From 154616a33166661702c14c20ad91b8ea601cf309 Mon Sep 17 00:00:00 2001
From: nservant <nservant@curie.fr>
Date: Mon, 15 Apr 2019 20:15:46 +0200
Subject: [PATCH] fix bug in travis
---
.travis.yml | 2 +-
conf/base.config | 2 +-
environment.yml | 3 ++-
nextflow.config | 16 +++-------------
4 files changed, 7 insertions(+), 16 deletions(-)
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' }
}
--
GitLab