Dev to master

.travis.yml

@@ -38,4 +38,6 @@ script:
   - 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 
+  # Test BAM Trimming
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --trim_bam 
 

CHANGELOG.md

@@ -4,15 +4,15 @@
 
 Initial release of nf-core/eager featuring:
 
-* QC Using FastQC/FastP
+* FastQC read quality control
+* (Optional) Read complexity filtering with FastP
 * Read merging and clipping using AdapterRemoval v2
 * Mapping using BWA
+* Library Complexity Estimation with Preseq
 * Conversion and Filtering of BAM files using Samtools
 * Damage assessment via DamageProfiler, additional filtering using PMDTools
-* Library Complexity Estimation with Preseq
-* BAM Clipping with BamUtil for UDGhalf protocols
-* QualiMap BAM QC 
 * Duplication removal via DeDup 
+* BAM Clipping with BamUtil for UDGhalf protocols
+* QualiMap BAM quality control analysis
 
-TODO sort this in order of analysis 
-
+Furthermore, this already creates an interactive report using MultiQC, which will be upgraded in V2.1 "Ulm" to contain more aDNA specific metrics.

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-2.0dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.0.0dev/bin:$PATH

README.md

@@ -8,23 +8,26 @@
 ![Singularity Container available](https://img.shields.io/badge/singularity-available-7E4C74.svg)
 
 ## Introduction
-THIS PIPELINE IS A WORK IN PROGRESS. Thanks for checking it out! Hopefully it will be functional soon.
 
 **nf-core/eager** is a bioinformatics best-practice analysis pipeline for ancient DNA data analysis.
 
 The pipeline uses [Nextflow](https://www.nextflow.io), a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results. It comes with docker / singularity containers making installation trivial and results highly reproducible.
 
 ### Pipeline steps
 
-* Make BWA reference genome index (optional)
-* FastQC
+* Create reference genome indices (optional)
+    * BWA 
+    * Samtools Index
+    * Sequence Dictionary
+* QC with FastQC
 * AdapterRemoval for read clipping and merging
-* Align with BWA
+* Read mapping with BWA
 * Samtools sort, index, stats & conversion to BAM
-* DeDup read deduplication or MarkDuplicates
+* DeDup read deduplication / MarkDuplicates
 * QualiMap BAM QC Checking
 * Preseq estimation
 * DamageProfiler damage profiling
+* PMDTools damagge filtering / assessment
 
 ### Documentation
 The nf-core/eager pipeline comes with documentation about the pipeline, found in the `docs/` directory:

Singularity

@@ -2,29 +2,17 @@ From:nfcore/base
 Bootstrap:docker
 
 %labels
-<<<<<<< HEAD
     MAINTAINER Alexander Peltzer <alexander.peltzer@qbic.uni-tuebingen.de>
-    DESCRIPTION Container image containing all requirements for the nf-core/EAGER2 pipeline
-    VERSION 2.0dev
+    DESCRIPTION Container image containing all requirements for the nf-core/eager pipeline
+    VERSION 2.0.0dev
 
 %environment
-    PATH=/opt/conda/envs/nf-core-eager-2.0dev/bin:$PATH
-=======
-    DESCRIPTION Singularity image containing all requirements for the nf-core/eager pipeline
-    VERSION 1.0dev
-
-%environment
-    PATH=/opt/conda/envs/nf-core-eager-1.0dev/bin:$PATH
->>>>>>> TEMPLATE
+    PATH=/opt/conda/envs/nf-core-eager-2.0.0dev/bin:$PATH
     export PATH
 
 %files
     environment.yml /
 
 %post
-<<<<<<< HEAD
     /opt/conda/bin/conda env create -f /environment.yml 
-=======
-    /opt/conda/bin/conda env create -f /environment.yml
->>>>>>> TEMPLATE
     /opt/conda/bin/conda clean -a

assets/where_are_my_files.txt

@@ -0,0 +1,29 @@
+=====================
+ Where are my files?
+=====================
+
+By default, the nfcore/eager pipeline does not save large intermediate files to the
+results directory. This is to try to conserve disk space.
+
+These files can be found in the pipeline `work` directory if needed.
+Alternatively, re-run the pipeline using `-resume` in addition to one of
+the below command-line options and they will be copied into the results directory:
+
+`--saveReference`
+Save any downloaded or generated reference genome files to your results folder.
+These can then be used for future pipeline runs, reducing processing times.
+
+-----------------------------------
+ Setting defaults in a config file
+-----------------------------------
+If you would always like these files to be saved without having to specify this on
+the command line, you can save the following to your personal configuration file
+(eg. `~/.nextflow/config`):
+
+params.saveReference = true
+
+For more help, see the following documentation:
+
+https://github.com/nf-core/eager/blob/master/docs/usage.md
+https://www.nextflow.io/docs/latest/getstarted.html
+https://www.nextflow.io/docs/latest/config.html

docs/installation.md

@@ -14,7 +14,6 @@ To start using the nf-core/eager pipeline, follow the steps below:
 4. [Reference genomes](#4-reference-genomes)
 5. [Appendices](#appendices)
     * [Running on UPPMAX](#running-on-uppmax)
->>>>>>> TEMPLATE
 
 ## 1) Install NextFlow
 Nextflow runs on most POSIX systems (Linux, Mac OSX etc). It can be installed by running the following commands:

docs/troubleshooting.md

@@ -1,9 +1,8 @@
 # nf-core/eager: Troubleshooting
->>>>>>> TEMPLATE
 
 ## Input files not found
 
-If only 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
+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
 
 1. The path must be enclosed in quotes (`'` or `"`)
 2. The path must have at least one `*` wildcard character. This is even if you are only running one paired end sample.