lll

Merge branch 'nf-core-master'

.github/workflows/main.yml

@@ -16,7 +16,49 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'biohpc_gen', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'lugh', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
+          profile:
+            - 'abims'
+            - 'awsbatch'
+            - 'aws_tower'
+            - 'bi'
+            - 'bigpurple'
+            - 'binac'
+            - 'biohpc_gen'
+            - 'cbe'
+            - 'ccga_dx'
+            - 'ccga_med'
+            - 'cfc'
+            - 'cfc_dev'
+            - 'crick'
+            - 'denbi_qbic'
+            - 'ebc'
+            - 'eddie'
+            - 'eva'
+            - 'genotoul'
+            - 'genouest'
+            - 'gis'
+            - 'google'
+            - 'hebbe'
+            - 'icr_davros'
+            - 'ifb_core'
+            - 'imperial'
+            - 'imperial_mb'
+            - 'jax'
+            - 'lugh'
+            - 'mpcdf'
+            - 'munin'
+            - 'oist'
+            - 'pasteur'
+            - 'phoenix'
+            - 'prince'
+            - 'sanger'
+            - 'seg_globe'
+            - 'shh'
+            - 'uct_hpc'
+            - 'uppmax'
+            - 'utd_ganymede'
+            - 'utd_sysbio'
+            - 'uzh'
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow

README.md

@@ -96,6 +96,7 @@ Currently documentation is available for the following systems:
 
 * [ABIMS](docs/abims.md)
 * [AWSBATCH](docs/awsbatch.md)
+* [AWS_TOWER](docs/aws_tower.md)
 * [BIGPURPLE](docs/bigpurple.md)
 * [BI](docs/bi.md)
 * [BINAC](docs/binac.md)
@@ -117,7 +118,6 @@ Currently documentation is available for the following systems:
 * [HEBBE](docs/hebbe.md)
 * [ICR_DAVROS](docs/icr_davros.md)
 * [JAX](docs/jax.md)
-* [KRAKEN](docs/kraken.md)
 * [LUGH](docs/lugh.md)
 * [MPCDF](docs/mpcdf.md)
 * [MUNIN](docs/munin.md)
@@ -131,6 +131,7 @@ Currently documentation is available for the following systems:
 * [UCT_HPC](docs/uct_hpc.md)
 * [UPPMAX](docs/uppmax.md)
 * [UTD_GANYMEDE](docs/utd_ganymede.md)
+* [UTD_SYSBIO](docs/utd_sysbio.md)
 * [UZH](docs/uzh.md)
 
 ### Uploading to `nf-core/configs`

bin/cchecker.py

@@ -10,6 +10,7 @@ import os
 import sys
 import argparse
 import re
+import yaml
 
 ############################################
 ############################################
@@ -51,19 +52,22 @@ def check_config(Config, Github):
     ### Ignore these profiles
     ignore_me = ['czbiohub_aws']
     tests.update(ignore_me)
+    # parse yaml GitHub actions file
+    try:
         with open(Github, 'r') as ghfile:
-        for line in ghfile:
+            wf = yaml.safe_load(ghfile)
-            if re.search('profile: ', line):
+            profile_list = wf["jobs"]["profile_test"]["strategy"]["matrix"]["profile"]
-                line = line.replace('\'','').replace('[','').replace(']','').replace('\n','')
+    except Exception as e:
-                profiles = line.split(':')[1].split(',')
+        print("Could not parse yaml file: {}, {}".format(Github, e))
-                for p in profiles:
+        sys.exit(1)
-                    tests.add(p.strip())
+    # Add profiles to test
+    for profile in profile_list:
+        tests.add(profile.strip())
 
