Merge branch 'master' into master

.github/workflows/main.yml

@@ -16,7 +16,7 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh']
+          profile: ['awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'utd_ganymede', 'uzh']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow
@@ -26,4 +26,5 @@ jobs:
       - name: Check ${{ matrix.profile }} profile
         env: 
           SCRATCH: '~'
+          NXF_GLOBAL_CONFIG: awsbatch.config
         run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }}

README.md

@@ -15,6 +15,7 @@ A repository for hosting Nextflow configuration files containing custom paramete
   * [Documentation](#documentation)
   * [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
 * [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config)
+  * [Pipeline-specific institutional documentation](#pipeline-specific-institutional-documentation)
   * [Pipeline-specific documentation](#pipeline-specific-documentation)
   * [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline)
   * [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files)
@@ -95,19 +96,21 @@ Currently documentation is available for the following systems:
 
 * [AWSBATCH](docs/awsbatch.md)
 * [BIGPURPLE](docs/bigpurple.md)
+* [BI](docs/bi.md)
 * [BINAC](docs/binac.md)
 * [CBE](docs/cbe.md)
-* [CCGA](docs/ccga.md)
 * [CCGA_DX](docs/ccga_dx.md)
 * [CCGA_MED](docs/ccga_med.md)
-* [CFC](docs/binac.md)
+* [CFC](docs/cfc.md)
 * [CRICK](docs/crick.md)
 * [CZBIOHUB_AWS](docs/czbiohub.md)
 * [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
 * [DENBI_QBIC](docs/denbi_qbic.md)
+* [EBC](docs/ebc.md)
 * [GENOTOUL](docs/genotoul.md)
 * [GENOUEST](docs/genouest.md)
 * [GIS](docs/gis.md)
+* [GOOGLE](docs/google.md)
 * [HEBBE](docs/hebbe.md)
 * [KRAKEN](docs/kraken.md)
 * [MUNIN](docs/munin.md)
@@ -117,6 +120,7 @@ Currently documentation is available for the following systems:
 * [SHH](docs/shh.md)
 * [UCT_HEX](docs/uct_hex.md)
 * [UPPMAX](docs/uppmax.md)
+* [UTD_GANYMEDE](docs/utd_ganymede.md)
 * [UZH](docs/uzh.md)
 
 ### Uploading to `nf-core/configs`
@@ -157,18 +161,28 @@ Each configuration file will add new params and overwrite the params already exi
 
 Note that pipeline-specific configs are not required and should only be added if needed.
 
-### Pipeline-specific documentation
+### Pipeline-specific institutional documentation
 
-Currently documentation is available for the following pipeline within the specific profile:
+Currently documentation is available for the following pipelines within specific profiles:
 
 * ampliseq
   * [BINAC](docs/pipeline/ampliseq/binac.md)
+  * [UPPMAX](docs/pipeline/ampliseq/uppmax.md)
 * eager
   * [SHH](docs/pipeline/eager/shh.md)
+* rnafusion
+  * [MUNIN](docs/pipeline/rnafusion/munin.md)
 * sarek
   * [MUNIN](docs/pipeline/sarek/munin.md)
   * [UPPMAX](docs/pipeline/sarek/uppmax.md)
 
+### Pipeline-specific documentation
+
+Currently documentation is available for the following pipeline:
+
+* viralrecon
+  * [genomes](docs/pipeline/viralrecon/genomes.md)
+
 ### Enabling pipeline-specific configs within a pipeline
 
 :warning: **This has to be done on a fork of the `nf-core/<PIPELINE>` repository.**

conf/bi.config

@@ -0,0 +1,18 @@
+params{
+  config_profile_description = 'Boehringer Ingelheim internal profile provided by nf-core/configs.'
+  config_profile_contact = 'Alexander Peltzer (@apeltzer)'
+  config_profile_url = 'https://www.boehringer-ingelheim.com/'
+}
+params.globalConfig = determine_global_config()
+
+includeConfig params.globalConfig
+
+def determine_global_config() {
+    if( System.getenv('NXF_GLOBAL_CONFIG') == null)
+    {
+        def errorMessage = "ERROR: Environment variable NXF_GLOBAL_CONFIG is missing. Set it to point to global.config file."
+        System.err.println(errorMessage)
+        throw new Exception(errorMessage)
+    }
+    return System.getenv('NXF_GLOBAL_CONFIG')   
+}

