Merge branch 'master' into biohpc_charliecloud_patch

.github/workflows/main.yml

@@ -62,6 +62,7 @@ jobs:
           - "google"
           - "hasta"
           - "hebbe"
+          - "hki"
           - "icr_davros"
           - "ifb_core"
           - "imperial"
@@ -83,6 +84,7 @@ jobs:
           - "sage"
           - "sahmri"
           - "sanger"
+          - "sbc_sharc"
           - "seg_globe"
           - "uct_hpc"
           - "unibe_ibu"

README.md

@@ -118,6 +118,7 @@ Currently documentation is available for the following systems:
 - [GOOGLE](docs/google.md)
 - [HASTA](docs/hasta.md)
 - [HEBBE](docs/hebbe.md)
+- [HKI](docs/hki.md)
 - [ICR_DAVROS](docs/icr_davros.md)
 - [IMPERIAL](docs/imperial.md)
 - [JAX](docs/jax.md)
@@ -137,6 +138,7 @@ Currently documentation is available for the following systems:
 - [ROSALIND](docs/rosalind.md)
 - [SAGE BIONETWORKS](docs/sage.md)
 - [SANGER](docs/sanger.md)
+- [SBC_SHARC](docs/sbc_sharc.md)
 - [SEG_GLOBE](docs/seg_globe.md)
 - [UCT_HPC](docs/uct_hpc.md)
 - [UNIBE_IBU](docs/unibe_ibu.md)
@@ -197,6 +199,10 @@ Currently documentation is available for the following pipelines within specific
 - ampliseq
   - [BINAC](docs/pipeline/ampliseq/binac.md)
   - [UPPMAX](docs/pipeline/ampliseq/uppmax.md)
+- atacseq
+  - [SBC_SHARC](docs/pipeline/atacseq/sbc_sharc.md)
+- chipseq
+  - [SBC_SHARC](docs/pipeline/chipseq/sbc_sharc.md)
 - eager
   - [EVA](docs/pipeline/eager/eva.md)
 - mag
@@ -204,11 +210,14 @@ Currently documentation is available for the following pipelines within specific
 - rnafusion
   - [HASTA](docs/pipeline/rnafusion/hasta.md)
   - [MUNIN](docs/pipeline/rnafusion/munin.md)
+- rnaseq
+  - [SBC_SHARC](docs/pipeline/rnaseq/sbc_sharc.md)
 - rnavar
   - [MUNIN](docs/pipeline/rnavar/munin.md)
 - sarek
   - [Cancer Research UK Manchester Institute](docs/pipeline/sarek/crukmi.md)
   - [MUNIN](docs/pipeline/sarek/munin.md)
+  - [SBC_SHARC](docs/pipeline/sarek/sbc_sharc.md)
   - [UPPMAX](docs/pipeline/sarek/uppmax.md)
 - taxprofiler
   - [EVA](docs/pipeline/taxprofiler/eva.md)

conf/cfc.config

@@ -12,7 +12,7 @@ singularity {
 
 process {
   executor = 'slurm'
-  queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' : 'compute' }
+  queue = 'qbic'
   scratch = 'true'
 }
 

conf/cfc_dev.config

@@ -11,7 +11,7 @@ singularity {
 
 process {
   executor = 'slurm'
-  queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' : 'compute' }
+  queue = 'qbic'
   scratch = 'true'
 }
 