     ###Check if sets are equal
-    if tests == config_profiles:
+    try:
-        sys.exit(0)
+        assert tests == config_profiles
-    else:
+    except (AssertionError):
-        #Maybe report what is missing here too
         print("Tests don't seem to test these profiles properly. Please check whether you added the profile to the Github Actions testing YAML.\n")
         print(config_profiles.symmetric_difference(tests))
         sys.exit(1)

conf/aws_tower.config

@@ -0,0 +1,21 @@
+//Nextflow config file for running on AWS batch
+params {
+    config_profile_description = 'AWS Batch with Tower Profile'
+    config_profile_contact = 'Gisela Gabernet (@ggabernet)'
+    config_profile_url = 'https://aws.amazon.com/batch/'
+}
+
+timeline {
+    overwrite = true
+}
+report {
+    overwrite = true
+}
+trace {
+    overwrite = true
+}
+dag {
+    overwrite = true
+}
+
+process.executor = 'awsbatch'

conf/cfc.config

@@ -11,7 +11,6 @@ singularity {
 }
 
 process {
-  beforeScript = 'module load devel/singularity/3.4.2'
   executor = 'slurm'
   queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' : 'compute' }
   scratch = 'true'

conf/cfc_dev.config

@@ -10,7 +10,6 @@ singularity {
 }
 
 process {
-  beforeScript = 'module load devel/singularity/3.4.2'
   executor = 'slurm'
   queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' : 'compute' }
   scratch = 'true'

conf/czbiohub_aws.config

@@ -27,7 +27,7 @@ process {
 workDir = "s3://czb-nextflow/intermediates/"
 
 aws.region = 'us-west-2'
-executor.awscli = '/home/ec2-user/miniconda/bin/aws'
+aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
 params.tracedir = './'
 
 params {

conf/eddie.config

@@ -31,7 +31,7 @@ process {
 params {
   saveReference = true
   // iGenomes reference base
-  igenomes_base = '/exports/igmm/eddie/NextGenResources/igenomes'
+  igenomes_base = '/exports/igmm/eddie/BioinformaticsResources/igenomes'
   max_memory = 384.GB
   max_cpus = 32
   max_time = 240.h
@@ -42,8 +42,8 @@ env {
 }
 
 singularity {
-  envWhitelist = "SINGULARITY_TMPDIR"
+  envWhitelist = "SINGULARITY_TMPDIR,TMPDIR"
-  runOptions = '-p'
+  runOptions = '-p -B "$TMPDIR"'
   enabled = true
   autoMounts = true
 }

conf/hebbe.config

@@ -14,7 +14,7 @@ process {
   clusterOptions = { "-A $params.project ${params.clusterOptions ?: ''}" }
 
   /* The Hebbe scheduler fails if you try to request an amount of memory for a job */
-  withName: '*' { memory = null }
+  withName: '.*' { memory = null }
 }
 
 params {

conf/jax.config

@@ -19,7 +19,7 @@ singularity{
     cacheDir = params.singularity_cache_dir
 }
 params {
-      max_memory = 768.GB
+      max_memory = 320.GB
-      max_cpus = 70
+      max_cpus = 32
       max_time = 336.h
     }

conf/kraken.config

@@ -1,24 +0,0 @@
-//Profile config names for nf-core/configs
-params {
-  config_profile_name = 'KRAKEN'
-  config_profile_description = 'Jenkins cluster provided by nf-core/configs.'
-  config_profile_contact = 'Maxime Garcia or Johannes Alneberg'
-  config_profile_url = 'kraken.dyn.scilifelab.se'
-}
-
-process {
-  executor = 'local'
-}
-
-docker {
-  enabled = true
-  mountFlags = 'z'
-  fixOwnership = true
-}
-
-params {
-  max_memory = 60.GB
-  max_cpus = 16
-  max_time = 72.h
-  igenomes_base = '/share/igenomes/'
-}

conf/munin.config

@@ -2,8 +2,8 @@
 
 params {
   // Specific nf-core/configs params
-  config_profile_contact = 'Szilveszter Juhos (@szilvajuhos)'
+  config_profile_contact = 'Maxime Garcia (@maxulysse)'
-  config_profile_description = 'MUNIN profile provided by nf-core/configs.'
+  config_profile_description = 'MUNIN profile provided by nf-core/configs'
   config_profile_url = 'https://ki.se/forskning/barntumorbanken'
 
   // Local AWS iGenomes reference file paths on munin
@@ -26,8 +26,12 @@ singularity {
 }
 