conf/cbe.config

@@ -14,7 +14,7 @@ process {
 
 singularity {
   enabled = true
-  cacheDir = '/scratch-cbe/shared/containers'
+  cacheDir = '/resources/containers'
 }
 
 params {

conf/ccga.config

@@ -1,41 +0,0 @@
-//Profile config names for nf-core/configs
-params {
-  config_profile_description = 'CCGA cluster profile provided by nf-core/configs.'
-  config_profile_contact = 'Marc Hoeppner (@marchoeppner)'
-  config_profile_url = 'https://www.ccga.uni-kiel.de/'
-}
-
-/*
- * -------------------------------------------------
- *  Nextflow config file for CCGA cluster in Kiel
- * -------------------------------------------------
- */
-
-singularity {
-  enabled = true
-  runOptions = "-B /ifs -B /scratch -B /work_beegfs"
-  cacheDir = "/ifs/data/nfs_share/ikmb_repository/singularity_cache/"
-}
-
-executor {
-  queueSize=100
-}
-
-process {
-
-  // Global process config
-  executor = 'slurm'
-  queue = 'ikmb_a'
-
-  clusterOptions = { "--qos=ikmb_a" }
-
-}
-
-params {
-  // illumina iGenomes reference file paths on RZCluster
-  igenomes_base = '/ifs/data/nfs_share/ikmb_repository/references/iGenomes/references/'
-  saveReference = true
-  max_memory = 128.GB
-  max_cpus = 16
-  max_time = 120.h
-}

conf/cfc.config

@@ -1,7 +1,7 @@
 //Profile config names for nf-core/configs
 params {
   config_profile_description = 'QBiC Core Facility cluster profile provided by nf-core/configs.'
-  config_profile_contact = 'Alexander Peltzer (@apeltzer)'
+  config_profile_contact = 'Gisela Gabernet (@ggabernet)'
   config_profile_url = 'http://qbic.uni-tuebingen.de/'
 }
 
@@ -13,6 +13,8 @@ singularity {
 process {
   beforeScript = 'module load devel/singularity/3.4.2'
   executor = 'slurm'
+  queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' : 'compute' }
+  scratch = 'true'
 }
 
 weblog{
@@ -22,7 +24,7 @@ weblog{
 
 params {
   igenomes_base = '/nfsmounts/igenomes'
-  max_memory = 498.GB
+  max_memory = 1999.GB
-  max_cpus = 20
+  max_cpus = 128
   max_time = 140.h
 }

conf/cfc_dev.config

@@ -0,0 +1,29 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'QBiC Core Facility cluster dev profile without container cache provided by nf-core/configs.'
+  config_profile_contact = 'Gisela Gabernet (@ggabernet)'
+  config_profile_url = 'http://qbic.uni-tuebingen.de/'
+}
+
+singularity {
+  enabled = true
+}
+
+process {
+  beforeScript = 'module load devel/singularity/3.4.2'
+  executor = 'slurm'
+  queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' : 'compute' }
+  scratch = 'true'
+}
+
+weblog{
+  enabled = true
+  url = 'https://services.qbic.uni-tuebingen.de/flowstore/workflows'
+}
+
+params {
+  igenomes_base = '/nfsmounts/igenomes'
+  max_memory = 1999.GB
+  max_cpus = 128
+  max_time = 140.h
+}

conf/czbiohub_aws.config

@@ -50,6 +50,7 @@ params {
   // No final slash because it's added later
   gencode_base = "s3://czbiohub-reference/gencode"
   transgenes_base = "s3://czbiohub-reference/transgenes"
+  refseq_base = "s3://czbiohub-reference/ncbi/genomes/refseq/"
 
   // AWS configurations
   awsregion = "us-west-2"
@@ -79,6 +80,12 @@ params {
       transcript_fasta  = "${params.gencode_base}/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa"
       star             = "${params.gencode_base}/mouse/vM21/STARIndex/"
     }
+    'AaegL5.0' {
+      fasta            = "${params.refseq_base}/invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna"
+      gtf              = "${params.refseq_base}/invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf"
+      bed              = "${params.refseq_base}/invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed"
+      star             = "${params.refseq_base}/invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/"
+    }
   }
 
