Merge pull request #4 from nservant/dev

fix bug in travis

.travis.yml

@@ -13,7 +13,7 @@ before_install:
   # Pull the docker image first so the test doesn't wait for this
   - docker pull nfcore/hic:dev
   # Fake the tag locally so that the pipeline runs properly
-  - docker tag nfcore/hic:dev nfcore/hic:latest
+  - docker tag nfcore/hic:dev nfcore/hic:dev
 
 install:
   # Install Nextflow

conf/base.config

@@ -11,7 +11,7 @@
 
 process {
 
-  container = params.container
+  container = process.container
 
   cpus = { check_max( 2, 'cpus' ) }
   memory = { check_max( 8.GB * task.attempt, 'memory' ) }

environment.yml

@@ -4,9 +4,10 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - python=2.7.11
+  - python=2.7.13
   - conda-forge::scipy=1.0.1
   - conda-forge::numpy=1.9.3
+  - conda-forge::r-markdown=0.9
   - bcbio::bx-python=0.7.3
   - bioconda::pysam=0.14.1
   - cooler=0.8.3

nextflow.config

@@ -11,11 +11,6 @@
 // Global default params, used in configs
 params {
 
-  // Container slug. Stable releases should specify release tag!
-  // Developmental code should specify :latest
-  //container = 'nfcore/hic:latest'
-  container = 'nfcore/hic:latest'
-
   // Workflow flags
   // TODO nf-core: Specify your pipeline's command line flags
   reads = "*{1,2}.fastq.gz"
@@ -42,6 +37,7 @@ params {
   custom_config_version = 'master'
 }
 
+process.container = 'nfcore/hic:dev'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -57,14 +53,8 @@ profiles {
   awsbatch { includeConfig 'conf/awsbatch.config' }
   conda { process.conda = "$baseDir/environment.yml" }
   debug { process.beforeScript = 'echo $HOSTNAME' }
-  docker {
-    docker.enabled = true
-    process.container = params.container
-  }
-  singularity {
-    singularity.enabled = true
-    process.container = {"shub://${params.container.replace('nfcore', 'nf-core')}"}
-  }
+  docker { docker.enabled = true }
+  singularity { singularity.enabled = true }
   test { includeConfig 'conf/test.config' }
 }