 // To use docker, use nextflow run -profile munin,docker
-docker {
+profiles {
+  docker {
+    docker {
       enabled = false
       mountFlags = 'z'
       fixOwnership = true
+    }
+  }
 }

conf/pipeline/eager/eva.config

@@ -61,7 +61,7 @@ process {
   // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
 
   withName: makeSeqDict {
-    clusterOptions = { "-S /bin/bash -v JAVA_OPTS='-XX:ParallelGCThreads=1' -l h_vmem=${(task.memory.toGiga() + 3)}G,virtual_free=${(task.memory.toGiga() + 3)}G" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
    }
       
   withName: fastqc {
@@ -69,7 +69,7 @@ process {
    }
 
   withName: adapter_removal {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 4)}G,virtual_free=${(task.memory.toGiga() * 4)}G" }
    }
 
   withName: dedup {
@@ -80,6 +80,10 @@ process {
     clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
    }
    
+  withName: library_merge {
+    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
+   }
+
   withName: malt {
     clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
    }
@@ -93,7 +97,7 @@ process {
    }
 
   withName: mtnucratio {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 4)}G,virtual_free=${(task.memory.toGiga() * 4)}G" }
    }
 
   withName: vcf2genome {

conf/pipeline/eager/shh.config

@@ -10,7 +10,7 @@ params {
 // Specific nf-core/eager process configuration
 process {
 
-  maxRetries = 2
+  maxRetries = 3
 
   withName: malt {
     maxRetries = 1
@@ -106,43 +106,43 @@ profiles {
         withLabel:'sc_tiny'{
           cpus = { check_max( 1, 'cpus' ) }
           memory = { check_max( 2.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
+          time = { task.attempt == 3 ? 1440.h : 48.h }
         }
 
         withLabel:'sc_small'{
           cpus = { check_max( 1, 'cpus' ) }
           memory = { check_max( 8.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
+          time = { task.attempt == 3 ? 1440.h : 48.h }
         }
 
         withLabel:'sc_medium'{
           cpus = { check_max( 1, 'cpus' ) }
           memory = { check_max( 16.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
+          time = { task.attempt == 3 ? 1440.h : 48.h }
         }
 
         withLabel:'mc_small'{
           cpus = { check_max( 2, 'cpus' ) }
           memory = { check_max( 8.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
+          time = { task.attempt == 3 ? 1440.h : 48.h }
         }
 
         withLabel:'mc_medium' {
           cpus = { check_max( 4, 'cpus' ) }
           memory = { check_max( 16.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
+          time = { task.attempt == 3 ? 1440.h : 48.h }
         }
 
         withLabel:'mc_large'{
            cpus = { check_max( 8, 'cpus' ) }
            memory = { check_max( 32.GB * task.attempt, 'memory' ) }
-           time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
+          time = { task.attempt == 3 ? 1440.h : 48.h }
         }
 
         withLabel:'mc_huge'{
            cpus = { check_max( 32, 'cpus' ) }
            memory = { check_max( 512.GB * task.attempt, 'memory' ) }
-           time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
+          time = { task.attempt == 3 ? 1440.h : 48.h }
          }
       }
   }
@@ -164,7 +164,7 @@ profiles {
     params {
       config_profile_description = 'Rough HOPS screening MPI-SHH profile, provided by nf-core/configs.'
       fasta = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta'
-      bwa_index = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta'
+      bwa_index = '/projects1/Reference_Genomes/Human/HG19/'
       fasta_index = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta.fai'
       seq_dict = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.dict'
       bwaalnn = 0.01

conf/pipeline/rnaseq/utd_sysbio.config

@@ -0,0 +1,19 @@
+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/'
+}
+
+process {
+
+  withName : "STAR_ALIGN" {
+    memory = 36.GB
+  }
+
+  withLabel:process_high {
+    cpus = { check_max( 16 * task.attempt, 'cpus' ) }
+    memory = { check_max( 60.GB * task.attempt, 'memory' ) }
+    time = { check_max( 16.h * task.attempt, 'time' ) }
+  }
+
+}

conf/pipeline/sarek/munin.config

@@ -2,8 +2,9 @@
 
 params {
   // Specific nf-core/configs params
-  config_profile_contact = 'Maxime Garcia (@MaxUlysse)'
+  config_profile_contact = 'Maxime Garcia (@maxulysse)'
   config_profile_description = 'nf-core/sarek MUNIN profile provided by nf-core/configs'
+  config_profile_url = 'https://ki.se/forskning/barntumorbanken'
 