   transgenes {

conf/ebc.config

@@ -0,0 +1,25 @@
+    //Profile config names for nf-core/configs
+    params {
+      config_profile_description = 'Generic Estonian Biocentre profile provided by nf-core/configs.'
+      config_profile_contact = 'Marcel Keller (@marcel-keller)'
+      config_profile_url = 'https://genomics.ut.ee/en/about-us/estonian-biocentre'
+    }
+
+    cleanup = true
+
+    conda {
+        cacheDir = '/ebc_data/nf-core/conda'
+    }
+    process {
+        executor = 'slurm'
+        conda = "$baseDir/environment.yml" 
+        beforeScript = 'module load nextflow'
+    }
+    executor {
+        queueSize = 16
+    }
+    params {
+      max_memory = 12.GB
+      max_cpus = 20
+      max_time = 120.h
+    }

conf/google.config

@@ -0,0 +1,21 @@
+// Nextflow config file for running on Google Cloud Life Sciences
+params {
+  config_profile_description = 'Google Cloud Life Sciences Profile'
+  config_profile_contact = 'Evan Floden, Seqera Labs (@evanfloden)'
+  config_profile_url = 'https://cloud.google.com/life-sciences'
+
+  google_zone = 'europe-west2-c'
+  google_bucket = false
+  google_debug = false
+  google_preemptible = true
+}
+
+process.executor = 'google-lifesciences'
+google.zone = params.google_zone
+google.lifeSciences.debug = params.google_debug
+workDir = params.google_bucket
+google.lifeSciences.preemptible = params.google_preemptible
+if (google.lifeSciences.preemptible) {
+  process.errorStrategy = { task.exitStatus==14 ? 'retry' : 'terminate' }
+  process.maxRetries = 5
+}

conf/pipeline/ampliseq/uppmax.config

@@ -0,0 +1,15 @@
+// Profile config names for nf-core/configs
+
+params {
+  // Specific nf-core/configs params
+  config_profile_contact = 'Daniel Lundin (daniel.lundin@lnu.se)'
+  config_profile_description = 'nf-core/ampliseq UPPMAX profile provided by nf-core/configs'
+}
+
+withName: make_SILVA_132_16S_classifier {
+  clusterOptions = { "-A $params.project -C fat -p node -N 1 ${params.clusterOptions ?: ''}" }
+}
+
+withName: classifier {
+  clusterOptions = { "-A $params.project -C fat -p node -N 1 ${params.clusterOptions ?: ''}" }
+}

conf/pipeline/eager/shh.config

@@ -5,6 +5,10 @@ params {
   config_profile_contact = 'James Fellows Yates (@jfy133)'
   config_profile_description = 'nf-core/eager SHH profile provided by nf-core/configs'
   igenomes_base = "/projects1/public_data/igenomes/"
+  
+  // default BWA
+   bwaalnn = 0.04
+   bwaalnl = 32
 }
 
 // Specific nf-core/eager process configuration
@@ -17,3 +21,27 @@ process {
     queue = { task.memory > 756.GB ? 'supercruncher' : 'long' }
   }
 }
+
+profiles {
+  pathogen_loose {
+    params {
+      config_profile_description = 'Pathogen (loose) MPI-SHH profile, provided by nf-core/configs.'
+      bwaalnn = 0.01
+      bwaalnl = 16
+    }
+  }
+  pathogen_strict {
+    params {
+      config_profile_description = 'Pathogen (strict) MPI-SHH SDAG profile, provided by nf-core/configs.'
+      bwaalnn = 0.1
+      bwaalnl = 32
+     }
+  }
+  human {
+      params {
+      config_profile_description = 'Human MPI-SHH SDAG profile, provided by nf-core/configs.'
+      bwaalnn = 0.01
+      bwaalnl = 16500
+     }
+  }
+}

conf/pipeline/rnafusion/munin.config

@@ -0,0 +1,10 @@
+// rnafusion/munin specific profile config
+
+params {
+  max_cpus = 24
+  max_memory = 256.GB
+  max_time = 72.h
+
+  // Paths
+  genomes_base = '/data1/references/rnafusion/dev/'
+}

conf/pipeline/sarek/munin.config

@@ -1,4 +1,4 @@
-// Profile config names for nf-core/configs
+// sarek/munin specific profile config
 
