From 22b7496bfd5710bc772887abe33fdf0adecd5b2a Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Thu, 21 Sep 2023 13:49:14 +0200 Subject: [PATCH 1/6] Create methylseq.config --- pipeline/methylseq.config | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 pipeline/methylseq.config diff --git a/pipeline/methylseq.config b/pipeline/methylseq.config new file mode 100644 index 000000000..02b09a434 --- /dev/null +++ b/pipeline/methylseq.config @@ -0,0 +1,9 @@ +/* + * ------------------------------------------------- + * nfcore/methylseq custom profile Nextflow config file + * ------------------------------------------------- + * Config options for custom environments. + * Cluster-specific config options should be saved + * in the conf/pipeline/methylseq folder and imported + * under a profile name here. + */ From 21f6cbcc94d9c173f209c368dc329329e3549d36 Mon Sep 17 00:00:00 2001 From: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> Date: Tue, 26 Sep 2023 15:00:25 +0000 Subject: [PATCH 2/6] Overhead vsc_kul_uhasselt fix --- conf/vsc_kul_uhasselt.config | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/conf/vsc_kul_uhasselt.config b/conf/vsc_kul_uhasselt.config index 051b05931..2ccaf741f 100644 --- a/conf/vsc_kul_uhasselt.config +++ b/conf/vsc_kul_uhasselt.config @@ -46,7 +46,7 @@ profiles { config_profile_description = 'HPC_GENIUS profile for use on the genius cluster of the VSC HPC.' config_profile_contact = 'joon.klaps@kuleuven.be' config_profile_url = 'https://docs.vscentrum.be/en/latest/index.html' - max_memory = 720.GB // 768 - 48 so 48GB for overhead + max_memory = 703.GB // 768 - 65 so 65GB for overhead, max is 720000MB max_time = 168.h max_cpus = 36 } @@ -55,7 +55,7 @@ profiles { executor = 'slurm' queue = { switch (task.memory) { - case { it >= 170.GB }: // 192 - 22 + case { it >= 175.GB }: // max is 180000 switch (task.time) { case { it >= 72.h }: return 'dedicated_big_bigmem' @@ -81,7 +81,7 @@ profiles { config_profile_description = 'HPC_WICE profile for use on the Wice cluster of the VSC HPC.' config_profile_contact = 'joon.klaps@kuleuven.be' config_profile_url = 'https://docs.vscentrum.be/en/latest/index.html' - max_memory = 2000.GB // 2048 - 48 so 48GB for overhead + max_memory = 1968.GB // max is 2016000 max_cpus = 72 max_time = 168.h } @@ -90,7 +90,7 @@ profiles { executor = 'slurm' queue = { switch (task.memory) { - case { it >= 220.GB }: // 256 - 36 + case { it >= 242.GB }: // max is 248800 switch (task.time) { case { it >= 72.h }: return 'dedicated_big_bigmem' @@ -116,7 +116,7 @@ profiles { config_profile_description = 'HPC_SUPERDOME profile for use on the genius cluster of the VSC HPC.' config_profile_contact = 'joon.klaps@kuleuven.be' config_profile_url = 'https://docs.vscentrum.be/en/latest/index.html' - max_memory = 708.GB // 756 - 48 + max_memory = 5772.GB // 6000 - 228 so 228GB for overhead, max is 5910888MB max_cpus = 14 max_time = 168.h } From 47fd0b8043090d6b2370cb585c564411d116a49e Mon Sep 17 00:00:00 2001 From: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> Date: Tue, 26 Sep 2023 15:27:42 +0000 Subject: [PATCH 3/6] wice_batch incorrect in 'sinfo' --- conf/vsc_kul_uhasselt.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/vsc_kul_uhasselt.config b/conf/vsc_kul_uhasselt.config index 2ccaf741f..bb202e8b2 100644 --- a/conf/vsc_kul_uhasselt.config +++ b/conf/vsc_kul_uhasselt.config @@ -90,7 +90,7 @@ profiles { executor = 'slurm' queue = { switch (task.memory) { - case { it >= 242.GB }: // max is 248800 + case { it >= 239.GB }: // max is 244800 switch (task.time) { case { it >= 72.h }: return 'dedicated_big_bigmem' From 21ce7aa6a3f04f5f72cd8ca9f251c5e6263ddaa1 Mon Sep 17 00:00:00 2001 From: LilyAnderssonLee Date: Wed, 27 Sep 2023 07:58:20 +0200 Subject: [PATCH 4/6] add new ignore names --- conf/pipeline/taxprofiler/hasta.