   // Specific nf-core/sarek params
   annotation_cache  = true

conf/pipeline/viralrecon/eddie.config

@@ -0,0 +1,13 @@
+env {
+  BLASTDB_LMDB_MAP_SIZE=100000000
+}
+
+process {
+  withName : '.*PICARD.*' {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+
+  withName : '.*SNPEFF.*' {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+}

conf/pipeline/viralrecon/genomes.config

@@ -20,21 +20,33 @@ params {
       primer_sets {
         artic {
           '1' {
-            fasta      = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V1/nCoV-2019.reference.fasta'
+            fasta      = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V1/nCoV-2019.reference.fasta'
             gff        = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
-            primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V1/nCoV-2019.primer.bed'
+            primer_bed = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V1/nCoV-2019.primer.bed'
             scheme     = 'nCoV-2019'
           }
           '2' {
-            fasta      = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V2/nCoV-2019.reference.fasta'
+            fasta      = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V2/nCoV-2019.reference.fasta'
             gff        = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
-            primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V2/nCoV-2019.primer.bed'
+            primer_bed = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V2/nCoV-2019.primer.bed'
             scheme     = 'nCoV-2019'
           }
           '3' {
-            fasta      = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta'
+            fasta      = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta'
             gff        = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
-            primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed'
+            primer_bed = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed'
+            scheme     = 'nCoV-2019'
+          }
+          '4' {
+            fasta      = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V4/SARS-CoV-2.reference.fasta'
+            gff        = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
+            primer_bed = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V4/SARS-CoV-2.scheme.bed'
+            scheme     = 'SARS-CoV-2'
+          }
+          '1200' {
+            fasta      = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/primer_schemes/artic/nCoV-2019/V1200/nCoV-2019.reference.fasta'
+            gff        = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
+            primer_bed = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/primer_schemes/artic/nCoV-2019/V1200/nCoV-2019.bed'
             scheme     = 'nCoV-2019'
           }
         }

conf/utd_sysbio.config

@@ -0,0 +1,35 @@
+//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_cache_dir = '/scratch/applied-genomics/singularity'
+}
+
+env {
+    TMPDIR = '/home/$USER/scratch/tmp'
+}
+
+singularity {
+  enabled = true
+  envWhitelist='SINGULARITY_BINDPATH'
+  autoMounts = true
+  cacheDir = params.singularity_cache_dir
+}
+
+process {
+  beforeScript = 'module load singularity/3.4.1'
+  executor = 'slurm'
+  queue = { task.memory >= 30.GB && task.cpu <= 16 ? 'normal': 'smallmem' }
+}
+
+// Preform work directory cleanup after a successful run
+cleanup = true
+
+params {
+  // TODO Need to initialize this
+  // igenomes_base = '/scratch/applied-genomics/references/iGenomes/references/'
+  max_memory = 90.GB
+  max_cpus = 16
+  max_time = 96.h
+}

docs/aws_tower.md

@@ -0,0 +1,5 @@
+# nf-core/configs: AWS Batch with Tower Configuration
+
+To be used when submitting jobs to AWS Batch by using Tower Forge. If you are not using Tower Forge, consider using the profile `awsbatch` where you can directly specify the Batch queue, AWS region and AWS cli path.
+
+This profile defines `awsbatch` as executor, and allows `overwrite` of `trace`, `timeline`, `report` and `dag` to allow resuming pipelines.

docs/eddie.md

@@ -1,10 +1,10 @@
 # nf-core/configs: Eddie Configuration
 
-nf-core pipelines sarek, rnaseq, and atacseq have all been tested on the University of Edinburgh Eddie HPC.
+nf-core pipelines sarek, rnaseq, atacseq, and viralrecon have all been tested on the University of Edinburgh Eddie HPC. All except atacseq have pipeline-specific config files; atacseq does not yet support this.
 
