From 122370b04dc6e4ef4acffce41bff6737f53565b6 Mon Sep 17 00:00:00 2001 From: ShahNiraj Date: Fri, 5 Jul 2024 11:03:56 +0100 Subject: [PATCH 1/6] Add files via upload First config --- conf/uondrs_ada.config | 45 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 conf/uondrs_ada.config diff --git a/conf/uondrs_ada.config b/conf/uondrs_ada.config new file mode 100644 index 000000000..bd5310528 --- /dev/null +++ b/conf/uondrs_ada.config @@ -0,0 +1,45 @@ +// definition of the slurm executor. Run the pipeline in a node able to submit jobs to a HPC via sbatch +singularity { + enabled = true + autoMounts = true + // Some processes don't respect the TMP environment variables: https://github.com/nf-core/rnaseq/issues/115 +} + +process { + // Global process config + executor = 'slurm' + queueSize = 10 + queue = 'defq' + submitRateLimit = '10/2min' +} + +process { + + // resources for default process execution +withLabel:process_low { + cpus = 2 + memory = 12.GB + time = 6.h + } + withLabel:process_medium { + cpus = 6 + memory = 36.GB + time = 6.h + } + withLabel:process_high { + cpus = 12 + memory = 240.GB + time = 6.h + } + withLabel:process_long { + time = 20.h + } + withLabel:error_ignore { + errorStrategy = 'ignore' + } + withLabel:error_retry { + errorStrategy = 'retry' + maxRetries = 2 + } + // resources for execution of processes / modules with the label "two cpus". This override the default ones. +} From cbe552388e0ac936f1de2d9aa85955675a7e52c5 Mon Sep 17 00:00:00 2001 From: ShahNiraj Date: Wed, 10 Jul 2024 11:35:35 +0100 Subject: [PATCH 2/6] Update uondrs_ada.config Added Profile config names for nf-core/configs --- conf/uondrs_ada.config | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/conf/uondrs_ada.config b/conf/uondrs_ada.config index bd5310528..a8af4a3f6 100644 --- a/conf/uondrs_ada.config +++ b/conf/uondrs_ada.config @@ -1,3 +1,13 @@ +//Profile config names for nf-core/configs + +params { + // Config Params + config_profile_description = 'University of Nottingham DRS - HPC Profile -- provided by nf-core/configs.' + config_profile_contact = 'Niraj Shah (@ShahNiraj)' + config_profile_url = 'https://forms.office.com/Pages/ResponsePage.aspx?id=7qe9Z4D970GskTWEGCkKHpYhN2mnMuNPm5Y3GQx5rlxUMzJQTDE0OUVSNUtHT0UyU0o2UTRCQzNaQSQlQCN0PWcu' + +} + // definition of the slurm executor. Run the pipeline in a node able to submit jobs to a HPC via sbatch singularity { enabled = true From 9a337abf8b65b94e9fcfa583f1b3b35fc190dbca Mon Sep 17 00:00:00 2001 From: ShahNiraj Date: Wed, 10 Jul 2024 11:36:19 +0100 Subject: [PATCH 3/6] Add files via upload --- docs/uondrs_ada.md | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 docs/uondrs_ada.md diff --git a/docs/uondrs_ada.md b/docs/uondrs_ada.md new file mode 100644 index 000000000..4a052da8f --- /dev/null +++ b/docs/uondrs_ada.md @@ -0,0 +1,29 @@ +# nf-core/configs: Ada HPC Configuration + +nfcore pipeline rnaseq have been tested on the Ada HPC. + +## Before running the pipeline + +- You will need an account to use the Ada HPC cluster in order to run the pipeline. +- Make sure that Singularity and Nextflow are installed. +- Downlode pipeline singularity images to a HPC system using [nf-core tools](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) + +``` +$ conda install nf-core +$ nf-core download +``` + + + + +## Running the pipeline using the adcra config profile + +- Run the pipeline within a [screen](https://linuxize.com/post/how-to-use-linux-screen/) or [tmux](https://linuxize.com/post/getting-started-with-tmux/) session. +- Specify the config profile with `-profile uondrs_ada`. + +``` +nextflow run /path/to/nf-core/rnaseq -profile uondrs_ada \ +--genome GRCh38 \ +--igenomes_base /path/to/genome_references/ \ +... # the rest of pipeline flags +``` \ No newline at end of file From 47e90ec8513099aee8d6027499d505c87862f101 Mon Sep 17 00:00:00 2001 From: ShahNiraj Date: Fri, 12 Jul 2024 11:07:53 +0100 Subject: [PATCH 4/6] Update nfcore_custom.config First nf-core config. --- nfcore_custom.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nfcore_custom.config b/nfcore_custom.config index 0512da1ba..1e1071910 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -10,6 +10,7 @@ //Please use a new line per include Config section to allow easier linting/parsing. Thank you. profiles { + uondrs_ada { includeConfig "${params.custom_config_base}/conf/uondrs_ada.config" } abims { includeConfig "${params.custom_config_base}/conf/abims.config" } adcra { includeConfig "${params.custom_config_base}/conf/adcra.config" } alice { includeConfig "${params.custom_config_base}/conf/alice.config" } From a32a6273305ea21408a66983c26502ddb1907dfd Mon Sep 17 00:00:00 2001 From: ShahNiraj Date: Fri, 12 Jul 2024 11:17:04 +0100 Subject: [PATCH 5/6] Update README.md Added 'uondrs_ada.md' in the pipeline specific documentation section of this page --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index 15cadcd08..90de1a636 100644 --- a/README.md +++ b/README.md @@ -296,6 +296,9 @@ Currently documentation is available for the following pipeline: - viralrecon - [genomes](docs/pipeline/viralrecon/genomes.md) + +- rnaseq + - [uondrs_ada](docs/pipeline/rnaseq/uondrs_ada.md) ### Enabling pipeline-specific configs within a pipeline From bf4f7c707c42a22f95a2001e5f73fc4c9f4672c9 Mon Sep 17 00:00:00 2001 From: ShahNiraj Date: Fri, 12 Jul 2024 11:29:51 +0100 Subject: [PATCH 6/6] Update main.yml Added "uondrs_ada" to the profiles section --- .github/workflows/main.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 223ec0325..a82f48dd1 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -34,6 +34,7 @@ jobs: strategy: matrix: profile: + - "uondrs_ada" - "abims" - "adcra" - "alice"