From 8e49f5f2faa79f76919dc75fdf4729eee45669d2 Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Tue, 2 Jan 2024 12:03:52 +0100 Subject: [PATCH 01/10] Update ku_sund_dangpu.md update instructions --- docs/ku_sund_dangpu.md | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 591f1e76d..3ab1cdce1 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -15,19 +15,28 @@ tmux new-session -s Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on DANGPU. Within the created session load Nextflow and Singularity and set up the environment by issuing the commands below: +first clear the environment and load Nextflow environment modules: ```bash -## Load Nextflow and Singularity environment modules module purge -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 +module load dangpu_libs openjdk/20.0.0 nextflow/23.04.1.5866 +``` + +for loading the older module nextflow/22.10.6 you can use `module load dangpu_libs java/11.0.15 nextflow/22.10.6` instead of `module load dangpu_libs openjdk/20.0.0 nextflow/23.04.1.5866`. + +next, load Singularity environment module: +```bash +module load singularity/3.8.0 python/3.7.13 nf-core/2.7.2 +``` -# set up bash environment variables for memory +set up bash environment variables for memory: +```bash export NXF_OPTS='-Xms1g -Xmx4g' export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home export NXF_TEMP=/scratch/temp/${USER} export NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images ``` -Create the user-specific nextflow directories if they don't exist yet: +Create the user-specific nextflow directories if they don't exist yet. You have to do this only once. ``` mkdir -p $NXF_SINGULARITY_CACHEDIR From c6bb615902f71e151b55510aefedccec18b67d70 Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Tue, 2 Jan 2024 13:22:47 +0100 Subject: [PATCH 02/10] Create ku_sund_dangpu.config create a methylseq setup that takes into account sources of potential problems in methyl -r 2.5.0: - do not use symlinks for reference genome - do not run Bismark in multicore mode --- conf/pipeline/methylseq/ku_sund_dangpu.config | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 conf/pipeline/methylseq/ku_sund_dangpu.config diff --git a/conf/pipeline/methylseq/ku_sund_dangpu.config b/conf/pipeline/methylseq/ku_sund_dangpu.config new file mode 100644 index 000000000..c37ace1e7 --- /dev/null +++ b/conf/pipeline/methylseq/ku_sund_dangpu.config @@ -0,0 +1,14 @@ +// Config profile metadata +params { + config_profile_contact = 'Adrija Kalvisa (@adrijak)' + config_profile_description = 'nf-core/methylseq ku_sund_dangpu profile provided by nf-core/configs' +} + +process { + withName: 'NFCORE_METHYLSEQ:METHYLSEQ:PREPARE_GENOME:BISMARK_GENOMEPREPARATION' { + stageInMode = 'copy' + } + withName: 'NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN' { + multicore = 2 + } +} From d2e2a4928bbb379c0f3a729ab30962f22a36a12b Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Tue, 2 Jan 2024 13:23:28 +0100 Subject: [PATCH 03/10] Update ku_sund_dangpu.config reduce n of cores for Bismark from 2 to 1 to avoid silent crashes when running in multicore mode --- conf/pipeline/methylseq/ku_sund_dangpu.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/pipeline/methylseq/ku_sund_dangpu.config b/conf/pipeline/methylseq/ku_sund_dangpu.config index c37ace1e7..718bdb27c 100644 --- a/conf/pipeline/methylseq/ku_sund_dangpu.config +++ b/conf/pipeline/methylseq/ku_sund_dangpu.config @@ -9,6 +9,6 @@ process { stageInMode = 'copy' } withName: 'NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN' { - multicore = 2 + multicore = 1 } } From 156d3ddbc3e5b501d0abe8523450674b883ab532 Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Wed, 3 Jan 2024 11:58:41 +0100 Subject: [PATCH 04/10] Update ku_sund_dangpu.config extend max_time from 72.h to 144.h --- conf/pipeline/methylseq/ku_sund_dangpu.config | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/conf/pipeline/methylseq/ku_sund_dangpu.config b/conf/pipeline/methylseq/ku_sund_dangpu.config index 718bdb27c..aa57270a4 100644 --- a/conf/pipeline/methylseq/ku_sund_dangpu.config +++ b/conf/pipeline/methylseq/ku_sund_dangpu.config @@ -1,14 +1,16 @@ -// Config profile metadata params { config_profile_contact = 'Adrija Kalvisa (@adrijak)' config_profile_description = 'nf-core/methylseq ku_sund_dangpu profile provided by nf-core/configs' + + // methylseq usually runs extremely long hours, use 2x the normal max_time allowance for this pipeline + max_time = 144.h } process { withName: 'NFCORE_METHYLSEQ:METHYLSEQ:PREPARE_GENOME:BISMARK_GENOMEPREPARATION' { stageInMode = 'copy' } - withName: 'NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN' { + withName: 'NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN' { multicore = 1 } } From b2d3b086197d86ce36f8c04eed4db7996790dbb6 Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Tue, 9 Jan 2024 14:40:35 +0100 Subject: [PATCH 05/10] Update ku_sund_dangpu.md update documentation --- docs/ku_sund_dangpu.md | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 3ab1cdce1..57faf5f8f 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -19,16 +19,12 @@ first clear the environment and load Nextflow environment modules: ```bash module purge module load dangpu_libs openjdk/20.0.0 nextflow/23.04.1.5866 +module load singularity/3.8.0 python/3.7.13 nf-core/2.7.2 ``` for loading the older module nextflow/22.10.6 you can use `module load dangpu_libs java/11.0.15 nextflow/22.10.6` instead of `module load dangpu_libs openjdk/20.0.0 nextflow/23.04.1.5866`. -next, load Singularity environment module: -```bash -module load singularity/3.8.0 python/3.7.13 nf-core/2.7.2 -``` - -set up bash environment variables for memory: +Next, set up bash environment variables for memory. (You can avoid repeatedly writing this every time by placing this code chunk into ${HOME}/.bash_profile and ${HOME}/.bashrc) ```bash export NXF_OPTS='-Xms1g -Xmx4g' export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home @@ -36,8 +32,7 @@ export NXF_TEMP=/scratch/temp/${USER} export NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images ``` -Create the user-specific nextflow directories if they don't exist yet. You have to do this only once. - +Create the user-specific nextflow directories if they don't exist yet. You have to do this only first time you run a nf-core pipeline. ``` mkdir -p $NXF_SINGULARITY_CACHEDIR mkdir -p $NXF_HOME @@ -51,13 +46,13 @@ To download and test a pipeline for the first time, use the `-profile test` and For example to run rnaseq: ``` -nextflow run nf-core/rnaseq -r 3.10.1 -profile test,ku_sund_dangpu --outdir +nextflow run nf-core/rnaseq -r 3.14.0 -profile test,ku_sund_dangpu --outdir ``` To run a pipeline: ``` -nextflow run nf-core/rnaseq -r 3.10.1 -profile ku_sund_dangpu --outdir --input +nextflow run nf-core/rnaseq -r 3.14.0 -profile ku_sund_dangpu --outdir --input ``` ## Notes From 536d0f3d048b022d85c8d36ea1b7ce8223282a3e Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Tue, 9 Jan 2024 14:45:49 +0100 Subject: [PATCH 06/10] Create ku_sund_dangpu.config Create pipeline-specific config for ku_sund_dangpu --- conf/pipeline/rnaseq/ku_sund_dangpu.config | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 conf/pipeline/rnaseq/ku_sund_dangpu.config diff --git a/conf/pipeline/rnaseq/ku_sund_dangpu.config b/conf/pipeline/rnaseq/ku_sund_dangpu.config new file mode 100644 index 000000000..9a5d5aeaa --- /dev/null +++ b/conf/pipeline/rnaseq/ku_sund_dangpu.config @@ -0,0 +1,7 @@ +process { + // Use more memory with processes labeled as 'process_high' to enable sufficient memory access to STAR_GENOMEGENERATE + // and other memory-intensive processes + withLabel: 'process_high' { + memory = 128.GB + } +} From 7550e1d7fd73f3b52731a0427d6c34f6cf30ebec Mon Sep 17 00:00:00 2001 From: Adrija Kalvisa Date: Mon, 25 Mar 2024 15:58:43 +0100 Subject: [PATCH 07/10] Update ku_sund_dangpu.md add NXF_WORK to stop draining dangpu nodes when running nf-core jobs --- docs/ku_sund_dangpu.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 57faf5f8f..8939dd5cc 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -29,6 +29,7 @@ Next, set up bash environment variables for memory. (You can avoid repeatedly wr export NXF_OPTS='-Xms1g -Xmx4g' export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home export NXF_TEMP=/scratch/temp/${USER} +export NXF_WORK=/scratch/temp/${USER} export NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images ``` From 4aa492e4736093b61a166a83828a59d0f4e5f7aa Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 25 Mar 2024 16:52:52 +0000 Subject: [PATCH 08/10] [automated] Fix code linting --- docs/ku_sund_dangpu.