@@ -25,4 +25,4 @@ params {
   max_memory = 1999.GB
   max_cpus = 128
   max_time = 140.h
-}
+}

conf/hki.config

@@ -0,0 +1,104 @@
+params {
+  config_profile_description = 'HKI clusters profile provided by nf-core/configs.'
+  config_profile_contact = 'James Fellows Yates (@jfy133)'
+  config_profile_url = 'https://leibniz-hki.de'
+}
+
+profiles {
+    apate {
+        params {
+            config_profile_description = 'apate HKI cluster profile provided by nf-core/configs'
+            config_profile_contact = 'James Fellows Yates (@jfy133)'
+            config_profile_url = 'https://leibniz-hki.de'
+            max_memory = 128.GB
+            max_cpus = 32
+            max_time = 1440.h
+        }
+        process {
+            executor = 'local'
+            maxRetries = 2
+        }
+
+        executor {
+            queueSize = 8
+        }
+
+        singularity {
+            enabled = true
+            autoMounts = true
+            cacheDir = '/Net/Groups/ccdata/apps/singularity'
+        }
+
+        conda {
+            cacheDir = '/Net/Groups/ccdata/apps/conda_envs'
+        }
+
+        cleanup = true
+    }
+
+    aither {
+        params {
+            config_profile_description = 'aither HKI cluster profile provided by nf-core/configs'
+            config_profile_contact = 'James Fellows Yates (@jfy133)'
+            config_profile_url = 'https://leibniz-hki.de'
+            max_memory = 128.GB
+            max_cpus = 32
+            max_time = 1440.h
+        }
+        process {
+            executor = 'local'
+            maxRetries = 2
+        }
+
+        executor {
+            queueSize = 8
+        }
+
+        singularity {
+            enabled = true
+            autoMounts = true
+            cacheDir = '/Net/Groups/ccdata/apps/singularity'
+        }
+
+        conda {
+            cacheDir = '/Net/Groups/ccdata/apps/conda_envs'
+        }
+
+        cleanup = true
+    }
+
+    arges {
+        params {
+            config_profile_description = 'arges HKI cluster profile provided by nf-core/configs'
+            config_profile_contact = 'James Fellows Yates (@jfy133)'
+            config_profile_url = 'https://leibniz-hki.de'
+            max_memory = 64.GB
+            max_cpus = 12
+            max_time = 1440.h
+        }
+        process {
+            executor = 'local'
+            maxRetries = 2
+        }
+
+        executor {
+            queueSize = 8
+        }
+
+        singularity {
+            enabled = true
+            autoMounts = true
+            cacheDir = '/Net/Groups/ccdata/apps/singularity'
+        }
+
+        conda {
+            cacheDir = '/Net/Groups/ccdata/apps/conda_envs'
+        }
+
+        cleanup = true
+    }
+
+    debug {
+        cleanup = false
+    }
+}

conf/pipeline/atacseq/sbc_sharc.config

@@ -0,0 +1,74 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+              
+              Sheffield Bioinformatics Core Configuration Profile - ShARC
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+					
+                  Custom Pipeline Resource Config for nf-core/atacseq
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+
+// process-specific resource requirements - reduced specification from those in atacseq/conf/base.config
+
+process {
+
+    withLabel:process_low {
+        cpus   = { check_max( 2 * task.attempt, 'cpus' ) }
+        memory = { check_max( 4.GB * task.attempt, 'memory' ) }
+        time   = { check_max( 4.h * task.attempt, 'time' ) }
+    }
+
+    withLabel:process_medium {
+        cpus   = { check_max( 4 * task.attempt, 'cpus' ) }
+        memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+        time   = { check_max( 6.h * task.attempt, 'time' ) }
+    }
+
+    withLabel:process_high {
+        cpus   = { check_max( 8 * task.attempt, 'cpus' ) }
+        memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+        time   = { check_max( 8.h * task.attempt, 'time' ) }
+    }
+
+    withLabel:process_long {
+        time   = { check_max( 12.h  * task.attempt, 'time' ) }
+    }
+
+}
+
+
+// function 'check_max()' to ensure that resource requirements don't go beyond maximum limit
+
+def check_max(obj, type) {
+  if (type == 'memory') {
+    try {
+      if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
+        return params.max_memory as nextflow.util.MemoryUnit
+      else
+        return obj
+    } catch (all) {
+      println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
+      return obj
+    }
+  } else if (type == 'time') {
+    try {
+      if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
+        return params.max_time as nextflow.util.Duration
+      else
+        return obj
+    } catch (all) {
+      println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
+      return obj
+    }
+  } else if (type == 'cpus') {
+    try {
+      return Math.min(obj, params.max_cpus as int)
+    } catch (all) {
+      println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
+      return obj
+    }
+  }
+}