 ## Getting help
 
-There is a Slack channel dedicated to eddie users on the MRC IGMM Slack: [https://igmm.slack.com/channels/eddie3](https://igmm.slack.com/channels/eddie3)
+There is a Slack channel dedicated to eddie users on the MRC IGC Slack: [https://igmm.slack.com/channels/eddie3](https://igmm.slack.com/channels/eddie3)
 
 ## Using the Eddie config profile
 
@@ -35,13 +35,13 @@ This config enables Nextflow to manage the pipeline jobs via the SGE job schedul
 
 ## Singularity set-up
 
-Load Singularity from the module system and, if you have access to `/exports/igmm/eddie/NextGenResources`, set the Singularity cache directory to the NextGenResources path below. If some containers for your pipeline run are not present, please contact the [IGMM Data Manager](data.manager@igmm.ed.ac.uk) to have them added. You can add these lines to the file `$HOME/.bashrc`, or you can run these commands before you run an nf-core pipeline.
+Load Singularity from the module system and, if you have access to `/exports/igmm/eddie/BioinformaticsResources`, set the Singularity cache directory to the BioinformaticsResources path below. If some containers for your pipeline run are not present, please contact the [IGC Data Manager](data.manager@igc.ed.ac.uk) to have them added. You can add these lines to the file `$HOME/.bashrc`, or you can run these commands before you run an nf-core pipeline.
 
-If you do not have access to `/exports/igmm/eddie/NextGenResources`, set the Singularity cache directory to somewhere sensible that is not in your `$HOME` area (which has limited space). It will take time to download all the Singularity containers, but you can use this again.
+If you do not have access to `/exports/igmm/eddie/BioinformaticsResources`, set the Singularity cache directory to somewhere sensible that is not in your `$HOME` area (which has limited space). It will take time to download all the Singularity containers, but you can use this again.
 
 ```bash
 module load singularity
-export NXF_SINGULARITY_CACHEDIR="/exports/igmm/eddie/NextGenResources/nextflow/singularity"
+export NXF_SINGULARITY_CACHEDIR="/exports/igmm/eddie/BioinformaticsResources/nf-core/singularity-images"
 ```
 
 Singularity will create a directory `.singularity` in your `$HOME` directory on eddie. Space on `$HOME` is very limited, so it is a good idea to create a directory somewhere else with more room and link the locations.
@@ -68,7 +68,7 @@ If your eddie terminal disconnects your Nextflow job will stop. You can run Next
 nohup ./nextflow_run.sh &
 ```
 
-### On a wild west node - IGMM only
+### On a wild west node - IGC only
 
 Wild west nodes on eddie can be accessed via ssh (node2c15, node2c16, node3g22). To run Nextflow on one of these nodes, do it within a [screen session](https://linuxize.com/post/how-to-use-linux-screen/).
 
@@ -92,12 +92,12 @@ screen -r <session_name>
 
 ## Using iGenomes references
 
-A local copy of the iGenomes resource has been made available on the Eddie HPC for those with access to `/exports/igmm/eddie/NextGenResources` so you should be able to run the pipeline against any reference available in the `igenomes.config`.
+A local copy of the iGenomes resource has been made available on the Eddie HPC for those with access to `/exports/igmm/eddie/BioinformaticsResources` so you should be able to run the pipeline against any reference available in the `igenomes.config`.
 You can do this by simply using the `--genome <GENOME_ID>` parameter.
 
 ## Adjusting maximum resources
 
-This config is set for IGMM standard nodes which have 32 cores and 384GB memory. If you are a non-IGMM user, please see the [ECDF specification](https://www.wiki.ed.ac.uk/display/ResearchServices/Memory+Specification) and adjust the `--clusterOptions` flag appropriately, e.g.
+This config is set for IGC standard nodes which have 32 cores and 384GB memory. If you are a non-IGC user, please see the [ECDF specification](https://www.wiki.ed.ac.uk/display/ResearchServices/Memory+Specification) and adjust the `--clusterOptions` flag appropriately, e.g.
 