 params {
   // Specific nf-core/configs params
@@ -7,16 +7,22 @@ params {
 
   // Specific nf-core/sarek params
   annotation_cache  = true
+  cadd_cache        = true
+  cadd_indels       = '/data1/cache/CADD/v1.4/InDels.tsv.gz'
+  cadd_indels_tbi   = '/data1/cache/CADD/v1.4/InDels.tsv.gz.tbi'
+  cadd_wg_snvs      = '/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz'
+  cadd_wg_snvs_tbi  = '/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz.tbi'
   pon               = '/data1/PON/vcfs/BTB.PON.vcf.gz'
   pon_index         = '/data1/PON/vcfs/BTB.PON.vcf.gz.tbi'
-  snpEff_cache = '/data1/cache/snpEff/'
+  snpeff_cache      = '/data1/cache/snpEff/'
   vep_cache         = '/data1/cache/VEP/'
+  vep_cache_version = '95'
 }
 
 // Specific nf-core/sarek process configuration
 process {
   withLabel:sentieon {
-    module = {params.sentieon ? 'sentieon/201808.05' : null}
+    module    = {params.sentieon ? 'sentieon/201911.00' : null}
     container = {params.sentieon ? null : container}
   }
 }

conf/pipeline/sarek/uppmax.config

@@ -9,9 +9,13 @@ params {
   igenomeIgnore = true
   genomes_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : '/sw/data/uppnex/ToolBox/hg38bundle'
 }
+
+def hostname = "hostname".execute().text.trim()
+
 if (hostname ==~ "r.*") {
   params.singleCPUmem = 6400.MB
 }
+
 if (hostname ==~ "i.*") {
   params.singleCPUmem = 15.GB
 }

conf/pipeline/viralrecon/genomes.config

@@ -0,0 +1,20 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/viralrecon custom profile Nextflow config file
+ * -------------------------------------------------
+ * Defines viral reference genomes for all environments.
+ */
+ 
+params {
+  // Genome reference file paths
+  genomes {
+    'NC_045512.2' {
+      fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz"
+      gff   = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.gff.gz"
+    }
+    'MN908947.3' {
+      fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz"
+      gff   = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz"
+    }
+  }
+}

conf/shh.config

@@ -3,6 +3,11 @@ params {
   config_profile_description = 'Generic MPI-SHH cluster(s) profile provided by nf-core/configs.'
   config_profile_contact = 'James Fellows Yates (@jfy133), Maxime Borry (@Maxibor)'
   config_profile_url = 'https://shh.mpg.de'
+  max_memory = 256.GB
+  max_cpus = 32
+  max_time = 720.h
+  //Illumina iGenomes reference file path
+  igenomes_base = "/projects1/public_data/igenomes/"
 }
 
 cleanup = true
@@ -23,21 +28,17 @@ executor {
     queueSize = 16
 }
 
-params {
-  max_memory = 256.GB
-  max_cpus = 32
-  max_time = 720.h
-  //Illumina iGenomes reference file path
-  igenomes_base = "/projects1/public_data/igenomes/"
-}
-
 profiles {
   cdag {
-      config_profile_description = 'MPI-SHH CDAG profile, provided by nf-core/configs.'
+    params {
+      config_profile_description = 'CDAG MPI-SHH profile, provided by nf-core/configs.'
+    }
   }
   sdag {
-      config_profile_description = 'MPI-SHH SDAG profile, provided by nf-core/configs.'
+    params {
+      config_profile_description = 'SDAG MPI-SHH profile, provided by nf-core/configs.'
       max_memory = 2.TB
       max_cpus = 128
      }
   }
+}

conf/uppmax.config

@@ -26,7 +26,7 @@ params {
 
 def hostname = "hostname".execute().text.trim()
 
-if (hostname ==~ "b.*") {
+if (hostname ==~ "b.*" || hostname ==~ "s.*") {
   params.max_memory = 109.GB
 }
 

conf/utd_ganymede.config

@@ -0,0 +1,24 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'University of Texas at Dallas HPC cluster profile provided by nf-core/configs'
+  config_profile_contact = 'Edmund Miller(@emiller88)'
+  config_profile_url = 'http://docs.oithpc.utdallas.edu/'
+}
+
+singularity {
+  enabled = true
+  envWhitelist='SINGULARITY_BINDPATH'
+  autoMounts = true
+}
+
+process {
+  beforeScript = 'module load singularity/2.4.5'
+  executor = 'slurm'
+  queue = 'genomics'
+}
+
+params {
+  max_memory = 32.GB
+  max_cpus = 16
+  max_time = 48.h
+}

docs/bi.md

@@ -0,0 +1,9 @@
+# nf-core/configs: BI Configuration
+
+All nf-core pipelines have been successfully configured for use at Boehringer Ingelheim.
+
+To use, run the pipeline with `-profile bi`. This will download and launch the [`bi.config`](../conf/bi.config) which has been pre-configured with a setup suitable for the BI systems. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
+
+Before running the pipeline you will need to follow the internal documentation to run Nextflow on our systems. Similar to that, you need to set an environment variable `NXF_GLOBAL_CONFIG` to the path of the internal global config which is not publicly available here.
+
+>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.

