Merge pull request #204 from apeltzer/dev

Fix DamageProfiler issues

Author: apeltzer

.travis.yml

@@ -14,7 +14,7 @@ before_install:
   - docker pull nfcore/eager:dev
   # Fake the tag locally so that the pipeline runs properly
   # Looks weird when this is :dev to :dev, but makes sense when testing code for a release (:dev to :1.0.1)
-  - docker tag nfcore/eager:dev nfcore/eager:2.0.7
+  - docker tag nfcore/eager:dev nfcore/eager:dev
 
 install:
   # Install Nextflow

Dockerfile

@@ -3,4 +3,4 @@ FROM nfcore/base
 LABEL description="Docker image containing all requirements for nf-core/eager pipeline"
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-eager-2.0.7/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.0.7dev/bin:$PATH

conf/base.config

@@ -61,11 +61,9 @@ process {
   withName: multiqc {
     errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
   }
-
   withName: damageprofiler {
-    params.large_ref ? "time = { check_max(8.h * task.attempt, 'time') }" : "time = { check_max(2.h * task.attempt, 'time') }"
+    time = params.large_ref ? { check_max(8.h * task.attempt, 'time') } : { check_max(2.h * task.attempt, 'time')}
   }
-
   withName: strip_input_fastq {
     cpus = { check_max(8 * task.attempt, 'cpus') }
     memory = { check_max( 8.GB * task.attempt, 'memory' ) }

environment.yml

@@ -1,4 +1,4 @@
-name: nf-core-eager-2.0.7
+name: nf-core-eager-2.0.7dev
 channels:
   - defaults
   - bioconda
@@ -17,7 +17,7 @@ dependencies:
   - bioconda::gatk4=4.1.1.0
   - bioconda::qualimap=2.2.2b
   - bioconda::vcf2genome=0.91
-  - bioconda::damageprofiler=0.4.5
+  - bioconda::damageprofiler=0.4.6
   - bioconda::multiqc=1.7
   - bioconda::pmdtools=0.60
   - conda-forge::r-rmarkdown=1.12
@@ -29,5 +29,5 @@ dependencies:
   - bioconda::bamutil=1.0.14
   - bioconda::mtnucratio=0.5
   - pysam=0.15.2
-  - python=3.6.7
+  - python=3.7.3
   #Missing Schmutzi,snpAD

nextflow.config

@@ -55,7 +55,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/eager:2.0.7'
+process.container = 'nfcore/eager:dev'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -111,7 +111,7 @@ manifest {
   name = 'nf-core/eager'
   author = 'Alexander Peltzer, Stephen Clayton, James A. Fellows Yates, Maxime Borry'
   homePage = 'https://github.com/nf-core/eager'
-  version = '2.0.7'
+  version = '2.0.7dev'
   description = 'A fully reproducible ancient and modern DNA pipeline in Nextflow and with cloud support.'
   mainScript = 'main.nf'
   nextflowVersion = '>=0.32.0'