conf/pipeline/chipseq/sbc_sharc.config

@@ -0,0 +1,74 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+              
+              Sheffield Bioinformatics Core Configuration Profile - ShARC
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+					
+                  Custom Pipeline Resource Config for nf-core/chipseq
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+
+// process-specific resource requirements - reduced specification from those in chipseq/conf/base.config
+
+process {
+
+    withLabel:process_low {
+        cpus   = { check_max( 2 * task.attempt, 'cpus' ) }
+        memory = { check_max( 4.GB * task.attempt, 'memory' ) }
+        time   = { check_max( 4.h * task.attempt, 'time' ) }
+    }
+
+    withLabel:process_medium {
+        cpus   = { check_max( 4 * task.attempt, 'cpus' ) }
+        memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+        time   = { check_max( 6.h * task.attempt, 'time' ) }
+    }
+
+    withLabel:process_high {
+        cpus   = { check_max( 8 * task.attempt, 'cpus' ) }
+        memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+        time   = { check_max( 8.h * task.attempt, 'time' ) }
+    }
+
+    withLabel:process_long {
+        time   = { check_max( 12.h  * task.attempt, 'time' ) }
+    }
+
+}
+
+
+// function 'check_max()' to ensure that resource requirements don't go beyond maximum limit
+
+def check_max(obj, type) {
+  if (type == 'memory') {
+    try {
+      if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
+        return params.max_memory as nextflow.util.MemoryUnit
+      else
+        return obj
+    } catch (all) {
+      println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
+      return obj
+    }
+  } else if (type == 'time') {
+    try {
+      if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
+        return params.max_time as nextflow.util.Duration
+      else
+        return obj
+    } catch (all) {
+      println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
+      return obj
+    }
+  } else if (type == 'cpus') {
+    try {
+      return Math.min(obj, params.max_cpus as int)
+    } catch (all) {
+      println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
+      return obj
+    }
+  }
+}

conf/pipeline/rnaseq/sbc_sharc.config

@@ -0,0 +1,79 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+              
+              Sheffield Bioinformatics Core Configuration Profile - ShARC
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+					
+                  Custom Pipeline Resource Config for nf-core/rnaseq
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+
+// process-specific resource requirements - reduced specification from those in rnaseq/conf/base.config
+
+process {
+
+    withLabel:process_low {
+        cpus   = { check_max( 2 * task.attempt, 'cpus' ) }
+        memory = { check_max( 4.GB * task.attempt, 'memory' ) }
+        time   = { check_max( 4.h * task.attempt, 'time' ) }
+    }
+
+    withLabel:process_medium {
+        cpus   = { check_max( 4 * task.attempt, 'cpus' ) }
+        memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+        time   = { check_max( 6.h * task.attempt, 'time' ) }
+    }
+
+    withLabel:process_high {
+        cpus   = { check_max( 8 * task.attempt, 'cpus' ) }
+        memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+        time   = { check_max( 8.h * task.attempt, 'time' ) }
+    }
+
+    withLabel:process_long {
+        time   = { check_max( 12.h  * task.attempt, 'time' ) }
+    }
+
+    withLabel:process_high_memory {
+        memory = { check_max( 60.GB * task.attempt, 'memory' ) }
+    }
+
+}
+
+
+// function 'check_max()' to ensure that resource requirements don't go beyond maximum limit
+
+def check_max(obj, type) {
+  if (type == 'memory') {
+    try {
+      if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
+        return params.max_memory as nextflow.util.MemoryUnit
+      else
+        return obj
+    } catch (all) {
+      println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
+      return obj
+    }
+  } else if (type == 'time') {
+    try {
+      if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
+        return params.max_time as nextflow.util.Duration
+      else
+        return obj
+    } catch (all) {
+      println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
+      return obj
+    }
+  } else if (type == 'cpus') {
+    try {
+      return Math.min(obj, params.max_cpus as int)
+    } catch (all) {
+      println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
+      return obj
+    }
+  }
+}
+