docs/ccga.md

@@ -1,18 +0,0 @@
-# nf-core/configs: CCGA Configuration
-
-Deployment and testing of nf-core pipelines at the CCGA cluster is on-going.
-
-To use, run the pipeline with `-profile ccga`. This will download and launch the [`ccga.config`](../conf/ccga.config) which has been pre-configured with a setup suitable for the CCGA cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
-
-Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on the cluster. You can do this by issuing the commands below:
-
-```bash
-## Load Nextflow and Singularity environment modules
-module purge
-module load IKMB
-module load Java/1.8.0
-module load Nextflow
-module load singularity3.1.0
-```
-
->NB: Access to the CCGA cluster is restricted to IKMB/CCGA employes. Please talk to Marc Hoeppner to get access (@marchoeppner).

docs/cfc.md

@@ -10,8 +10,10 @@ Before running the pipeline you will need to load Nextflow and Singularity using
 ## Load Nextflow and Singularity environment modules
 module purge
 module load devel/java_jdk/1.8.0u121
-module load qbic/singularity_slurm/3.0.3
+module load devel/singularity/3.4.2
 ```
 
 >NB: You will need an account to use the HPC cluster CFC in order to run the pipeline. If in doubt contact IT.
 >NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.
+
+The queues are set to be `qbic` or `compute` and will be chosen automatically for you depending on your job submission.

docs/ebc.md

@@ -0,0 +1,11 @@
+# nf-core/configs: EBC Configuration
+
+All nf-core pipelines have been successfully configured for use on the [Estonian Biocentre (EBC)](https://genomics.ut.ee/en/about-us/estonian-biocentre) cluster at the [High Performance Computing Center](https://hpc.ut.ee/en) of the the University of Tartu.
+To use, run the pipeline with `-profile ebc`. This will download and launch the [`ebc.config`](../conf/ebc.config) which has been pre-configured with a setup suitable for the EBC cluster. Using this profile, currently, a conda environment containing all of the required software will be downloaded and stored in a central location.
+
+> :warning: You must install your own [conda binary](conda.io) to run nf-core pipelines in a conda environment. Running with singularity will be added soon.
+
+The profile will put a maximum job limit of 12 GB, 20 CPUs and a maximum wall time of 120 hours.
+
+NB: You will need an account to use the HPC cluster on EBC cluster in order to run the pipeline. If in doubt contact IT.
+NB: Nextflow will need to submit the jobs via the SLURM scheduler to the HPC cluster and as such the commands above will have to be executed on one of the head nodes. If in doubt contact IT.

docs/google.md

@@ -0,0 +1,37 @@
+# nf-core/configs: Google Cloud Life Sciences Configuration
+
+To be used with the `google` profile by specifying the `-profile google` when running nf-core pipelines.
+
+![Google Cloud](images/google-cloud-logo.svg "https://cloud.google.com/life-sciences/docs/tutorials/nextflow")
+
+## Quick Start
+
+```bash
+GOOGLE_APPLICATION_CREDENTIALS=<your_key>.json
+NXF_MODE=google
+nextflow run nf-core/rnaseq -profile test,google --google_bucket <gs://your_bucket/work>
+```
+
+### Required Parameters
+
+#### `--google-bucket`
+
+The Google Cloud Storage bucket location to be used as a Nextflow work directory. Can also be specified with (`-w gs://your_bucket/work`).
+
+### Optional Parameters
+
+#### `--google-zone`
+
+The Google zone where the computation is executed in Compute Engine VMs. Multiple zones can be provided separating them by a comma. Default (`europe-west2-c`).
+
+#### `--google-preemptible`
+
+Enables the usage of preemptible virtual machines with a retry error statergy for up to 5 retries. Default (`true`).
+
+#### `--google-debug`
+
+Copies the /google debug directory from the VM to the task bucket directory. Useful for debugging. Default (`false`).
