diff --git a/.travis.yml b/.travis.yml index feb74c6..2eaea15 100644 --- a/.travis.yml +++ b/.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 diff --git a/conf/base.config b/conf/base.config index 98c3861..ba72768 100644 --- a/conf/base.config +++ b/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' ) } diff --git a/environment.yml b/environment.yml index b5cee2f..90ae5f5 100644 --- a/environment.yml +++ b/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 diff --git a/nextflow.config b/nextflow.config index c9f2203..5cd6dfe 100644 --- a/nextflow.config +++ b/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' } }