Merge remote-tracking branch 'upstream/master' into UPPMAX

.github/workflows/main.yml

@@ -16,7 +16,7 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'utd_ganymede', 'uzh']
+          profile: ['awsbatch', '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

README.md

@@ -167,6 +167,8 @@ Currently documentation is available for the following pipeline within the speci
   * [BINAC](docs/pipeline/ampliseq/binac.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)

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/'
 }
 

conf/cfc_dev.config

@@ -0,0 +1,28 @@
+//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' }
+}
+
+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/pipeline/rnafusion/munin.config

@@ -0,0 +1,60 @@
+// rnafusion/munin specific profile config
+
+params {
+  max_cpus = 24
+  max_memory = 256.GB
+  max_time = 72.h
+  container_version = '1.1.0'
+
+  // Tool versions
+  arriba_version = '1.1.0'
+  ericscript_version = '0.5.5'
+  fusioncatcher_version = '1.20'
+  fusion_inspector_version = '1.3.1-star2.7.0f'
+  pizzly_version = '0.37.3'
+  squid_version = '1.5-star2.7.0f'
+  star_fusion_version = '1.6.0'
+
+  // Paths
+  reference_base = '/data1/references/rnafusion'
+  containerPath = "file:///data1/containers/rnafusion_containers_v${container_version}"
+  containerPathCommon = "file:///data1/containers/rnafusion_common"
+  
+  // References
+  fasta = "${params.reference_base}/1.1.0/Homo_sapiens.GRCh38_r97.all.fa"
+  gtf = "${params.reference_base}/1.1.0/Homo_sapiens.GRCh38_r97.gtf"
+  transcript = "${params.reference_base}/1.1.0/Homo_sapiens.GRCh38_r97.cdna.all.fa.gz"
+  databases = "${params.reference_base}/1.1.0/databases"
+  
+  star_index = "${params.reference_base}/1.1.0/star_index/star"
+  arriba_ref = "${params.reference_base}/arriba_ref"
+  fusioncatcher_ref = "${params.reference_base}/fusioncatcher_ref/human_v98"
+  star_fusion_ref = "${params.reference_base}/star_fusion/1.6.0/ensembl/ctat_genome_lib_build_dir"
+  ericscript_ref = "${params.reference_base}/ericscript_ref/ericscript_db_homosapiens_ensembl84" 
+}
+
+process {
+  container = "${params.containerPath}/rnafusion_1.1.0.img"
+
+  withName: "arriba|arriba_visualization" {
+    container = "${params.containerPath}/rnafusion_arriba_v${params.arriba_version}.img"
+  }
+  withName: "star_fusion|download_star_fusion" {
+    container = "${params.containerPath}/rnafusion_star-fusion_v${params.star_fusion_version}.img"
+  }
+  withName:fusioncatcher {
+    container = "${params.containerPath}/rnafusion_fusioncatcher_v${params.fusioncatcher_version}.img"
+  }
+  withName:fusion_inspector {
+    container = "${params.containerPath}/rnafusion_fusion-inspector_v${params.fusion_inspector_version}.img"
+  }
+  withName:ericscript {
+    container = "${params.containerPathCommon}/rnafusion_ericscript_v${params.ericscript_version}.img"
+  }
+  withName:pizzly {
+    container = "${params.containerPathCommon}/rnafusion_pizzly_v${params.pizzly_version}.img"
+  }
+  withName:squid {
+    container = "${params.containerPath}/rnafusion_squid_v${params.squid_version}.img"
+  }
+}

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/utd_ganymede.config

@@ -12,7 +12,7 @@ singularity {
 }
 
 process {
-  beforeScript = 'module load singularity'
+  beforeScript = 'module load singularity/2.4.5'
   executor = 'slurm'
   queue = 'genomics'
 }

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/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`
 

docs/pipeline/rnafusion/munin.md

@@ -0,0 +1,19 @@
+# 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 containers
+* 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`
-* Path to `snpEff_cache`: `/data1/cache/snpEff/`
+* Params `annotation_cache` and `cadd_cache` set to `true`
+* 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`
 

nfcore_custom.config

@@ -17,6 +17,7 @@ profiles {
   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 {
@@ -47,7 +48,9 @@ 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'],
     genotoul: ['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'],
     genouest: ['.genouest.org'],