+
+## Cloud Life Sciences Setup
+
+Please refer to the [Google Cloud](https://cloud.google.com/life-sciences/docs/tutorials/nextflow) and [Nextflow](https://www.nextflow.io/docs/latest/google.html#cloud-life-sciences) documentation which describe how to setup the Google Cloud environment.

docs/images/google-cloud-logo.svg

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docs/pipeline/ampliseq/binac.md

@@ -6,7 +6,7 @@ Extra specific configuration for the ampliseq pipeline.
 
 To use, run the pipeline with `-profile binac`.
 
-This will download and launch the ampliseq specific [`binac.config`](../conf/pipeline/ampliseq/binac.config) which has been pre-configured with a setup suitable for the BINAC cluster.
+This will download and launch the ampliseq specific [`binac.config`](../../../conf/pipeline/ampliseq/binac.config) which has been pre-configured with a setup suitable for the BINAC cluster.
 
 Example: `nextflow run nf-core/ampliseq -profile binac`
 

docs/pipeline/ampliseq/uppmax.md

@@ -0,0 +1,17 @@
+# nf-core/configs: uppmax ampliseq specific configuration
+
+Extra specific configuration for the ampliseq pipeline.
+
+## Usage
+
+To use, run the pipeline with `-profile uppmax`.
+
+This will download and launch the ampliseq specific [`uppmax.config`](../../../conf/pipeline/ampliseq/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX cluster.
+
+Example: `nextflow run nf-core/ampliseq -profile uppmax`
+
+## ampliseq specific configurations for uppmax
+
+Specific configurations for UPPMAX has been made for ampliseq.
+
+* Makes sure that a fat node is allocated for training and applying a Bayesian classifier.

docs/pipeline/eager/shh.md

@@ -6,7 +6,7 @@ Extra specific configuration for eager pipeline
 
 To use, run the pipeline with `-profile shh`.
 
-This will download and launch the eager specific [`shh.config`](../conf/pipeline/eager/shh.config) which has been pre-configured with a setup suitable for the shh cluster.
+This will download and launch the eager specific [`shh.config`](../../../conf/pipeline/eager/shh.config) which has been pre-configured with a setup suitable for the shh cluster.
 
 Example: `nextflow run nf-core/eager -profile shh`
 
@@ -14,4 +14,5 @@ Example: `nextflow run nf-core/eager -profile shh`
 
 Specific configurations for shh has been made for eager.
 
-* If running with the MALT module turned on, the MALT process by default will be sent  to the long queue with a resource requirement minimum of 725GB and 64 cores. If this fails, the process will be tried once more only and sent to the supercruncher queue. The module will not retry after this, and pipeline will fail.
+* If running with the MALT module turned on, the MALT process by default will be sent  to the long queue with a resource requirement minimum of 725GB and 64 cores. If this fails, the process will be tried once more only and sent to the supercruncher queue. The module will not retry after this, and pipeline will fail. Note, this will only work on SDAG.
+* Provides additional group specific profiles, which adapt the `bwa aln` mapping parameters to each context: `pathogens_loose` (`-l 0.01 -n 16`), `pathogens_strict` (`-l 32, -n 0.1`) and `human` (`-l 16500, -n 0.01`).

docs/pipeline/rnafusion/munin.md

@@ -0,0 +1,18 @@
+# nf-core/configs: MUNIN rnafusion specific configuration
+
+Extra specific configuration for rnafusion pipeline
+
+## Usage
+
+To use, run the pipeline with `-profile munin`.
+
+This will download and launch the rnafusion specific [`munin.config`](../../../conf/pipeline/rnafusion/munin.config) which has been pre-configured with a setup suitable for the `MUNIN` cluster.
+
+Example: `nextflow run nf-core/rnafusion -profile munin`
+
+## rnafusion specific configurations for MUNIN
+
+Specific configurations for `MUNIN` has been made for rnafusion.