 ```bash
 --clusterOptions "-C mem256GB" --max_memory "256GB"

docs/kraken.md

@@ -1,10 +0,0 @@
-# nf-core/configs: KRAKEN Configuration
-
-This profile can be **only** combined with `jenkins.config`. It is used for
-testing pipeline with real data on **in-house** cluster located at SciLifeLab.
-
-To use, run the pipeline with `-profile kraken`. This will download and launch
-the [`kraken.config`](../conf/kraken.config) which has been pre-configured to
-test the pipeline using `docker` by default.
-
-Example: `nextflow run -profile kraken,jenkins`

docs/pipeline/rnaseq/utd_sysbio.md

@@ -0,0 +1,23 @@
+# nf-core/configs: UTD sysbio rnaseq specific configuration
+
+Extra specific configuration for rnaseq pipeline
+
+## Usage
+
+To use, run the pipeline with `-profile sysbio`.
+
+This will download and launch the eager specific [`utd_sysbio.config`](../../../conf/pipeline/rnaseq/utd_sysbio.config) which has been pre-configured with a setup suitable for the shh cluster.
+
+Example: `nextflow run nf-core/rnaseq -profile sysbio`
+
+## rnaseq specific configurations for UTD sysbio
+
+Specific configurations for UTD Sysbio has been made for rnaseq.
+
+### General profiles
+
+<!-- TODO -->
+
+### Contextual profiles
+
+<!-- TODO -->

docs/utd_sysbio.md

@@ -0,0 +1,16 @@
+# nf-core/configs: UTD Sysbio Configuration
+
+All nf-core pipelines have been successfully configured for use on the Sysbio HPC cluster at the [The Univeristy of Texas at Dallas](https://www.utdallas.edu/).
+
+To use, run the pipeline with `-profile utd_sysbio`. This will download and launch the [`utd_sysbio.config`](../conf/utd_sysbio.config) which has been pre-configured with a setup suitable for the Sysbio 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 Sysbio. You can do this by issuing the commands below:
+
+```bash
+## Singularity environment modules
+module purge
+module load singularity
+```
+
+>NB: You will need an account to use the HPC cluster on Sysbio in order to run the pipeline. If in doubt contact OIT.
+>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 OIT.

nfcore_custom.config

@@ -12,6 +12,7 @@
 profiles {
   abims        { includeConfig "${params.custom_config_base}/conf/abims.config" }
   awsbatch     { includeConfig "${params.custom_config_base}/conf/awsbatch.config" }
+  aws_tower    { includeConfig "${params.custom_config_base}/conf/aws_tower.config" }
   bi           { includeConfig "${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" }
@@ -36,7 +37,6 @@ profiles {
   genouest     { includeConfig "${params.custom_config_base}/conf/genouest.config" }
   gis          { includeConfig "${params.custom_config_base}/conf/gis.config" }
   hebbe        { includeConfig "${params.custom_config_base}/conf/hebbe.config" }
-  kraken       { includeConfig "${params.custom_config_base}/conf/kraken.config" }
   lugh         { includeConfig "${params.custom_config_base}/conf/lugh.config"}
   mpcdf        { includeConfig "${params.custom_config_base}/conf/mpcdf.config" }
   munin        { includeConfig "${params.custom_config_base}/conf/munin.config" }
@@ -50,6 +50,7 @@ profiles {
   uct_hpc      { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }
   uppmax       { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
   utd_ganymede { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" }
+  utd_sysbio   { includeConfig "${params.custom_config_base}/conf/utd_sysbio.config" }
   uzh          { includeConfig "${params.custom_config_base}/conf/uzh.config" }
   jax          { includeConfig "${params.custom_config_base}/conf/jax.config" }
 }
@@ -70,6 +71,7 @@ params {
     genotoul: ['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'],
     genouest: ['.genouest.org'],
     uppmax: ['.uppmax.uu.se'],
-    utd_ganymede: ['ganymede.utdallas.edu']
+    utd_ganymede: ['ganymede.utdallas.edu'],
+    utd_sysbio: ['sysbio.utdallas.edu']
   ]
 }

pipeline/rnaseq.config

@@ -10,4 +10,5 @@
 
 profiles {
   eddie { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/eddie.config" }
+  utd_sysbio { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/utd_sysbio.config" }
 }

pipeline/viralrecon.config

@@ -5,3 +5,7 @@
  */
 
 includeConfig "${params.custom_config_base}/conf/pipeline/viralrecon/genomes.config"
+
+profiles {
+  eddie { includeConfig "${params.custom_config_base}/conf/pipeline/viralrecon/eddie.config" }
+}