conf/pipeline/sarek/sbc_sharc.config

@@ -0,0 +1,114 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+              
+              Sheffield Bioinformatics Core Configuration Profile - ShARC
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+                    
+                  Custom Pipeline Resource Config for nf-core/sarek
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+
+// process-specific resource requirements - reduced specification from those in sarek/conf/base.config
+
+process {
+
+    
+    // process labels
+
+    withLabel:process_low {
+        cpus   = { check_max( 2 * task.attempt, 'cpus' ) }
+        memory = { check_max( 4.GB * task.attempt, 'memory' ) }
+        time   = { check_max( 4.h * task.attempt, 'time' ) }
+    }
+
+    withLabel:process_medium {
+        cpus   = { check_max( 4 * task.attempt, 'cpus' ) }
+        memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+        time   = { check_max( 6.h * task.attempt, 'time' ) }
+    }
+
+    withLabel:process_high {
+        cpus   = { check_max( 8 * task.attempt, 'cpus' ) }
+        memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+        time   = { check_max( 8.h * task.attempt, 'time' ) }
+    }
+
+    withLabel:process_long {
+        time   = { check_max( 12.h  * task.attempt, 'time' ) }
+    }
+
+    withLabel:process_high_memory {
+        memory = { check_max( 60.GB * task.attempt, 'memory' ) }
+    }
+
+
+    // process name
+
+    withName:'BWAMEM1_MEM|BWAMEM2_MEM' {
+        cpus    = { check_max( 12 * task.attempt, 'cpus' ) }
+        memory  = { check_max( 16.GB * task.attempt, 'memory' ) }
+        time    = { check_max( 8.h  * task.attempt, 'time' ) }
+    }
+
+    withName:'FASTP' {
+        cpus    = { check_max( 12 * task.attempt, 'cpus' ) }
+    }
+
+    withName:'FASTQC|FASTP|MOSDEPTH|SAMTOOLS_CONVERT' {
+        memory  = { check_max( 4.GB * task.attempt, 'memory' ) }
+    }
+
+    withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|SAMTOOLS_STATS' {
+        cpus    = { check_max( 4 * task.attempt, 'cpus' ) }
+    }
+
+    withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_GATHERBQSRREPORTS' {
+        memory  = { check_max( 16.GB * task.attempt, 'memory' ) }
+    }
+
+    withName:'GATK4_MARKDUPLICATES' {
+        memory  = { check_max( 16.GB * task.attempt, 'memory' ) }
+    }
+
+    withName:'FREEBAYES|SAMTOOLS_STATS|SAMTOOLS_INDEX|UNZIP' {
+        cpus    = { check_max( 1 * task.attempt, 'cpus' ) }
+    }
+
+}
+
+
+// function 'check_max()' to ensure that resource requirements don't go beyond maximum limit
+
+def check_max(obj, type) {
+  if (type == 'memory') {
+    try {
+      if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
+        return params.max_memory as nextflow.util.MemoryUnit
+      else
+        return obj
+    } catch (all) {
+      println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
+      return obj
+    }
+  } else if (type == 'time') {
+    try {
+      if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
+        return params.max_time as nextflow.util.Duration
+      else
+        return obj
+    } catch (all) {
+      println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
+      return obj
+    }
+  } else if (type == 'cpus') {
+    try {
+      return Math.min(obj, params.max_cpus as int)
+    } catch (all) {
+      println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
+      return obj
+    }
+  }
+}

