Merge pull request #134 from nf-core/dev

PR release 2.0.5

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:2.0.4
+  - docker tag nfcore/eager:dev nfcore/eager:2.0.5
 
 install:
   # Install Nextflow
@@ -39,16 +39,16 @@ script:
   # Run the basic pipeline with the test profile
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --saveReference
   # Run the basic pipeline with single end data (pretending its single end actually)
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --singleEnd --bwa_index results/reference_genome/bwa_index/
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --singleEnd --bwa_index results/reference_genome/bwa_index/bwa_index/
   # Run the same pipeline testing optional step: fastp, complexity 
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --complexity_filter --bwa_index results/reference_genome/bwa_index/
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --complexity_filter --bwa_index results/reference_genome/bwa_index/bwa_index/
   # Test BAM Trimming
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --trim_bam --bwa_index results/reference_genome/bwa_index/
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --trim_bam --bwa_index results/reference_genome/bwa_index/bwa_index/
   # Test running with CircularMapper
   - 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/
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --bwamem --bwa_index results/reference_genome/bwa_index/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/
+  # Run the basic pipeline with the bam input profile
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile testbam,docker --bam

CHANGELOG.md

@@ -6,6 +6,21 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## [Unpublished / Dev Branch]
 
+## [2.0.5] - 2019-01-28
+
+### `Added`
+* [#127](https://github.com/nf-core/eager/pull/127) - Added a second testcase for testing the pipeline properly
+* [#129](https://github.com/nf-core/eager/pull/129) - Support BAM files as [input format](https://github.com/nf-core/eager/issues/41)
+* [#131](https://github.com/nf-core/eager/pull/131) - Support different [reference genome file extensions](https://github.com/nf-core/eager/issues/130)
+
+### `Fixed`
+* [#128](https://github.com/nf-core/eager/issues/128) - Fixed reference genome handling errors
+
+### `Dependencies`
+* Picard Tools 2.18.21 -> 2.18.23
+* R-Markdown 1.10 -> 1.11 
+* FastP 0.19.5 -> 0.19.6 
+
 ## [2.0.4] - 2019-01-09
 
 ### `Added`

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-2.0.4/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.0.5/bin:$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 2.0.4
+    VERSION 2.0.5
 
 %environment
-    PATH=/opt/conda/envs/nf-core-eager-2.0.4/bin:$PATH
+    PATH=/opt/conda/envs/nf-core-eager-2.0.5/bin:$PATH
     export PATH
 
 %files

conf/base.config

@@ -28,7 +28,10 @@ process {
     //errorStrategy = 'ignore'
   }
 
-
+  withName:convertBam {
+    cpus = { check_max(8 * task.attempt, 'cpus') }
+  }
+  
   withName:bwa {
     memory = { check_max( 16.GB * task.attempt, 'memory' ) }
     cpus = { check_max(8 * task.attempt, 'cpus') }

conf/test.config

@@ -15,6 +15,7 @@ params {
   //Input data
   singleEnd = false
   readPaths = [['JK2782_TGGCCGATCAACGA_L008', ['https://github.com/nf-core/test-datasets/raw/eager2/testdata/Mammoth/JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq.gz','https://github.com/nf-core/test-datasets/raw/eager2/testdata/Mammoth/JK2782_TGGCCGATCAACGA_L008_R2_001.fastq.gz.tengrand.fq.gz']],
+  ['JK2785_TGGCCGATCAACGA_L008', ['https://github.com/nf-core/test-datasets/raw/eager2/testdata/Mammoth/JK2785_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq.gz','https://github.com/nf-core/test-datasets/raw/eager2/testdata/Mammoth/JK2785_TGGCCGATCAACGA_L008_R2_001.fastq.gz.tengrand.fq.gz']],
   ]
   // Genome references
   fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager2/reference/Mammoth_MT_Krause.fasta'

conf/testbam.config

@@ -0,0 +1,22 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ * nextflow run nf-core/eager -profile test, docker (or singularity, or conda)
+ */
+
+params {
+  max_cpus = 2
+  max_memory = 6.GB
+  max_time = 48.h
+  genome = "Custom"
+  //Input data
+  readPaths = [
+    'https://github.com/nf-core/test-datasets/raw/eager2/testdata/Mammoth/bam/test1.bam',
+    'https://github.com/nf-core/test-datasets/raw/eager2/testdata/Mammoth/bam/test2.bam'
+  ]
+  // Genome references
+  fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager2/reference/Mammoth_MT_Krause.fasta'
+}

docs/faq.md

@@ -0,0 +1 @@
+# Frequently Asked Questions

docs/troubleshooting.md

@@ -1,5 +1,22 @@
 # nf-core/eager: Troubleshooting
 
+## My pipeline update doesn't seem to do anything!
+
+To download a new version of a pipeline, you can use the following, replacing `<VERSION>` the the corresponding verison.
+
+```bash
+nextflow pull nf-core/eager -r <VERSION>
+```
+However, in very rare cases, minor fixes to a version will be pushed out without a version number bump. This can confuse nextflow slightly, as it thinks you already have the 'broken' version from your original pipeline download.
+
+If when running the pipeline you don't see any changes in the fixed version when running it, you can try removing your nextflow EAGER cache typically stored in your home directory with
+
+```bash
+rm -r ~/.nextflow/assets/nf-core/eager
+```
+
+And re-pull the pipeline with the command above. This will install a fresh version of the version with the fixes.
+
 ## Input files not found
 
 If no file, only one input file, or only read one and not read two is picked up then something is wrong with your input file declaration
@@ -26,3 +43,4 @@ If you still have an issue with running the pipeline then feel free to contact u
 Have a look at the [pipeline website](https://github.com/nf-core/eager) to find out how.
 
 If you have problems that are related to Nextflow and not our pipeline then check out the [Nextflow gitter channel](https://gitter.im/nextflow-io/nextflow) or the [google group](https://groups.google.com/forum/#!forum/nextflow).
+