+
+* `cpus`, `memory` and `time` max requirements.
+* Paths to specific references and indexes

docs/pipeline/sarek/munin.md

@@ -6,17 +6,22 @@ Extra specific configuration for sarek pipeline
 
 To use, run the pipeline with `-profile munin`.
 
-This will download and launch the sarek specific [`munin.config`](../conf/pipeline/sarek/munin.config) which has been pre-configured with a setup suitable for the MUNIN cluster.
+This will download and launch the sarek specific [`munin.config`](../../../conf/pipeline/sarek/munin.config) which has been pre-configured with a setup suitable for the `MUNIN` cluster.
 
 Example: `nextflow run nf-core/sarek -profile munin`
 
 ## Sarek specific configurations for MUNIN
 
-Specific configurations for MUNIN has been made for sarek.
+Specific configurations for `MUNIN` has been made for sarek.
 
-* Params `annotation_cache` set to `true`
+* Params `annotation_cache` and `cadd_cache` set to `true`
-* Path to `snpEff_cache`: `/data1/cache/snpEff/`
+* Params `vep_cache_version` set to `95`
+* Path to `snpeff_cache`: `/data1/cache/snpEff/`
 * Path to `vep_cache`: `/data1/cache/VEP/`
 * Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz`
 * Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi`
+* Path to `cadd_indels`: `/data1/cache/CADD/v1.4/InDels.tsv.gz`
+* Path to `cadd_indels_tbi`: `/data1/cache/CADD/v1.4/InDels.tsv.gz.tbi`
+* Path to `cadd_wg_snvs`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz`
+* Path to `cadd_wg_snvs_tbi`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz.tbi`
 * Load module `Sentieon` for Processes with `sentieon` labels

docs/pipeline/sarek/uppmax.md

@@ -6,7 +6,7 @@ Extra specific configuration for sarek pipeline
 
 To use, run the pipeline with `-profile uppmax`.
 
-This will download and launch the sarek specific [`uppmax.config`](../conf/pipeline/sarek/uppmax.config) which has been pre-configured with a setup suitable for uppmax clusters.
+This will download and launch the sarek specific [`uppmax.config`](../../../conf/pipeline/sarek/uppmax.config) which has been pre-configured with a setup suitable for uppmax clusters.
 
 Example: `nextflow run nf-core/sarek -profile uppmax`
 

docs/pipeline/viralrecon/genomes.md

@@ -0,0 +1,9 @@
+# nf-core/configs: viralrecon specific configuration
+
+Extra specific configuration for viralrecon pipeline
+
+## Usage
+
+Will be used automatically when running the pipeline with the shared configs in the nf-core/configs repository
+
+This will download and launch the viralrecon specific [`viralrecon.config`](../../../conf/pipeline/viralrecon/genomes.config) which has been pre-configured with custom genomes.

docs/shh.md

@@ -2,7 +2,7 @@
 
 All nf-core pipelines have been successfully configured for use on the Department of Archaeogenetic's SDAG/CDAG clusters at the [Max Planck Institute for the Science of Human History (MPI-SHH)](http://shh.mpg.de).
 
-To use, run the pipeline with `-profile ssh`. You can further with optimise submissions by specifying which cluster you are using with `-profile shh,sdag` or `-profile ssh,cdag`. This will download and launch the [`shh.config`](../conf/shh.config) which has been pre-configured with a setup suitable for the SDAG and CDAG clusters respectively. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. The image will currently be centrally stored here:
+To use, run the pipeline with `-profile shh`. You can further with optimise submissions by specifying which cluster you are using with `-profile shh,sdag` or `-profile shh,cdag`. This will download and launch the [`shh.config`](../conf/shh.config) which has been pre-configured with a setup suitable for the SDAG and CDAG clusters respectively. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. The image will currently be centrally stored here:
 