conf/sage.config

@@ -30,11 +30,14 @@ aws {
   client {
     uploadChunkSize = 209715200
   }
+  batch {
+    maxParallelTransfers = 1
+  }
 }
 executor {
     name = 'awsbatch'
     // Ensure unlimited queue size on AWS Batch
-    queueSize = 100000
+    queueSize = 500
     // Slow down the rate at which AWS Batch jobs accumulate in
     // the queue (an attempt to prevent orphaned EBS volumes)
     submitRateLimit = '5 / 1 sec'

conf/sbc_sharc.config

@@ -0,0 +1,57 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+              
+              Sheffield Bioinformatics Core Configuration Profile - ShARC
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+          
+                            Base Institutional Configuration
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+
+params {
+  
+  // nf-core specific parameters displayed in header summary of each run
+
+  config_profile_description = 'Sheffield Bioinformatics Core - ShARC'
+  config_profile_contact = 'Lewis Quayle (l.quayle@sheffield.ac.uk)'
+  config_profile_url = 'https://docs.hpc.shef.ac.uk/en/latest/sharc/index.html'
+  
+  // hpc resource limits
+
+  max_cpus = 16
+  max_memory = 64.GB
+  max_time = 96.h
+
+}
+
+
+// container engine
+
+singularity {
+
+  enabled = true
+  autoMounts = true
+
+}
+
+
+// hpc configuration specific to ShARC
+
+process {
+
+  // scheduler
+
+  executor = 'sge'
+  penv = 'smp'
+  queue = { task.time <= 6.h ? 'shortint.q' : 'all.q' }
+  clusterOptions = { "-l rmem=${task.memory.toGiga()}G" }
+
+  // error and retry handling
+
+  errorStrategy = { task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish' }
+  maxRetries = 2
+
+}

docs/hki.md

@@ -0,0 +1,24 @@
+# nf-core/configs: HKI Configuration
+
+All nf-core pipelines have been successfully configured for use on clusters at the [Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute](https://www.leibniz-hki.de/en).
+
+To use, run the pipeline with `-profile hki,<cluster>`. This will download and launch the [`hki.config`](../conf/hki.config) which contains specific profiles for each cluster. The number of parallel jobs that run is currently limited to 8.
+
+The currently available profiles are:
+
+- apate (uses singularity, cleanup set to true by default)
+- arges (uses singularity, cleanup set to true by default)
+- aither (uses singularity, cleanup set to true by default)
+- debug (sets cleanup to false for debugging purposes, use e.g. `profile hki,<cluster>,debug`)
+
+Note that Nextflow is not necessarily installed by default on the HKI HPC cluster(s). You will need to install it into a directory you have write access to.
+Follow these instructions from the Nextflow documentation.
+
+- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
+
+All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline
+has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
+
+> NB: You will need an account to use the HKI HPC clusters in order to run the pipeline. If in doubt contact the ICT Service Desk.
+> NB: Nextflow will need to submit the jobs via SLURM to the HKI HPC clusters and as such the commands above will have to be executed on the login
+> node. If in doubt contact ICT.

docs/pipeline/atacseq/sbc_sharc.md

@@ -0,0 +1,11 @@
+# nf-core/configs: ATAC-Seq Specific Configuration - Sheffield Bioinformatics Core Facility ShARC
+
+Specific configuration for [nf-co.re/atacseq](https://nf-co.re/atacseq) pipeline
+
+## Usage
+
+To use, run nextflow with the pipeline using `-profile sbc_sharc` (note the single hyphen).
+
+This will download and launch the atacseq specific [`sbc_sharc.config`](../../../conf/pipeline/atacseq/sbc_sharc.config) which has been pre-configured with a setup suitable for the [University of Sheffield ShARC cluster](https://docs.hpc.shef.ac.uk/en/latest/index.html) and will automatically load the appropriate pipeline-specific configuration file.
+
+Example: `nextflow run nf-core/atacseq -profile sbc_sharc`

