From badc2799738a75f9585e2c50718fd8abca0493cc Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Tue, 14 Feb 2023 13:39:08 +0100 Subject: [PATCH 01/17] update nextflow version nextflow/22.10.6 --- docs/ku_sund_dangpu.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 3bae7baab..142a75850 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -19,7 +19,7 @@ Within the created session load Nextflow and Singularity and set up the environm ```bash ## Load Nextflow and Singularity environment modules module purge -module load java/11.0.15 nextflow/22.04.4 singularity/3.8.0 +module load java/11.0.15 nextflow/22.10.6 singularity/3.8.0 # set up bash environment variables for memory export NXF_OPTS='-Xms1g -Xmx4g' From 9329abc34b8124c03aaeef7b2e826bd2f7fcce34 Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Tue, 14 Feb 2023 13:46:16 +0100 Subject: [PATCH 02/17] add tmux instructions --- docs/ku_sund_dangpu.md | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 142a75850..29de191ff 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -54,4 +54,22 @@ nextflow run nf-core/rnaseq -r 3.8.1 -profile ku_sund_dangpu --outdir Date: Tue, 14 Feb 2023 13:47:18 +0100 Subject: [PATCH 03/17] fix typos --- docs/ku_sund_dangpu.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 29de191ff..cb925444d 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -62,14 +62,14 @@ tmux new-session -s mysessionname # load modules, define variables, run nfcore pipeline here ``` -detach a session use control+B and then press d +Detach a session use control+B and then press d. -to attach a previously detached session again: +To attach a previously detached session again: ``` tmux atttach-session -t mysessionname ``` -to exit a tmux session when the job is done: +To exit a tmux session when the job is done: ``` exit ``` From 9e7954162fc486cb2dbe617978de26449466cc6c Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Tue, 14 Feb 2023 14:06:20 +0100 Subject: [PATCH 04/17] update rnaseq pipeline --- docs/ku_sund_dangpu.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index cb925444d..4a7b0447d 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -43,13 +43,13 @@ To download and test a pipeline for the first time, use the `-profile test` and For example to run rnaseq: ``` -nextflow run nf-core/rnaseq -r 3.8.1 -profile test,ku_sund_dangpu --outdir +nextflow run nf-core/rnaseq -r 3.10.1 -profile test,ku_sund_dangpu --outdir ``` To run a pipeline: ``` -nextflow run nf-core/rnaseq -r 3.8.1 -profile ku_sund_dangpu --outdir +nextflow run nf-core/rnaseq -r 3.10.1 -profile ku_sund_dangpu --outdir ``` ## Notes From 540fb7dc0a8f4c494e4a8c6dc9ef2768cc988d29 Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Wed, 15 Feb 2023 13:30:15 +0100 Subject: [PATCH 05/17] change tmp to temp tmp does not have write persmissions for many users, so change to temp. --- docs/ku_sund_dangpu.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 4a7b0447d..26e81e4cb 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -24,7 +24,7 @@ module load java/11.0.15 nextflow/22.10.6 singularity/3.8.0 # set up bash environment variables for memory export NXF_OPTS='-Xms1g -Xmx4g' export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home -export NXF_TEMP=/scratch/tmp/${USER} +export NXF_TEMP=/scratch/temp/${USER} export NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images ``` From cd20b8d750ad61b70001ec756fdf993cb7722e96 Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Wed, 15 Feb 2023 13:31:20 +0100 Subject: [PATCH 06/17] add --input to rnaseq pipeline add a css file to input requirements when running a pipeline example --- docs/ku_sund_dangpu.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 26e81e4cb..d24676564 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -49,7 +49,7 @@ nextflow run nf-core/rnaseq -r 3.10.1 -profile test,ku_sund_dangpu --outdir +nextflow run nf-core/rnaseq -r 3.10.1 -profile ku_sund_dangpu --outdir --input ``` ## Notes From c57b76e0d066ef38d7016ab8e46239aba1af2c52 Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Fri, 17 Mar 2023 12:00:40 +0100 Subject: [PATCH 07/17] add nf-core module module load dangpu_libs python/3.7.13 nf-core/2.7.2 --- docs/ku_sund_dangpu.