Merge pull request #61 from nf-core/dev

version 1.2.0 nf-core-hic

nextflow.config

@@ -9,43 +9,62 @@
 params {
 
   // Workflow flags
-  // Specify your pipeline's command line flags
-  reads = "*{1,2}.fastq.gz"
+  genome = false
+  reads = "data/*{1,2}.fastq.gz"
+  single_end = false
+
   outdir = './results'
   genome = false
   readPaths = false
   chromosome_size = false
   restriction_fragments = false
-  skipMaps = false
-  skipIce = false
-  skipCool = false
-  skipMultiQC = false
+  skip_maps = false
+  skip_ice = false
+  skip_cool = false
+  skip_multiqc = false
+  save_reference = false
+  save_interaction_bam = false
+  save_aligned_intermediates = false
+  
   dnase = false
+  rm_dup = false
+  rm_singleton = false
+  rm_multi = false
+  min_restriction_fragment_size = false
+  max_restriction_fragment_size = false
+  min_insert_size = false
+  max_insert_size = false
+  min_cis_dist = false
 
   // Boilerplate options
+  multiqc_config = false
   name = false
-  multiqc_config = "$baseDir/assets/multiqc_config.yaml"
   email = false
-  maxMultiqcEmailFileSize = 25.MB
+  email_on_fail = false
+  max_multiqc_email_size = 25.MB
   plaintext_email = false
   monochrome_logs = false
   help = false
-  igenomes_base = "./iGenomes"
+  igenomes_base = 's3://ngi-igenomes/igenomes/'
   tracedir = "${params.outdir}/pipeline_info"
-  awsqueue = false
-  awsregion = 'eu-west-1'
-  igenomesIgnore = false
+  igenomes_ignore = false
+
   custom_config_version = 'master'
   custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
   hostnames = false
   config_profile_description = false
   config_profile_contact = false
   config_profile_url = false
+
+  // Defaults only, expecting to be overwritten
+  max_memory = 24.GB
+  max_cpus = 8
+  max_time = 240.h
 }
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/hic:1.1.0'
+process.container = 'nfcore/hic:1.2.0'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -62,19 +81,33 @@ includeConfig 'conf/hicpro.config'
 
 // Create profiles
 profiles {
-  awsbatch { includeConfig 'conf/awsbatch.config' }
   conda { process.conda = "$baseDir/environment.yml" }
   debug { process.beforeScript = 'echo $HOSTNAME' }
-  docker { docker.enabled = true }
-  singularity { singularity.enabled = true }
+  docker {
+    docker.enabled = true
+    // Avoid this error:
+    //   WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
+    // Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351
+    // once this is established and works well, nextflow might implement this behavior as new default.
+    docker.runOptions = '-u \$(id -u):\$(id -g)'
+  }
+  singularity {
+    singularity.enabled = true
+    singularity.autoMounts = true
+  }
   test { includeConfig 'conf/test.config' }
 }
 
 // Load igenomes.config if required
-if(!params.igenomesIgnore){
+if (!params.igenomes_ignore) {
   includeConfig 'conf/igenomes.config'
 }
 
+// Export this variable to prevent local Python libraries from conflicting with those in the container
+env {
+  PYTHONNOUSERSITE = 1
+}
+
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
@@ -101,8 +134,8 @@ manifest {
   homePage = 'https://github.com/nf-core/hic'
   description = 'Analysis of Chromosome Conformation Capture data (Hi-C)'
   mainScript = 'main.nf'
-  nextflowVersion = '>=19.04.0'
-  version = '1.1.0'
+  nextflowVersion = '>=19.10.0'
+  version = '1.2.0'
 }
 
 // Function to ensure that resource requirements don't go beyond