Fixed reported bugs, updated docs and added custom config option

.travis.yml

@@ -1,38 +1,37 @@
-sudo: required
-language: python
-jdk: openjdk8
-services: docker
-python: '3.6'
-cache: pip
-matrix:
-  fast_finish: true
-
-before_install:
-  # PRs to master are only ok if coming from dev branch
-  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])'
-  # Pull the docker image first so the test doesn't wait for this
-  - docker pull nfcore/chipseq
-  # Fake the tag locally so that the pipeline runs properly
-  - docker tag nfcore/chipseq nfcore/chipseq:latest
-
-install:
-  # Install Nextflow
-  - mkdir /tmp/nextflow && cd /tmp/nextflow
-  - wget -qO- get.nextflow.io | bash
-  - sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
-  # Install nf-core/tools
-  - pip install nf-core
-  # Reset
-  - mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
-
-env:
-  - NXF_VER='0.31.1' # Specify a minimum NF version that should be tested and work
-  - NXF_VER='' # Plus: get the latest NF version and check that it works
-
-script:
-  # Lint the pipeline code
-  - "nf-core lint ${TRAVIS_BUILD_DIR}"
-  # Run, build reference genome
-  - travis_wait 20 nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --saveReference
-  # Basic run with supplied reference
-  - travis_wait 20 nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --bwa_index ${TRAVIS_BUILD_DIR}/tests/results/reference_genome/BWAIndex/
+sudo: required
+language: python
+jdk: openjdk8
+services: docker
+python: '3.6'
+cache: pip
+matrix:
+  fast_finish: true
+
+before_install:
+  # PRs to master are only ok if coming from dev branch
+  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])'
+  # Pull the docker image first so the test doesn't wait for this
+  - docker pull nfcore/chipseq:dev
+  # Fake the tag locally so that the pipeline runs properly
+  - docker tag nfcore/chipseq:dev nfcore/chipseq:latest
+
+install:
+  # Install Nextflow
+  - mkdir /tmp/nextflow && cd /tmp/nextflow
+  - wget -qO- get.nextflow.io | bash
+  - sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
+  # Install nf-core/tools
+  - pip install --upgrade pip # Get rid of dependency resolve issues from older pip versions
+  - pip install nf-core
+  # Reset
+  - mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
+
+env:
+  - NXF_VER='0.32.0' # Specify a minimum NF version that should be tested and work
+  - NXF_VER='' # Plus: get the latest NF version and check that it works
+
+script:
+  # Lint the pipeline code
+  - nf-core lint ${TRAVIS_BUILD_DIR}
+  # Run the pipeline with the test profile
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker

CHANGELOG.md

@@ -1,5 +1,5 @@
-## nf-core/chipseq v1.0
-v1.0 release of nf-core/chipseq
+## nf-core/chipseq v1.0dev
+v1.0dev nf-core/chipseq
 * Add option for building BWA index for larger ref
 * Update software versions in uppmax-modules
 * Add function to validate input files in MACS config file
@@ -9,5 +9,17 @@ v1.0 release of nf-core/chipseq
 * Add blacklist files for ce10, dm3, hg38, and mm9
 * Documents revised accordingly.
 
+05/02/2019 17:11:13
+* Major overhaul of docs and assets in-line with nf-core/tools v1.4
+* Added ability to use nf-core/configs along with associated docs
+* Updated manifest scope to deal with pipeline version
+* Removed NGI and SciLifeLab logos, and changed name of pipeline logo
+* Added awsbatch configuration
+* Put file() calls in fromFilePath()
+* Removed --project param specific to UPPMAX
+* Moved appropriate default params variables to nextflow.config
+* Changed Picard memory specification
+* Changed version number back to 1.0dev from 1.0
+* Updated conda packages
 
 Repository moved from https://github.com/SciLifeLab/NGI-ChIPseq

CODE_OF_CONDUCT.md

@@ -0,0 +1,46 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on the [Gitter channel](https://gitter.im/nf-core/Lobby). The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

Dockerfile

@@ -5,4 +5,4 @@ LABEL authors="[email protected]" \
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-chipseq-1.0/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-chipseq-1.0dev/bin:$PATH

