From e609a13a0147706edf4720763d857500bacedbff Mon Sep 17 00:00:00 2001 From: Falko Date: Tue, 14 Jan 2025 13:53:11 +0100 Subject: [PATCH 1/7] Changed to apptainer --- conf/fgcz.config | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/conf/fgcz.config b/conf/fgcz.config index dbbf729f7..d48125566 100644 --- a/conf/fgcz.config +++ b/conf/fgcz.config @@ -1,9 +1,6 @@ params { config_profile_description = "FGCZ ETH/UZH" - config_profile_contact = "natalia.zajac@fgcz.ethz.ch" - max_memory = 500.GB - max_cpus = 64 - max_time = 240.h + config_profile_contact = "falnoe@ethz.ch" } process { @@ -20,10 +17,8 @@ executor { queueSize = 30 } - - -singularity { +apptainer { enabled = true autoMounts = true - cacheDir = "/srv/GT/nextflow/singularity/" + cacheDir = "/srv/GT/software/apptainer/cache" } From ee61ba68eb90f97dbba65354eb7dd84750247377 Mon Sep 17 00:00:00 2001 From: Falko Date: Tue, 14 Jan 2025 13:57:03 +0100 Subject: [PATCH 2/7] update with new info --- docs/fgcz.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/fgcz.md b/docs/fgcz.md index 0fe0c689f..3016ac7da 100644 --- a/docs/fgcz.md +++ b/docs/fgcz.md @@ -2,17 +2,17 @@ Configuration file to run nf-core pipelines on the cluster of the [Functional Genomics Center Zurich](https://fgcz.ch/), a research and training facility of the ETH Zürich and the University of Zurich. -Note that, at present, this config has only been tested with nf-core/viralrecon, but should function similarly for other nf-core pipelines. +Note that, at present, this config has only been tested with `nf-core/viralrecon` and `nf-core/atacseq`, but should function similarly for other nf-core pipelines. -To use, run the pipeline with `-profile fgcz`. This will download and launch the profile.config which has been pre-configured with a setup suitable for the FGCZ 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. **This requires a local installation of singularity**. It is easiest to submit the pipeline from a compute node. Once the image is cached, you can also submit from the login node. -The config places the singularity cache in your /srv/GT/ directory for access by all projects. +To use, run the pipeline with `-profile fgcz`. This will download and launch the profile.config which has been pre-configured with a setup suitable for the FGCZ cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to an apptainer image before execution of the pipeline. **This requires a local installation of apptainer**. It is easiest to submit the pipeline from a compute node. Once the image is cached, you can also submit from the login node. +The config places the apptainer cache in your /srv/GT/software/apptainer/cache directory for access by all projects. -Example: /usr/local/ngseq/src/nextflow/nextflow run -profile fgcz +Example: nextflow run -profile fgcz ## Before running the pipeline -Load the following modules before running any nf-core pipelines. +You may need to load the jdk module before running any nextflow pipelines. ```bash -module load Dev/Python/3.8.3 +module load Dev/jdk/21 ``` From b987d53fb7565bf95f0ab55a202c7af55a1b08e8 Mon Sep 17 00:00:00 2001 From: Falko Date: Tue, 14 Jan 2025 13:57:47 +0100 Subject: [PATCH 3/7] code block formatting --- docs/fgcz.md | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/docs/fgcz.md b/docs/fgcz.md index 3016ac7da..fe9d11c84 100644 --- a/docs/fgcz.md +++ b/docs/fgcz.md @@ -7,12 +7,16 @@ Note that, at present, this config has only been tested with `nf-core/viralrecon To use, run the pipeline with `-profile fgcz`. This will download and launch the profile.config which has been pre-configured with a setup suitable for the FGCZ cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to an apptainer image before execution of the pipeline. **This requires a local installation of apptainer**. It is easiest to submit the pipeline from a compute node. Once the image is cached, you can also submit from the login node. The config places the apptainer cache in your /srv/GT/software/apptainer/cache directory for access by all projects. -Example: nextflow run -profile fgcz +Example: + +```shell +nextflow run -profile fgcz ... +``` ## Before running the pipeline You may need to load the jdk module before running any nextflow pipelines. -```bash +```shell module load Dev/jdk/21 ``` From 1029bb8f1b6e6f3b18cf6f88f6962dd36680f87f Mon Sep 17 00:00:00 2001 From: Falko Date: Tue, 14 Jan 2025 14:01:33 +0100 Subject: [PATCH 4/7] Added max settings back into params --- conf/fgcz.config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/conf/fgcz.config b/conf/fgcz.config index d48125566..41d38cbdb 100644 --- a/conf/fgcz.config +++ b/conf/fgcz.config @@ -1,6 +1,9 @@ params { config_profile_description = "FGCZ ETH/UZH" config_profile_contact = "falnoe@ethz.ch" + max_memory = 500.GB + max_cpus = 64 + max_time = 240.h } process { From dfb35b27e52649b8b2afc4f78fae539012d8f20d Mon Sep 17 00:00:00 2001 From: Falko Date: Tue, 14 Jan 2025 14:19:07 +0100 Subject: [PATCH 5/7] Change queueSize to 10 --- conf/fgcz.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/fgcz.config b/conf/fgcz.config index 41d38cbdb..8257511a8 100644 --- a/conf/fgcz.config +++ b/conf/fgcz.config @@ -17,7 +17,7 @@ process { } executor { - queueSize = 30 + queueSize = 10 } apptainer { From ab89c2683672405aae5f4b67ab125167b7185f40 Mon Sep 17 00:00:00 2001 From: Falko Date: Tue, 14 Jan 2025 14:26:41 +0100 Subject: [PATCH 6/7] Formatting --- docs/fgcz.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/fgcz.md b/docs/fgcz.md index fe9d11c84..eba187ec1 100644 --- a/docs/fgcz.md +++ b/docs/fgcz.md @@ -5,7 +5,7 @@ Configuration file to run nf-core pipelines on the cluster of the [Functional Ge Note that, at present, this config has only been tested with `nf-core/viralrecon` and `nf-core/atacseq`, but should function similarly for other nf-core pipelines. To use, run the pipeline with `-profile fgcz`. This will download and launch the profile.config which has been pre-configured with a setup suitable for the FGCZ cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to an apptainer image before execution of the pipeline. **This requires a local installation of apptainer**. It is easiest to submit the pipeline from a compute node. Once the image is cached, you can also submit from the login node. -The config places the apptainer cache in your /srv/GT/software/apptainer/cache directory for access by all projects. +The config places the apptainer cache in your `/srv/GT/software/apptainer/cache` directory for access by all projects. Example: From 580b17ab9ef563e9df9eb10d7ba07c091c990a36 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 15 Jan 2025 14:08:06 +0100 Subject: [PATCH 7/7] Update docs/fgcz.md --- docs/fgcz.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/fgcz.md b/docs/fgcz.md index eba187ec1..f6b1072b2 100644 --- a/docs/fgcz.md +++ b/docs/fgcz.md @@ -7,7 +7,7 @@ Note that, at present, this config has only been tested with `nf-core/viralrecon To use, run the pipeline with `-profile fgcz`. This will download and launch the profile.config which has been pre-configured with a setup suitable for the FGCZ cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to an apptainer image before execution of the pipeline. **This requires a local installation of apptainer**. It is easiest to submit the pipeline from a compute node. Once the image is cached, you can also submit from the login node. The config places the apptainer cache in your `/srv/GT/software/apptainer/cache` directory for access by all projects. -Example: +For example: ```shell nextflow run -profile fgcz ...