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index d24676564..21749163d 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -19,7 +19,7 @@ Within the created session load Nextflow and Singularity and set up the environm ```bash ## Load Nextflow and Singularity environment modules module purge -module load java/11.0.15 nextflow/22.10.6 singularity/3.8.0 +module load dangpu_libs java/11.0.15 nextflow/22.10.6 singularity/3.8.0 python/3.7.13 nf-core/2.7.2 # set up bash environment variables for memory export NXF_OPTS='-Xms1g -Xmx4g' From e99a7511905bb7f2d7e1f7ba0fbfe59770836b66 Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Fri, 17 Mar 2023 15:20:41 +0100 Subject: [PATCH 08/17] add explanation for -r parameter --- docs/ku_sund_dangpu.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 21749163d..1844976b9 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -38,7 +38,7 @@ mkdir $NXF_TEMP ## How to run a pipeline with institution profile -To download and test a pipeline for the first time, use the `-profile test` and specify `--outdir`. It is a good practice to use the pipeline version with specifying `-r` each time you run a pipeline. +To download and test a pipeline for the first time, use the `-profile test` and specify `--outdir`. It is a good practice to use the pipeline version with specifying `-r` each time you run a pipeline. `-r` refers to a revision version and is useful to ensurereproducibility when rerunning the pipeline. You can read more on nf-core pipeline reproducibility [here](https://nf-co.re/rnaseq/3.10.1/usage#reproducibility) For example to run rnaseq: From e467acb120c413c42efb776a1b84e334b918a668 Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Fri, 17 Mar 2023 15:21:15 +0100 Subject: [PATCH 09/17] fix typo --- docs/ku_sund_dangpu.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 1844976b9..6514de1bf 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -38,7 +38,7 @@ mkdir $NXF_TEMP ## How to run a pipeline with institution profile -To download and test a pipeline for the first time, use the `-profile test` and specify `--outdir`. It is a good practice to use the pipeline version with specifying `-r` each time you run a pipeline. `-r` refers to a revision version and is useful to ensurereproducibility when rerunning the pipeline. You can read more on nf-core pipeline reproducibility [here](https://nf-co.re/rnaseq/3.10.1/usage#reproducibility) +To download and test a pipeline for the first time, use the `-profile test` and specify `--outdir`. It is a good practice to use the pipeline version with specifying `-r` each time you run a pipeline. `-r` refers to a revision version and is useful to ensure reproducibility when rerunning the pipeline. You can read more on nf-core pipeline reproducibility [here](https://nf-co.re/rnaseq/3.10.1/usage#reproducibility) For example to run rnaseq: From 4f03f9c8e96458be4d5eaa7ad3aa18dc75091343 Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Wed, 9 Aug 2023 11:47:00 +0200 Subject: [PATCH 10/17] Update ku_sund_dangpu.config update queue size --- conf/ku_sund_dangpu.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/ku_sund_dangpu.config b/conf/ku_sund_dangpu.config index 51ca462cd..894bfb5d9 100644 --- a/conf/ku_sund_dangpu.config +++ b/conf/ku_sund_dangpu.config @@ -4,7 +4,7 @@ params { config_profile_url = '' // General cpus/memory/time requirements - max_cpus = 30 + max_cpus = 8 max_memory = 200.GB max_time = 72.h } @@ -22,4 +22,4 @@ singularity { enabled = true autoMounts = true runOptions = '--bind /projects:/projects' -} \ No newline at end of file +} From 86385c00a8d24c046b8fa168065c621fa527a036 Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Wed, 9 Aug 2023 11:48:59 +0200 Subject: [PATCH 11/17] Update ku_sund_dangpu.md update docs --- docs/ku_sund_dangpu.