Update to 2.0.4dev

Author: apeltzer

.travis.yml

@@ -13,7 +13,7 @@ before_install:
   # Pull the docker image first so the test doesn't wait for this
   - docker pull nfcore/eager:dev
   # Fake the tag locally so that the pipeline runs properly
-  - docker tag nfcore/eager:dev nfcore/eager:2.0.3
+  - docker tag nfcore/eager:dev nfcore/eager:latest
 
 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-2.0.3/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.0.4dev/bin:$PATH

Singularity

@@ -4,10 +4,10 @@ Bootstrap:docker
 %labels
     MAINTAINER Alexander Peltzer <alexander.peltzer@qbic.uni-tuebingen.de>
     DESCRIPTION Container image containing all requirements for the nf-core/eager pipeline
-    VERSION 2.0.3
+    VERSION 2.0.4dev
 
 %environment
-    PATH=/opt/conda/envs/nf-core-eager-2.0.3/bin:$PATH
+    PATH=/opt/conda/envs/nf-core-eager-2.0.4dev/bin:$PATH
     export PATH
 
 %files

environment.yml

@@ -1,4 +1,4 @@
-name: nf-core-eager-2.0.3
+name: nf-core-eager-2.0.4dev
 channels:
   - defaults
   - bioconda
@@ -9,22 +9,22 @@ dependencies:
   - bioconda::adapterremoval=2.2.2
   - bioconda::adapterremovalfixprefix=0.0.4
   - bioconda::bwa=0.7.17
-  - bioconda::picard=2.18.15
+  - bioconda::picard=2.18.21
   - bioconda::samtools=1.9
   - bioconda::dedup=0.12.3
   - bioconda::angsd=0.923
   - bioconda::circularmapper=1.93.4
-  - bioconda::gatk4=4.0.11.0
+  - bioconda::gatk4=4.0.12.0
   - bioconda::qualimap=2.2.2b
   - bioconda::vcf2genome=0.91
-  - bioconda::damageprofiler=0.3.11
-  - bioconda::multiqc=1.6
+  - bioconda::damageprofiler=0.4.4
+  - bioconda::multiqc=1.7
   - bioconda::pmdtools=0.60
   - conda-forge::r-rmarkdown=1.10
   - conda-forge::libiconv=1.15
   - conda-forge::pigz=2.3.4
   - bioconda::sequencetools=1.2.2
   - bioconda::preseq=2.0.3
-  - bioconda::fastp=0.19.4
+  - bioconda::fastp=0.19.5
   - bioconda::bamutil=1.0.14
   #Missing Schmutzi,snpAD

nextflow.config

@@ -10,7 +10,7 @@
 
 // Global default params, used in configs
 params {
-  container = 'nfcore/eager:dev'
+  container = 'nfcore/eager:latest'
 
   //Pipeline options
   aligner = 'bwa'
@@ -107,7 +107,7 @@ manifest {
   name = 'nf-core/eager'
   author = 'Alexander Peltzer, Stephen Clayton, James A Fellows-Yates'
   homePage = 'https://github.com/nf-core/eager'
-  version = '2.0.3'
+  version = '2.0.4dev'
   description = 'A fully reproducible and modern ancient DNA pipeline in Nextflow and with cloud support.'
   mainScript = 'main.nf'
   nextflowVersion = '>=0.32.0'