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/pipeline/taxprofiler/hasta.config b/conf/pipeline/taxprofiler/hasta.config index 4aef6cc63..9e9a980a3 100644 --- a/conf/pipeline/taxprofiler/hasta.config +++ b/conf/pipeline/taxprofiler/hasta.config @@ -2,6 +2,7 @@ params { // Specific nf-core/configs params config_profile_contact = 'Sofia Stamouli (@sofstam)' config_profile_description = 'nf-core/taxprofiler HASTA profile provided by nf-core/configs' + validationSchemaIgnoreParams = "priority,clusterOptions,schema_ignore_params,genomes,fasta" } process { From 4491908f75aa71514531e1ae3c666abf85dba564 Mon Sep 17 00:00:00 2001 From: cruk-mi <93599115+cruk-mi@users.noreply.github.com> Date: Tue, 3 Oct 2023 15:12:16 +0000 Subject: [PATCH 5/6] Some changes regarding definition of software versions --- conf/crukmi.config | 2 +- docs/crukmi.md | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/crukmi.config b/conf/crukmi.config index 7f5c2b74b..e20003457 100644 --- a/conf/crukmi.config +++ b/conf/crukmi.config @@ -12,7 +12,7 @@ singularity { } process { - beforeScript = 'module load apps/apptainer/1.2.0' + beforeScript = 'module load apps/apptainer' executor = 'slurm' queue = { task.memory <= 240.GB ? 'compute' : 'hmem' } diff --git a/docs/crukmi.md b/docs/crukmi.md index 769295af2..b2226b872 100644 --- a/docs/crukmi.md +++ b/docs/crukmi.md @@ -2,14 +2,14 @@ All nf-core pipelines have been successfully configured for the use on the HPC (griffin) at Cancer Research UK Manchester Institute. -To use, run the pipeline with `-profile crukmi`. This will download and launch the [`crukmi.config`](../conf/crukmi.config) which has been pre-configured with a setup suitable for the griffin HPC. Using this profile, singularity images will be downloaded to run on the cluster and stored in a centralised location. +To use, run the pipeline with `-profile crukmi`. This will download and launch the [`crukmi.config`](../conf/crukmi.config) which has been pre-configured with a setup suitable for the Griffin HPC. Using this profile, Apptainer/Singularity images will be downloaded to run on the cluster and stored in a centralised location. Before running the pipeline you will need to load Nextflow using the environment module system, for example via: ```bash ## Load Nextflow environment modules module purge -module load apps/nextflow/22.04.5 +module load apps/nextflow ``` The pipeline should always be executed inside a workspace on the `/scratch/` system. All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large. From 884f03b6cba6ed91045b967ec60d640d34b2228f Mon Sep 17 00:00:00 2001 From: Margherita <86382379+daisymut@users.noreply.github.com> Date: Thu, 5 Oct 2023 03:33:46 +0200 Subject: [PATCH 6/6] Update README.md to fix a link fixed a link rendering in the Adding a new config section --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 11896c95b..d8064cab3 100644 --- a/README.md +++ b/README.md @@ -62,7 +62,7 @@ If you decide to upload your custom config file to `nf-core/configs` then this w You will simply have to specify `-profile ` in the command used to run the pipeline. See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples. -Before adding your config file to nf-core/configs, we highly recommend writing and testing your own custom config file (as described [above](Using an existing config)), and then continuing with the next steps. +Before adding your config file to nf-core/configs, we highly recommend writing and testing your own custom config file (as described [above](https://github.com/nf-core/configs#using-an-existing-config)), and then continuing with the next steps. N.B. In your config file, please also make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` and `params.config_profile_url` set to reasonable values. Users will get information on who wrote the configuration profile then when executing a nf-core pipeline and can report back if there are things missing for example.