docs/pipeline/chipseq/sbc_sharc.md

@@ -0,0 +1,11 @@
+# nf-core/configs: ChIP-Seq Specific Configuration - Sheffield Bioinformatics Core Facility ShARC
+
+Specific configuration for [nf-co.re/chipseq](https://nf-co.re/chipseq) pipeline
+
+## Usage
+
+To use, run nextflow with the pipeline using `-profile sbc_sharc` (note the single hyphen).
+
+This will download and launch the chipseq specific [`sbc_sharc.config`](../../../conf/pipeline/chipseq/sbc_sharc.config) which has been pre-configured with a setup suitable for the [University of Sheffield ShARC cluster](https://docs.hpc.shef.ac.uk/en/latest/index.html) and will automatically load the appropriate pipeline-specific configuration file.
+
+Example: `nextflow run nf-core/chipseq -profile sbc_sharc`

docs/pipeline/rnaseq/sbc_sharc.md

@@ -0,0 +1,11 @@
+# nf-core/configs: RNA-Seq Specific Configuration - Sheffield Bioinformatics Core Facility ShARC
+
+Specific configuration for [nf-co.re/rnaseq](https://nf-co.re/rnaseq) pipeline
+
+## Usage
+
+To use, run nextflow with the pipeline using `-profile sbc_sharc` (note the single hyphen).
+
+This will download and launch the rnaseq specific [`sbc_sharc.config`](../../../conf/pipeline/rnaseq/sbc_sharc.config) which has been pre-configured with a setup suitable for the [University of Sheffield ShARC cluster](https://docs.hpc.shef.ac.uk/en/latest/index.html) and will automatically load the appropriate pipeline-specific configuration file.
+
+Example: `nextflow run nf-core/rnaseq -profile sbc_sharc`

docs/pipeline/sarek/sbc_sharc.md

@@ -0,0 +1,11 @@
+# nf-core/configs: Sarek Specific Configuration - Sheffield Bioinformatics Core Facility ShARC
+
+Specific configuration for [nf-co.re/sarek](https://nf-co.re/sarek) pipeline
+
+## Usage
+
+To use, run nextflow with the pipeline using `-profile sbc_sharc` (note the single hyphen).
+
+This will download and launch the sarek specific [`sbc_sharc.config`](../../../conf/pipeline/sarek/sbc_sharc.config) which has been pre-configured with a setup suitable for the [University of Sheffield ShARC cluster](https://docs.hpc.shef.ac.uk/en/latest/index.html) and will automatically load the appropriate pipeline-specific configuration file.
+
+Example: `nextflow run nf-core/sarek -profile sbc_sharc`