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 6514de1bf..896f27013 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -59,7 +59,10 @@ Note that normally on dangpu server you are required to run resource-intensive c Start a new session and enter the vitual screen named `mysessionname`: ``` tmux new-session -s mysessionname -# load modules, define variables, run nfcore pipeline here + +# load modules +# define variables +# run nfcore pipeline here ``` Detach a session use control+B and then press d. From 72444ba27ccb0ec2be0312af27249084bf9dbbea Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Wed, 9 Aug 2023 11:50:03 +0200 Subject: [PATCH 12/17] Update ku_sund_dangpu.md update docs --- docs/ku_sund_dangpu.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 896f27013..341d684bc 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -1,9 +1,8 @@ # nf-core/configs: ku_sund_dangpu configuration -All nf-core pipelines have been successfully configured for use on the DANGPU at the -Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) and the Novo Nordisk Foundation Center for Protein Research (CPR) at the University of Copenhagen. +All nf-core pipelines have been successfully configured for use on the DANGPU server at the Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) at the University of Copenhagen. -To use, run the pipeline with `-profile ku_sund_dangpu`. This will download and launch the [`ku_sund_dangpu.config`](../conf/ku_sund_dangpu.config) which has been pre-configured with a setup suitable for the DANGPU. +To use the institution profile, run the pipeline with `-profile ku_sund_dangpu`. This will download and launch the [`ku_sund_dangpu.config`](../conf/ku_sund_dangpu.config) which has been pre-configured with a setup suitable for the DANGPU. ## Prepare the environment From 3f04f4c39ec7c58947097538a0c20c1acd89b7b8 Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Wed, 9 Aug 2023 12:01:05 +0200 Subject: [PATCH 13/17] Update ku_sund_dangpu.config update RAM --- conf/ku_sund_dangpu.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/ku_sund_dangpu.config b/conf/ku_sund_dangpu.config index 894bfb5d9..8c82a746e 100644 --- a/conf/ku_sund_dangpu.config +++ b/conf/ku_sund_dangpu.config @@ -5,7 +5,7 @@ params { // General cpus/memory/time requirements max_cpus = 8 - max_memory = 200.GB + max_memory = 64.GB max_time = 72.h } From 21b5b5ca9c27ea0baf5a5c0ef8443e140ef75ffa Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Wed, 9 Aug 2023 12:03:34 +0200 Subject: [PATCH 14/17] Update docs/ku_sund_dangpu.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- docs/ku_sund_dangpu.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 341d684bc..64aa818d3 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -56,7 +56,7 @@ nextflow run nf-core/rnaseq -r 3.10.1 -profile ku_sund_dangpu --outdir Date: Wed, 9 Aug 2023 12:03:45 +0200 Subject: [PATCH 15/17] Update docs/ku_sund_dangpu.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- docs/ku_sund_dangpu.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 64aa818d3..1c6d2ed70 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -67,7 +67,7 @@ tmux new-session -s mysessionname Detach a session use control+B and then press d. To attach a previously detached session again: -``` +```bash tmux atttach-session -t mysessionname ``` From e8ec1e8e023184938e8d808df36af5d477c8d19c Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Wed, 9 Aug 2023 12:03:52 +0200 Subject: [PATCH 16/17] Update docs/ku_sund_dangpu.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- docs/ku_sund_dangpu.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 1c6d2ed70..07e9549aa 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -72,6 +72,6 @@ tmux atttach-session -t mysessionname ``` To exit a tmux session when the job is done: -``` +```bash exit ``` From 55668821d761234a5e87727afb90d9a462dbd5ad Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 10 Aug 2023 08:52:00 +0000 Subject: [PATCH 17/17] [automated] Fix linting with Prettier --- docs/ku_sund_dangpu.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 07e9549aa..591f1e76d 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -53,9 +53,10 @@ nextflow run nf-core/rnaseq -r 3.10.1 -profile ku_sund_dangpu --outdir