile_url = 'https://www.scilifelab.se/units/clinical-genomics-goteborg/' + config_profile_contact = 'Clinical Genomics, Gothenburg' + config_profile_url = 'https://www.scilifelab.se/units/clinical-genomics-goteborg/' } //Nextflow parameters singularity { - enabled = true + enabled = true cacheDir = "/apps/bio/dependencies/nf-core/singularities" } @@ -15,26 +15,32 @@ profiles { wgs { process { - queue = 'wgs.q' - executor = 'sge' - penv = 'mpi' + queue = 'wgs.q' + executor = 'sge' + penv = 'mpi' process.clusterOptions = '-l excl=1' - params.max_cpus = 40 - params.max_time = 48.h - params.max_memory = 128.GB + params.max_cpus = 40 + params.max_time = 48.h + params.max_memory = 128.GB } } production { process { - queue = 'production.q' - executor = 'sge' - penv = 'mpi' + queue = 'production.q' + executor = 'sge' + penv = 'mpi' process.clusterOptions = '-l excl=1' - params.max_cpus = 40 - params.max_time = 480.h - params.max_memory = 128.GB + params.max_cpus = 40 + params.max_time = 480.h + params.max_memory = 128.GB } } } +//Specific parameter for pipelines that can use Sentieon (e.g. nf-core/sarek, nf-core/raredisease) +process { + withLabel:'sentieon' { + container = "/apps/bio/singularities/sentieon-211204-peta.simg" + } +} From 6b9cdc8ef3c959cf7a4c2137a1b6bf80ee970a07 Mon Sep 17 00:00:00 2001 From: Gwenna Breton Date: Thu, 7 Jul 2022 14:24:15 +0200 Subject: [PATCH 17/21] Added info about Sentieon singularities --- docs/medair.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/medair.md b/docs/medair.md index 5eb1c46..7b0c7d7 100644 --- a/docs/medair.md +++ b/docs/medair.md @@ -64,3 +64,7 @@ For example, the following job would run with the `wgs` profile: ```bash run nextflow nf-core/raredisease -profile medair,wgs ``` + +### Sentieon + +In some pipelines (sarek, raredisease) it is possible to use Sentieon for alignment and variant calling. If ones uses the label `sentieon` for running a process, the config file contains the path to the Sentieon singularity image on Medair. From 648025c1ceea79460eb1f064d72d49d25f3ee942 Mon Sep 17 00:00:00 2001 From: Gwenna Breton Date: Mon, 8 Aug 2022 16:04:21 +0200 Subject: [PATCH 18/21] Clarified where to store singularity images --- docs/medair.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/medair.md b/docs/medair.md index 7b0c7d7..48ad557 100644 --- a/docs/medair.md +++ b/docs/medair.md @@ -24,9 +24,9 @@ source activate nf-core ### Storage of Singularity images -When downloading a nf-core pipeline for the first time (or a specific version of a pipeline), you can choose to store the Singularity image for future use. A central location for these images is: `/apps/bio/dependencies/nf-core/singularities`. +When downloading a nf-core pipeline for the first time (or a specific version of a pipeline), you can choose to store the Singularity image for future use. We chose to have a central location for these images on medair: `/apps/bio/dependencies/nf-core/singularities`. -If you run or add the following to your `.bashrc`, Nexflow will know where to store the images: +For Nexflow to know where to store new images, run or add the following to your `.bashrc`: ```bash export NXF_SINGULARITY_CACHEDIR="/apps/bio/dependencies/nf-core/singularities" From 2740b5efbfc62aed864c027396fd33cbc075d07a Mon Sep 17 00:00:00 2001 From: Gwenna Breton Date: Mon, 8 Aug 2022 16:08:05 +0200 Subject: [PATCH 19/21] Update docs/medair.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fixed typo Co-authored-by: Matthias Hörtenhuber --- docs/medair.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/medair.md b/docs/medair.md index 48ad557..bd13e84 100644 --- a/docs/medair.md +++ b/docs/medair.md @@ -57,7 +57,7 @@ module load singularity ### Choose a profile -Depending on what you are running, you can choose between the `wgs` and `production` profiles. Jobs running with the `wgs` profile run on a queue with higher priority. Jobs running with the `production` profile can last longer (max time: 20 times, versus 2 days for the `wgs` profile). +Depending on what you are running, you can choose between the `wgs` and `production` profiles. Jobs running with the `wgs` profile run on a queue with higher priority. Jobs running with the `production` profile can last longer (max time: 20 days, versus 2 days for the `wgs` profile). For example, the following job would run with the `wgs` profile: From ffefefe0ab95dec7e7ba45fbe7fb777972b276f6 Mon Sep 17 00:00:00 2001 From: Gwenna Breton Date: Mon, 8 Aug 2022 16:11:55 +0200 Subject: [PATCH 20/21] Added contact emails --- conf/medair.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/medair.config b/conf/medair.config index eeda705..d147643 100644 --- a/conf/medair.config +++ b/conf/medair.config @@ -1,7 +1,7 @@ //Profile config names for nf-core/configs params { config_profile_description = 'Cluster profile for medair (local cluster of Clinical Genomics Gothenburg)' - config_profile_contact = 'Clinical Genomics, Gothenburg' + config_profile_contact = 'Clinical Genomics, Gothenburg (cgg-rd@gu.se, cgg-it@gu.se)' config_profile_url = 'https://www.scilifelab.se/units/clinical-genomics-goteborg/' } From 0e4f2b40d3f0e2873a34569dc440858f871241e1 Mon Sep 17 00:00:00 2001 From: Gwenna Breton Date: Mon, 8 Aug 2022 16:14:17 +0200 Subject: [PATCH 21/21] Added email of IT group --- docs/medair.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/medair.md b/docs/medair.md index bd13e84..706332f 100644 --- a/docs/medair.md +++ b/docs/medair.md @@ -42,7 +42,7 @@ Use the `nf-core download --singularity-cache-only` command to start a download. ## Run nf-core pipelines -Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands below will have to be executed on one of the login nodes. If in doubt contact cgg-it. +Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands below will have to be executed on one of the login nodes. If in doubt contact cgg-it (cgg-it[at]gu.se). ### Set-up: load Nextflow and Singularity