docs/sbc_sharc.md

@@ -0,0 +1,40 @@
+# nf-core/configs: Sheffield Bioinformatics Core Facility ShARC Configuration
+
+## Using the SBC_ShARC Institutional Configuration Profile
+
+To use [`sbc_sharc.config`](../conf/sbc_sharc.config), run nextflow with an nf-core pipeline using `-profile sbc_sharc` (note the single hyphen).
+
+This will download and launch [`sbc_sharc.config`](../conf/sbc_sharc.config) which has been pre-configured with a setup suitable for the ShARC cluster and will automatically load the appropriate pipeline-specific configuration file.
+
+The following nf-core pipelines have been successfully configured for use on the the [University of Sheffield ShARC cluster](https://docs.hpc.shef.ac.uk/en/latest/index.html):
+
+- [nf-co.re/atacseq](https://nf-co.re/atacseq)
+- [nf-co.re/chipseq](https://nf-co.re/chipseq)
+- [nf-co.re/rnaseq](https://nf-co.re/rnaseq)
+- [nf-co.re/sarek](https://nf-co.re/sarek)
+
+When using [`sbc_sharc.config`](../conf/sbc_sharc.config) with the pipelines listed above, the appropriate configuration file from the list below will be loaded automatically:
+
+- [atacseq sbc_sharc.config](../conf/pipeline/atacseq/sbc_sharc.config)
+- [chipseq sbc_sharc.config](../conf/pipeline/chipseq/sbc_sharc.config)
+- [rnaseq sbc_sharc.config](../conf/pipeline/rnaseq/sbc_sharc.config)
+- [sarek sbc_sharc.config](../conf/pipeline/sarek/sbc_sharc.config)
+
+The [`sbc_sharc.config`](../conf/sbc_sharc.config) configuration file might work with other nf-core pipelines as it stands but we cannot guarantee they will run without issue. We will be continuing to create, test and optimise configurations for new pipelines in the future.
+
+## A Note on Singularity Containers
+
+The [`sbc_sharc.config`](../conf/sbc_sharc.config) configuration file supports running nf-core pipelines with Singularity containers; Singularity images will be downloaded automatically before execution of the pipeline.
+
+When you run nextflow for the first time, Singularity will create a hidden directory `.singularity` in your `$HOME` directory `/home/$USER` which has very very limited (10GB) space available. It is therefore a good idea to create a directory somewhere else (e.g., `/data/$USER`) with more room and link the locations. To do this, run the following series of commands:
+
+```shell
+# change directory to $HOME
+cd $HOME
+
+# make the directory that will be linked to
+mkdir /data/$USER/.singularity
+
+# link the new directory with the existing one
+ln -s /data/$USER/.singularity .singularity
+```

nfcore_custom.config

@@ -44,6 +44,7 @@ profiles {
   google       { includeConfig "${params.custom_config_base}/conf/google.config" }
   hasta        { includeConfig "${params.custom_config_base}/conf/hasta.config" }
   hebbe        { includeConfig "${params.custom_config_base}/conf/hebbe.config" }
+  hki          { includeConfig "${params.custom_config_base}/conf/hki.config"}
   icr_davros   { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
   ifb_core     { includeConfig "${params.custom_config_base}/conf/ifb_core.config" }
   imperial     { includeConfig "${params.custom_config_base}/conf/imperial.config" }
@@ -65,6 +66,7 @@ profiles {
   sage         { includeConfig "${params.custom_config_base}/conf/sage.config" }
   sahmri       { includeConfig "${params.custom_config_base}/conf/sahmri.config" }
   sanger       { includeConfig "${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"}
   uct_hpc      { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }
   unibe_ibu    { includeConfig "${params.custom_config_base}/conf/unibe_ibu.config" }

pipeline/atacseq.config

@@ -0,0 +1,13 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/atacseq custom profile Nextflow config file
+ * -------------------------------------------------
+ * Config options for custom environments.
+ * Cluster-specific config options should be saved
+ * in the conf/pipeline/atacseq folder and imported
+ * under a profile name here.
+ */
+
+profiles {
+  sbc_sharc { includeConfig "${params.custom_config_base}/conf/pipeline/atacseq/sbc_sharc.config" }
+}

pipeline/chipseq.config

@@ -0,0 +1,13 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/chipseq custom profile Nextflow config file
+ * -------------------------------------------------
+ * Config options for custom environments.
+ * Cluster-specific config options should be saved
+ * in the conf/pipeline/chipseq folder and imported
+ * under a profile name here.
+ */
+
+profiles {
+  sbc_sharc { includeConfig "${params.custom_config_base}/conf/pipeline/chipseq/sbc_sharc.config" }
+}

pipeline/rnaseq.config

@@ -11,5 +11,6 @@
 profiles {
   eddie { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/eddie.config" }
   mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/mpcdf.config" }
+  sbc_sharc { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/sbc_sharc.config" }
   utd_sysbio { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/utd_sysbio.config" }
 }

pipeline/sarek.config

@@ -15,5 +15,6 @@ profiles {
   eddie { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/eddie.config" }
   icr_davros { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/icr_davros.config" }
   munin { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/munin.config" }
+  sbc_sharc { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/sbc_sharc.config" }
   uppmax { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/uppmax.config" }
 }