 ```bash
 /projects1/singularity_scratch/cache/
@@ -10,7 +10,7 @@ To use, run the pipeline with `-profile ssh`. You can further with optimise subm
 
 however this will likely change to a read-only directory in the future that will be managed by the IT team.
 
-This configuration will automatically choose the correct SLURM queue (`short`,`medium`,`long`) depending on the time and memory required by each process. `-profile ssh,sdag` additionally allows for submission of jobs to the `supercruncher` queue when a job's requested memory exceeds 756GB.
+This configuration will automatically choose the correct SLURM queue (`short`,`medium`,`long`) depending on the time and memory required by each process. `-profile shh,sdag` additionally allows for submission of jobs to the `supercruncher` queue when a job's requested memory exceeds 756GB.
 
 >NB: You will need an account and VPN access to use the cluster at MPI-SHH in order to run the pipeline. If in doubt contact the IT team.
 >NB: Nextflow will need to submit the jobs via SLURM to the clusters and as such the commands above will have to be executed on one of the head nodes. If in doubt contact IT.

docs/utd_ganymede.md

@@ -0,0 +1,18 @@
+# nf-core/configs: UTD Ganymede Configuration
+
+All nf-core pipelines have been successfully configured for use on the Ganymede HPC cluster at the [The Univeristy of Texas at Dallas](https://www.utdallas.edu/).
+
+To use, run the pipeline with `-profile utd_ganymede`. This will download and launch the [`utd_ganymede.config`](../conf/utd_ganymede.config) which has been pre-configured with a setup suitable for the Ganymede HPC cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
+
+Before running the pipeline you will need to load Singularity using the environment module system on Ganymede. You can do this by issuing the commands below:
+
+```bash
+## Singularity environment modules
+module purge
+module load singularity
+```
+
+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 HPC cluster on Ganymede in order to run the pipeline. If in doubt contact Ganymedeadmins.
+>NB: Nextflow will need to submit the jobs via SLURM to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact GanymedeAdmins.

nfcore_custom.config

@@ -11,20 +11,23 @@
 //Please use a new line per include Config section to allow easier linting/parsing. Thank you.
 profiles {
   awsbatch     { includeConfig "${params.custom_config_base}/conf/awsbatch.config" }
+  bi           { includeConfig "${params.custom_config_base}/conf/bi.config" }
   bigpurple    { includeConfig "${params.custom_config_base}/conf/bigpurple.config" }
   binac        { includeConfig "${params.custom_config_base}/conf/binac.config" }
   cbe          { includeConfig "${params.custom_config_base}/conf/cbe.config" }
-  ccga         { includeConfig "${params.custom_config_base}/conf/ccga.config" }
   ccga_dx      { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" }
   ccga_med     { includeConfig "${params.custom_config_base}/conf/ccga_med.config" }
   cfc          { includeConfig "${params.custom_config_base}/conf/cfc.config" }
+  cfc_dev      { includeConfig "${params.custom_config_base}/conf/cfc_dev.config" }
   crick        { includeConfig "${params.custom_config_base}/conf/crick.config" }
   czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
   czbiohub_aws_highpriority {
                  includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config";
                  includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config"}
+  ebc          { includeConfig "${params.custom_config_base}/conf/ebc.config" }
   icr_davros   { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
   genotoul     { includeConfig "${params.custom_config_base}/conf/genotoul.config" }
+  google       { includeConfig "${params.custom_config_base}/conf/google.config" }
   denbi_qbic   { includeConfig "${params.custom_config_base}/conf/denbi_qbic.config" }
   genouest     { includeConfig "${params.custom_config_base}/conf/genouest.config" }
   gis          { includeConfig "${params.custom_config_base}/conf/gis.config" }
@@ -37,6 +40,7 @@ profiles {
   shh          { includeConfig "${params.custom_config_base}/conf/shh.config" }
   uct_hex      { includeConfig "${params.custom_config_base}/conf/uct_hex.config" }
   uppmax       { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
+  utd_ganymede { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" }
   uzh          { includeConfig "${params.custom_config_base}/conf/uzh.config" }
 }
 
@@ -46,11 +50,14 @@ profiles {
 params {
   // This is a groovy map, not a nextflow parameter set
   hostnames = [
+    binac: ['.binac.uni-tuebingen.de'],
     cbe: ['.cbe.vbc.ac.at'],
+    cfc: ['.hpc.uni-tuebingen.de'],
     crick: ['.thecrick.org'],
     icr_davros: ['.davros.compute.estate'],
     genotoul: ['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'],
     genouest: ['.genouest.org'],
-    uppmax: ['.uppmax.uu.se']
+    uppmax: ['.uppmax.uu.se'],
+    utd_ganymede: ['ganymede.utdallas.edu']
   ]
 }

pipeline/ampliseq.config

@@ -10,4 +10,5 @@
 
 profiles {
   binac { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/binac.config" }
+  uppmax { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/uppmax.config" }
 }

pipeline/rnafusion.config

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

pipeline/viralrecon.config

@@ -0,0 +1,7 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/viralrecon custom profile Nextflow config file
+ * -------------------------------------------------
+ */
+
+includeConfig "${params.custom_config_base}/conf/pipeline/viralrecon/genomes.config"