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fix bug in travis #4

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Apr 15, 2019
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2 changes: 1 addition & 1 deletion .travis.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion conf/base.config
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@

process {

container = params.container
container = process.container

cpus = { check_max( 2, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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3 changes: 2 additions & 1 deletion environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
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16 changes: 3 additions & 13 deletions nextflow.config
Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand All @@ -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'
Expand All @@ -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' }
}

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