Merge pull request nf-core#659 from AdrijaK/master

update ku_sund_dangpu profile

conf/pipeline/methylseq/ku_sund_dangpu.config

@@ -0,0 +1,16 @@
+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' {
+        multicore = 1
+    }
+}

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
+    }
+}

docs/ku_sund_dangpu.md

@@ -15,19 +15,27 @@ tmux new-session -s <session-name>
 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
+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`.
 
-# 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
 export NXF_TEMP=/scratch/temp/${USER}
+export NXF_WORK=/scratch/temp/${USER}
 export NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images
 ```
 
-Create the user-specific nextflow directories if they don't exist yet:
+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
@@ -42,13 +50,13 @@ 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 <name-of-output-directory>
+nextflow run nf-core/rnaseq -r 3.14.0 -profile test,ku_sund_dangpu --outdir <name-of-output-directory>
 ```
 
 To run a pipeline:
 
 ```
-nextflow run nf-core/rnaseq  -r 3.10.1 -profile ku_sund_dangpu --outdir <name-of-output-directory> --input <name-of-input-csv-file>
+nextflow run nf-core/rnaseq  -r 3.14.0 -profile ku_sund_dangpu --outdir <name-of-output-directory> --input <name-of-input-csv-file>
 ```
 
 ## Notes