Merge branch 'master' into crukmi

.github/workflows/main.yml

@@ -30,6 +30,7 @@ jobs:
       matrix:
         profile:
           - "abims"
+          - "adcra"
           - "alice"
           - "aws_tower"
           - "awsbatch"

README.md

@@ -86,6 +86,7 @@ See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs
 Currently documentation is available for the following systems:
 
 - [ABIMS](docs/abims.md)
+- [ADCRA](docs/adcra.md)
 - [ALICE](docs/alice.md)
 - [AWSBATCH](docs/awsbatch.md)
 - [AWS_TOWER](docs/aws_tower.md)

conf/adcra.config

@@ -0,0 +1,40 @@
+/*
+* --------------------------------------------------------------
+*   nf-core pipelines config file for AD project using CRA HPC
+* --------------------------------------------------------------
+*/
+
+params {
+  config_profile_name = 'adcra'
+  config_profile_description = 'CRA HPC profile provided by nf-core/configs'
+  config_profile_contact = 'Kalayanee Chairat (@kalayaneech)'
+  config_profile_url = 'https://bioinformatics.kmutt.ac.th/'
+  }
+  
+params {  
+  max_cpus = 16
+  max_memory = 128.GB
+  max_time = 120.h
+}
+
+// Specify the job scheduler
+executor {  
+  name = 'slurm'
+  queueSize = 20
+  submitRateLimit = '6/1min'
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+}
+
+process {
+  scratch = true
+  queue = 'unlimit'
+  queueStatInterval = '10 min'
+  maxRetries = 3
+  errorStrategy = { task.attempt <=3 ? 'retry' : 'finish' }
+  cache = 'lenient'
+  exitStatusReadTimeoutMillis = '2700000'
+}

docs/adcra.md

@@ -0,0 +1,39 @@
+# nf-core/configs: CRA HPC Configuration
+
+nfcore pipeline sarek and rnaseq have been tested on the CRA HPC.
+
+## Before running the pipeline
+
+- You will need an account to use the CRA HPC cluster in order to run the pipeline.
+- Make sure that Singularity and Nextflow are installed.
+- Downlode pipeline singularity images to a HPC system using [nf-core tools](https://nf-co.re/tools/#downloading-pipelines-for-offline-use)
+
+```
+$ conda install nf-core
+$ nf-core download
+```
+
+- You will need to specify a Singularity cache directory in your ~./bashrc. This will store your container images in this cache directory without repeatedly downloading them every time you run a pipeline. Since space on home directory is limited, using lustre file system is recommended.
+
+```
+export NXF_SINGULARITY_CACHEDIR = "/lustre/fs0/storage/yourCRAAccount/cache_dir"
+```
+
+- Download iGenome reference to be used as a local copy.
+
+```
+$ aws s3 --no-sign-request --region eu-west-1 sync s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/ /lustre/fs0/storage/yourCRAAccount/references/Homo_sapiens/GATK/GRCh38/
+```
+
+## Running the pipeline using the adcra config profile
+
+- Run the pipeline within a [screen](https://linuxize.com/post/how-to-use-linux-screen/) or [tmux](https://linuxize.com/post/getting-started-with-tmux/) session.
+- Specify the config profile with `-profile adcra`.
+- Using lustre file systems to store results (`--outdir`) and intermediate files (`-work-dir`) is recommended.
+
+```
+nextflow run /path/to/nf-core/<pipeline-name> -profile adcra \
+--genome GRCh38 \
+--igenomes_base /path/to/genome_references/ \
+... # the rest of pipeline flags
+```

nfcore_custom.config

@@ -11,6 +11,7 @@
 //Please use a new line per include Config section to allow easier linting/parsing. Thank you.
 profiles {
   abims        { includeConfig "${params.custom_config_base}/conf/abims.config" }
+  adcra        { includeConfig "${params.custom_config_base}/conf/adcra.config" }
   alice        { includeConfig "${params.custom_config_base}/conf/alice.config" }
   aws_tower    { includeConfig "${params.custom_config_base}/conf/aws_tower.config" }
   awsbatch     { includeConfig "${params.custom_config_base}/conf/awsbatch.config" }