Merge pull request #66 from nf-core/dev

Release 2.0.0 PR

.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
   # Fake the tag locally so that the pipeline runs properly
-  - docker tag nfcore/eager nfcore/eager:latest
+  - docker tag nfcore/eager nfcore/eager:2.0.0
 
 install:
   # Install Nextflow
@@ -33,11 +33,14 @@ script:
   # Lint the pipeline code
   - nf-core lint ${TRAVIS_BUILD_DIR}
   # Run the basic pipeline with the test profile
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd
   # Run the basic pipeline with single end data (pretending its single end actually)
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --singleEnd 
   # Run the same pipeline testing optional step: fastp, complexity 
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --complexity_filter 
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --complexity_filter 
   # Test BAM Trimming
-  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --trim_bam 
-
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --trim_bam 
+  # 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

CHANGELOG.md

@@ -1,13 +1,13 @@
 # nf-core/eager: Changelog
 
-## 2.0 "Kaufbeuren" - 2018-10-14
+## 2.0 "Kaufbeuren" - 2018-10-17
 
 Initial release of nf-core/eager featuring:
 
 * FastQC read quality control
 * (Optional) Read complexity filtering with FastP
 * Read merging and clipping using AdapterRemoval v2
-* Mapping using BWA
+* Mapping using BWA / BWA Mem or CircularMapper
 * Library Complexity Estimation with Preseq
 * Conversion and Filtering of BAM files using Samtools
 * Damage assessment via DamageProfiler, additional filtering using PMDTools

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-2.0.0dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.0.0/bin:$PATH

README.md

@@ -21,13 +21,14 @@ The pipeline uses [Nextflow](https://www.nextflow.io), a bioinformatics workflow
     * Sequence Dictionary
 * QC with FastQC
 * AdapterRemoval for read clipping and merging
-* Read mapping with BWA
+* Read mapping with BWA, BWA Mem or CircularMapper
 * Samtools sort, index, stats & conversion to BAM
-* DeDup read deduplication / MarkDuplicates
+* DeDup or MarkDuplicates read deduplication
 * QualiMap BAM QC Checking
-* Preseq estimation
+* Preseq Library Complexity Estimation
 * DamageProfiler damage profiling
-* PMDTools damagge filtering / assessment
+* BAM Clipping for UDG+/UDGhalf protocols
+* PMDTools damage filtering / assessment
 
 ### Documentation
 The nf-core/eager pipeline comes with documentation about the pipeline, found in the `docs/` directory:

Singularity

@@ -4,10 +4,10 @@ Bootstrap:docker
 %labels
     MAINTAINER Alexander Peltzer <[email protected]>
     DESCRIPTION Container image containing all requirements for the nf-core/eager pipeline
-    VERSION 2.0.0dev
+    VERSION 2.0.0
 
 %environment
-    PATH=/opt/conda/envs/nf-core-eager-2.0.0dev/bin:$PATH
+    PATH=/opt/conda/envs/nf-core-eager-2.0.0/bin:$PATH
     export PATH
 
 %files

docs/usage.md

@@ -136,14 +136,23 @@ Please note the following requirements:
 If left unspecified, a default pattern is used: `data/*{1,2}.fastq.gz`
 
 ### `--singleEnd`
-By default, the pipeline expects paired-end data. If you have single-end data, you need to specify `--singleEnd` on the command line when you launch the pipeline. A normal glob pattern, enclosed in quotation marks, can then be used for `--reads`. For example:
+If you have single-end data, you need to specify `--singleEnd` on the command line when you launch the pipeline. A normal glob pattern, enclosed in quotation marks, can then be used for `--reads`. For example:
 
 ```bash
 --singleEnd --reads '*.fastq'
 ```
 
 It is not possible to run a mixture of single-end and paired-end files in one run.
 
+### `--pairedEnd`
+If you have paired-end data, you need to specify `--pairedEnd` on the command line when you launc hthe pipeline. 
+
+A normal glob pattern, enclosed in quotation marks, can then be used for `--reads`. For example:
+
+```bash
+--pairedEnd --reads '*.fastq'
+```
+
 ## Reference Genomes
 
 The pipeline config files come bundled with paths to the illumina iGenomes reference index files. If running with docker or AWS, the configuration is set up to use the [AWS-iGenomes](https://ewels.github.io/AWS-iGenomes/) resource.
@@ -327,6 +336,7 @@ Turns off duplicate removal methods DeDup and MarkDuplicates respectively. No du
 Performs a poly-G complexity filtering step in the beginning of the pipeline if turne on. This can be useful for especially assembly projects where low-complexity regions might dramatically influence the assembly of contigs.
 
 ## Complexity Filtering Options
+
 ### `--complexity_filter_poly_g_min`
 
 This option can be used to define the minimum value for the poly-G filtering step in low complexity filtering. By default, this is set to a value of `10` unless the user has chosen something specifically using this option.
@@ -355,6 +365,8 @@ Sets the minimum overlap between two reads when read merging is performed. Defau
 
 ## Read Mapping Parameters
 
+## BWA (default)
+
 These parameters configure mapping algorithm parameters. 
 
 ### `--bwaalnn`
@@ -369,13 +381,37 @@ Configures the `bwa aln -k` parameter for the seeding phase in the mapping algor
 
 Configures the length of the seed used in `bwa aln -l`. Default is set to BWA default of `32`.
 
+## CircularMapper
+
+### `--circularmapper`
+
+This turns on the CircularMapper application, that enhances the mapping procedure with the BWA algorithm on circular references utilizing a extend-remap procedure (see Peltzer et al 2016, Genome Biology for details). 
+
+### `--circularextension`
+
+The number of bases to extend the reference genome with. By default this is set to `500` if not specified otherwise.
+
+### `--circulartarget`
+
+The chromosome in your FastA reference that you'd like to be treated as circular. By default this is set to `MT` but can be configured to match any other chromosome. 
+
+### `--circularfilter`
+
+If you want to filter out reads that don't map to a circular chromosome, turn this on. By default this option is turned off.
+
+## BWA Mem
+
+### `--bwamem`
+
+Turn this on to utilize BWA Mem instead of `bwa aln` for alignment. Can be quite useful for modern DNA, but is rarely used in projects for ancient DNA.
+
 ## Read Filtering and Conversion Parameters
 
 Users can configure to keep/discard/extract certain groups of reads efficiently in the nf-core/eager pipeline. 
 
 ### `--bam_keep_mapped_only`
 
-This can be used to only keep mapped reads for downstream analysis. By default turned off, all reads are kept in the BAM file.
+This can be used to only keep mapped reads for downstream analysis. By default turned off, all reads are kept in the BAM file. Unmapped reads are stored both in BAM and FastQ format e.g. for different downstream processing.
 
 ### `--bam_keep_all`
 

environment.yml

@@ -1,4 +1,4 @@
-name: nf-core-eager-2.0.0dev
+name: nf-core-eager-2.0.0
 channels:
   - defaults
   - conda-forge