Updates to fix new lint tests. Simpler travis config.

.travis.yml

@@ -20,7 +20,7 @@ install:
   - cd /tmp/nf-core-tools
   - pip install --user -e .
   # Reset
-  - cd ${TRAVIS_BUILD_DIR}
+  - cd ${TRAVIS_BUILD_DIR}/tests
 
 env:
   - ALIGNER=bismark NXF_VER=0.27.6
@@ -30,7 +30,7 @@ env:
 
 script:
   - "nf-core lint ${TRAVIS_BUILD_DIR}"
-  - "cd ${TRAVIS_BUILD_DIR}/tests && ./run_test.sh -a $ALIGNER -b" # Run, build reference genome
-  - "cd ${TRAVIS_BUILD_DIR}/tests && ./run_test.sh -a $ALIGNER"    # Basic run
-  - "cd ${TRAVIS_BUILD_DIR}/tests && ./run_test.sh -a $ALIGNER -r" # Run, RRBS mode
-  - "cd ${TRAVIS_BUILD_DIR}/tests && ./run_test.sh -a $ALIGNER -n" # Run, no-trimming mode
+  - "./run_test.sh -a $ALIGNER -b" # Run, build reference genome
+  - "./run_test.sh -a $ALIGNER"    # Basic run
+  - "./run_test.sh -a $ALIGNER -r" # Run, RRBS mode
+  - "./run_test.sh -a $ALIGNER -n" # Run, no-trimming mode

environment.yml

@@ -7,15 +7,15 @@ channels:
   - bioconda
 dependencies:
   # Default bismark
-  - conda-forge::openjdk # Needed for FastQC docker - see bioconda/bioconda-recipes#5026
-  - fastqc=0.11.5
+  - conda-forge::openjdk=8.0.144 # Needed for FastQC docker - see bioconda/bioconda-recipes#5026
+  - fastqc=0.11.7
   - trim-galore=0.4.5
   - samtools=1.7
   - bowtie2=2.3.4.1
   - bismark=0.19.0
   - qualimap=2.2.2a
-  - multiqc=1.4
+  - multiqc=1.5
   # bwa-meth aligner
-  - picard=2.17.8
+  - picard=2.18.0
   - bwameth=0.2.0
   - methyldackel=0.3.0

nextflow.config

@@ -92,12 +92,12 @@ trace {
 }
 dag {
   enabled = true
-  file = "${params.outdir}/pipeline_info/MethylSeq_dag.html"
+  file = "${params.outdir}/pipeline_info/MethylSeq_dag.svg"
 }
 
 manifest {
   homePage = 'https://github.com/nf-core/methylseq'
-  description = 'Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.'
+  description = 'Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community.'
   mainScript = 'main.nf'
 }