Merge branch 'nf-core:master' into sbc_sharc

.github/workflows/main.yml

@@ -69,6 +69,7 @@ jobs:
           - "jax"
           - "ku_sund_dangpu"
           - "lugh"
+          - "mana"
           - "marvin"
           - "medair"
           - "mjolnir_globe"
@@ -87,6 +88,7 @@ jobs:
           - "sanger"
           - "sbc_sharc"
           - "seg_globe"
+          - "tigem"
           - "uct_hpc"
           - "unibe_ibu"
           - "uppmax"

README.md

@@ -125,6 +125,7 @@ Currently documentation is available for the following systems:
 - [KU SUND DANGPU](docs/ku_sund_dangpu.md)
 - [LUGH](docs/lugh.md)
 - [MAESTRO](docs/maestro.md)
+- [Mana](docs/mana.md)
 - [MARVIN](docs/marvin.md)
 - [MEDAIR](docs/medair.md)
 - [MJOLNIR_GLOBE](docs/mjolnir_globe.md)
@@ -141,6 +142,7 @@ Currently documentation is available for the following systems:
 - [SANGER](docs/sanger.md)
 - [SBC_SHARC](docs/sbc_sharc.md)
 - [SEG_GLOBE](docs/seg_globe.md)
+- [TIGEM](docs/tigem.md)
 - [UCT_HPC](docs/uct_hpc.md)
 - [UNIBE_IBU](docs/unibe_ibu.md)
 - [UPPMAX](docs/uppmax.md)

conf/ccga_med.config

@@ -13,8 +13,8 @@ params {
 
 singularity {
   enabled = true
-  runOptions = "-B /work_ifs -B /scratch"
-  cacheDir = "/work_ifs/ikmb_repository/singularity_cache/"
+  runOptions = "-B /work_ifs -B /scratch -B /work_beegfs"
+  cacheDir = "/work_beegfs/ikmb_repository/singularity_cache/"
 }
 
 executor {
@@ -31,7 +31,7 @@ process {
 
 params {
   // illumina iGenomes reference file paths on RZCluster
-  igenomes_base = '/work_ifs/ikmb_repository/references/iGenomes/references/'
+  igenomes_base = '/work_beegfs/ikmb_repository/references/iGenomes/references/'
   saveReference = true
   max_memory = 250.GB
   max_cpus = 24

conf/mana.config

@@ -0,0 +1,21 @@
+params {
+  config_profile_description = 'University of Hawaii at Manoa'
+  config_profile_url = 'http://www.hawaii.edu/its/ci/'
+  config_profile_contact = 'Cedric Arisdakessian'
+
+  max_memory = 400.GB
+  max_cpus = 96
+  max_time = 72.h
+}
+
+process {
+  executor = 'slurm'
+  queue = 'shared,exclusive,kill-shared,kill-exclusive'
+  module = 'tools/Singularity'
+}
+
+singularity {
+  enabled = true
+  cacheDir = "$HOME/.singularity_images_cache"
+  autoMounts = true
+}

conf/pipeline/mag/eva.config

@@ -4,6 +4,11 @@ params {
   config_profile_description = 'nf-core/mag EVA profile provided by nf-core/configs'
 }
 
+env {
+    OPENBLAS_NUM_THREADS=1
+    OMP_NUM_THREADS=1
+}
+
 process {
 
     withName: FASTQC {

conf/tigem.config

@@ -0,0 +1,14 @@
+params {
+  config_profile_description = 'Telethon Institute of Genetic and Medicine (TIGEM) provided by nf-core/configs.'
+  config_profile_contact = 'Giuseppe Martone (@giusmar)'
+  config_profile_url = 'https://github.com/giusmar'
+}
+
+process.executor = 'slurm'
+google.zone = 'europe-west1'
+
+singularity {
+    enabled = true
+    autoMounts = true
+    cacheDir = 'work/singularity'
+}

docs/mana.md

@@ -0,0 +1,45 @@
+# nf-core/configs Mana (at University of Hawaii at Manoa) Configuration
+
+To use, run the pipeline with `-profile mana`. It will use the following parameters for Mana (UHM HPCC):
+
+- Load singularity and use it as default container technology
+- Setup a container cache directory in your home (~/.singularity_images_cache)
+- Select appropriate queues (currently: `shared,exclusive,kill-shared,kill-exclusive`)
+- Set the maximum available resources (available in 09/02/2022):
+  - CPUs: 96
+  - Memory: 400.GB
+  - Time: 72.h
+
+## Pre-requisites
+
+In order to run a nf-core pipeline on Mana, you will need to setup nextflow in your environment.
+At the moment, nextflow is not available as a module (but might be in the future).
+
+### Install nextflow in a conda environment
+
+Before we start, we will need to work on an interactive node (currently, mana doesn't let you execute any program in the login node):
+
+```bash
+# Request an interactive sandbox node for 30 min
+srun --pty -t 30 -p sandbox /bin/bash
+```
+
+To setup nextflow on your account, follow these steps.
+
+```bash
+# Load the latest anaconda3 module
+module load lang/Anaconda3/2022.05
+
+# Initialize environment
+. $(conda info --base)/etc/profile.d/conda.sh
+
+# Install nextflow (here in base environment, but you can create a new one if you'd like)
+conda install -c bioconda nextflow
+```
+
+If you want these settings to be persistent, you can add the first 2 commands in your .bash_profile file like this:
+
+```bash
+echo "module load lang/Anaconda3/2022.05" >> ~/.bash_profile
+echo "$(conda info --base)/etc/profile.d/conda.sh" >> ~/.bash_profile
+```

docs/tigem.md

@@ -0,0 +1,7 @@
+# nf-core/configs: TIGEM configuration
+
+To use, run the pipeline with `-profile tigem`. This will download and launch the tigem.config which has been pre-configured with a setup suitable for the TIGEM personal biocluster.
+
+---
+
+This configuration profile can be used on TIGEM clusters, with the pre-installed SLURM job scheduling system. An additional parameter is `google.zone` to allow downloading data from GCP for a specific time zone. It should not interfere with any local or other AWS configuration.

nfcore_custom.config

@@ -52,6 +52,7 @@ profiles {
   ku_sund_dangpu {includeConfig "${params.custom_config_base}/conf/ku_sund_dangpu.config"}
   lugh         { includeConfig "${params.custom_config_base}/conf/lugh.config" }
   maestro      { includeConfig "${params.custom_config_base}/conf/maestro.config" }
+  mana         { includeConfig "${params.custom_config_base}/conf/mana.config" }
   marvin       { includeConfig "${params.custom_config_base}/conf/marvin.config" }
   medair       { includeConfig "${params.custom_config_base}/conf/medair.config" }
   mjolnir_globe { includeConfig "${params.custom_config_base}/conf/mjolnir_globe.config" }
@@ -69,6 +70,7 @@ profiles {
   sanger       { includeConfig "${params.custom_config_base}/conf/sanger.config"}
   sbc_sharc    { includeConfig "${params.custom_config_base}/conf/sbc_sharc.config"}
   seg_globe    { includeConfig "${params.custom_config_base}/conf/seg_globe.config"}
+  tigem        { includeConfig "${params.custom_config_base}/conf/tigem.config"}
   uct_hpc      { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }
   unibe_ibu    { includeConfig "${params.custom_config_base}/conf/unibe_ibu.config" }
   uppmax       { includeConfig "${params.custom_config_base}/conf/uppmax.config" }