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/docs/ku_sund_dangpu.md b/docs/ku_sund_dangpu.md index 8939dd5cc..1488ce3e4 100644 --- a/docs/ku_sund_dangpu.md +++ b/docs/ku_sund_dangpu.md @@ -16,6 +16,7 @@ Before running the pipeline you will need to load Nextflow and Singularity using Within the created session load Nextflow and Singularity and set up the environment by issuing the commands below: first clear the environment and load Nextflow environment modules: + ```bash module purge module load dangpu_libs openjdk/20.0.0 nextflow/23.04.1.5866 @@ -24,7 +25,8 @@ module load singularity/3.8.0 python/3.7.13 nf-core/2.7.2 for loading the older module nextflow/22.10.6 you can use `module load dangpu_libs java/11.0.15 nextflow/22.10.6` instead of `module load dangpu_libs openjdk/20.0.0 nextflow/23.04.1.5866`. -Next, set up bash environment variables for memory. (You can avoid repeatedly writing this every time by placing this code chunk into ${HOME}/.bash_profile and ${HOME}/.bashrc) +Next, set up bash environment variables for memory. (You can avoid repeatedly writing this every time by placing this code chunk into ${HOME}/.bash_profile and ${HOME}/.bashrc) + ```bash export NXF_OPTS='-Xms1g -Xmx4g' export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home @@ -33,7 +35,8 @@ export NXF_WORK=/scratch/temp/${USER} export NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images ``` -Create the user-specific nextflow directories if they don't exist yet. You have to do this only first time you run a nf-core pipeline. +Create the user-specific nextflow directories if they don't exist yet. You have to do this only first time you run a nf-core pipeline. + ``` mkdir -p $NXF_SINGULARITY_CACHEDIR mkdir -p $NXF_HOME From 9646b00efe2b4d9765896f36c73784d707bc7eb9 Mon Sep 17 00:00:00 2001 From: Martin Porks Date: Mon, 25 Mar 2024 17:59:44 +0100 Subject: [PATCH 09/10] fix: linting --- conf/pipeline/methylseq/ku_sund_dangpu.config | 2 +- conf/pipeline/rnaseq/ku_sund_dangpu.config | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/conf/pipeline/methylseq/ku_sund_dangpu.config b/conf/pipeline/methylseq/ku_sund_dangpu.config index aa57270a4..fa1bca494 100644 --- a/conf/pipeline/methylseq/ku_sund_dangpu.config +++ b/conf/pipeline/methylseq/ku_sund_dangpu.config @@ -12,5 +12,5 @@ process { } withName: 'NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN' { multicore = 1 - } + } } diff --git a/conf/pipeline/rnaseq/ku_sund_dangpu.config b/conf/pipeline/rnaseq/ku_sund_dangpu.config index 9a5d5aeaa..7e46348d5 100644 --- a/conf/pipeline/rnaseq/ku_sund_dangpu.config +++ b/conf/pipeline/rnaseq/ku_sund_dangpu.config @@ -1,7 +1,7 @@ process { - // Use more memory with processes labeled as 'process_high' to enable sufficient memory access to STAR_GENOMEGENERATE + // Use more memory with processes labeled as 'process_high' to enable sufficient memory access to STAR_GENOMEGENERATE // and other memory-intensive processes - withLabel: 'process_high' { - memory = 128.GB + withLabel: 'process_high' { + memory = 128.GB } } From cf1cc808b8e1ebe2b5295377e6801c86057af90a Mon Sep 17 00:00:00 2001 From: Martin Porks Date: Mon, 25 Mar 2024 18:02:59 +0100 Subject: [PATCH 10/10] fix: linting one more time --- conf/pipeline/rnaseq/ku_sund_dangpu.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/pipeline/rnaseq/ku_sund_dangpu.config b/conf/pipeline/rnaseq/ku_sund_dangpu.config index 7e46348d5..703c56759 100644 --- a/conf/pipeline/rnaseq/ku_sund_dangpu.config +++ b/conf/pipeline/rnaseq/ku_sund_dangpu.config @@ -1,6 +1,6 @@ process { - // Use more memory with processes labeled as 'process_high' to enable sufficient memory access to STAR_GENOMEGENERATE - // and other memory-intensive processes + // Use more memory with processes labeled as 'process_high' to enable sufficient memory access to STAR_GENOMEGENERATE + // and other memory-intensive processes withLabel: 'process_high' { memory = 128.GB }