Merge pull request #120 from nf-core/dev

Release 2.0.4

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:2.0.4
 
 install:
   # Install Nextflow
@@ -48,5 +48,7 @@ script:
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --circularmapper --circulartarget 'NC_007596.2'
   # Test running with BWA Mem
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --bwamem --bwa_index results/reference_genome/bwa_index/
+  # Test with zipped reference input
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --fasta 'https://raw.githubusercontent.com/nf-core/test-datasets/eager2/reference/Test.fasta.gz'
   # Test basic pipeline with Conda too 
   - travis_wait 25 nextflow run ${TRAVIS_BUILD_DIR} -profile test,conda --pairedEnd --bwa_index results/reference_genome/bwa_index/

CHANGELOG.md

@@ -4,7 +4,20 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## [Unpublished]
+## [Unpublished / Dev Branch]
+
+## [2.0.4] - 2019-01-07
+
+### `Added`
+* [#111](https://github.com/nf-core/eager/pull/110) - Allow [Zipped FastA reference input](https://github.com/nf-core/eager/issues/91)
+* [#113](https://github.com/nf-core/eager/pull/113) - All files are now staged via channels, which is considered best practice by Nextflow 
+* [#114](https://github.com/nf-core/eager/pull/113) - Add proper runtime defaults for multiple processes 
+* [#118](https://github.com/nf-core/eager/pull/118) - Add centralized configs handling by https://github.com/nf-core/configs
+* [#115](https://github.com/nf-core/eager/pull/115) - Add DamageProfiler MultiQC support
+
+### `Fixed`
+* [#110](https://github.com/nf-core/eager/pull/110) - Fix for [MultiQC Missing Second FastQC report](https://github.com/nf-core/eager/issues/107)
+* [#112](https://github.com/nf-core/eager/pull/112) - Remove [redundant UDG options](https://github.com/nf-core/eager/issues/89)
 
 ## [2.0.3] - 2018-12-12
 

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:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.0.4/bin:$PATH

README.md

@@ -55,7 +55,7 @@ nextflow pull nf-core/eager
 4. Set up your job with default parameters
 
 ```bash
-nextflow run nf-core -profile <docker/singularity/conda> --reads'*_R{1,2}.fastq.gz' --fasta '<REFERENCE.fasta'
+nextflow run nf-core -profile <docker/singularity/conda> --reads'*_R{1,2}.fastq.gz' --fasta '<REFERENCE>.fasta'
 ```
 
 5. See the overview of the run with under `<OUTPUT_DIR>/MultiQC/multiqc_report.html`

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 2.0.4
 
 %environment
-    PATH=/opt/conda/envs/nf-core-eager-2.0.3/bin:$PATH
+    PATH=/opt/conda/envs/nf-core-eager-2.0.4/bin:$PATH
     export PATH
 
 %files

bin/scrape_software_versions.py

@@ -16,6 +16,7 @@
     'GATK': ['v_gatk.txt', r"Version:([\d\.]+)"],
     'bamUtil' : ['v_bamutil.txt', r"Version: ([\d\.]+)"],
     'fastP': ['v_fastp.txt', r"([\d\.]+)"],
+    'DamageProfiler' : ['v_damageprofiler.txt', r"version\": \"([\d\.]+)"],
 }
 results = OrderedDict()
 results['nf-core/eager'] = '<span style="color:#999999;\">N/A</span>'
@@ -30,6 +31,7 @@
 results['GATK'] = '<span style="color:#999999;\">N/A</span>'
 results['bamUtil'] = '<span style="color:#999999;\">N/A</span>'
 results['fastP'] = '<span style="color:#999999;\">N/A</span>'
+results['DamageProfiler'] = '<span style="color:#999999;\">N/A</span>'
 
 # Search each file using its regex
 for k, v in regexes.items():

conf/acad-pheonix.config

@@ -34,6 +34,20 @@ process {
     cpus = { check_max(8 * task.attempt, 'cpus') }
     time = { check_max(8.h * task.attempt, 'time') }
   }
+  withName:bwamem{
+    memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+    cpus = { check_max(8 * task.attempt, 'cpus') }
+    time = { check_max(8.h * task.attempt, 'time') }
+  }
+  withName:qualimap{
+    cpus = { check_max(8 * task.attempt, 'cpus') }
+  }
+  withName:bam_trim{
+    cpus = { check_max(4 * task.attempt, 'cpus') }
+  }
+  withName:markDup{
+    cpus = { check_max(8 * task.attempt, 'cpus') }
+  }
   withName:preseq {
     errorStrategy = 'ignore'
   }