README.md

@@ -1,13 +1,10 @@
-# ![nf-core/chipseq](docs/images/chipseq_logo.png)
+# ![nf-core/chipseq](docs/images/nfcore-chipseq_logo.png)
 
 [![Build Status](https://travis-ci.org/nf-core/chipseq.svg?branch=master)](https://travis-ci.org/nf-core/chipseq)
-[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.31.1-brightgreen.svg)](https://www.nextflow.io/)
-[![Gitter](https://img.shields.io/badge/gitter-%20join%20chat%20%E2%86%92-4fb99a.svg)](https://gitter.im/nf-core/Lobby)
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.32.0-brightgreen.svg)](https://www.nextflow.io/)
 
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
-[![Docker Container available](https://img.shields.io/docker/automated/nfcore/chipseq.svg)](https://hub.docker.com/r/nfcore/chipseq/)
-[![https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://singularity-hub.org/collections/1123)
-
+[![Docker](https://img.shields.io/docker/automated/nfcore/chipseq.svg)](https://hub.docker.com/r/nfcore/chipseq/)
 
 ## Introduction
 **nf-core/chipseq** is a bioinformatics best-practice analysis pipeline used for chromatin immunoprecipitation (ChIP-seq) data analysis.
@@ -17,29 +14,30 @@ The pipeline uses [Nextflow](https://www.nextflow.io), a bioinformatics workflow
 ### Pipeline Steps
 
 * Make BWA reference genome index (optional)
-* FastQC
-* TrimGalore!
-* Align with BWA
-* Samtools sort, index, stats & convert to BED
-* Samtools idxstats
-* Picard MarkDuplicates
-* Count read statistics
-* PhantomPeakQualTools
-* SPP: Calculate NSCRSC and cross correlation
-* DeepTools bamPEFragmentSize, plotFingerprint, bamCoverage, multiBamSummary, plotCorrelation, plotPCA, computeMatrix, plotProfile
+* FastQC raw sequencing reads quality control
+* TrimGalore! adapter trimming
+* BWA alignment against reference genome
+* Samtools post-alignment processing and format conversion
+* Picard duplicate read identification
+* Statistics about read counts
+* PhantomPeakQualTools normalized strand cross-correlation (NSC) and relative strand cross-correlation (RSC)
+* deepTools fingerprint, coverage bigwig, correlation plots of reads over genome-wide bins, and distribution of reads around gene bodies
 * MACS2 peak calling
-* Saturation analysis
-* ChIP peak annotation
+* Saturation analysis (optional)
+* Post peak calling processing: blacklist filtering and annotation
 * MultiQC
 
-
 ### Documentation
 The nf-core/chipseq pipeline comes with documentation about the pipeline, found in the `docs/` directory:
 
-1. [Installation and configuration](docs/installation.md)
-2. [Running the pipeline](docs/usage.md)
-3. [Output and how to interpret the results](docs/output.md)
-
+1. [Installation](docs/installation.md)
+2. Pipeline configuration
+    * [Local installation](docs/configuration/local.md)
+    * [Adding your own system](docs/configuration/adding_your_own.md)
+    * [Reference genomes](docs/configuration/reference_genomes.md)
+3. [Running the pipeline](docs/usage.md)
+4. [Output and how to interpret the results](docs/output.md)
+5. [Troubleshooting](docs/troubleshooting.md)
 
 ## Credits
 These scripts were written for use at the [National Genomics Infrastructure](https://portal.scilifelab.se/genomics/)

Singularity

@@ -4,10 +4,10 @@ Bootstrap:docker
 %labels
     MAINTAINER Alexander Peltzer <[email protected]>
     DESCRIPTION Container image containing all requirements for the nf-core/chipseq pipeline
-    VERSION 1.0
+    VERSION 1.0dev
 
 %environment
-    PATH=/opt/conda/envs/nf-core-chipseq-1.0/bin:$PATH
+    PATH=/opt/conda/envs/nf-core-chipseq-1.0dev/bin:$PATH
     export PATH
 
 %files

assets/email_template.html

@@ -1,21 +1,20 @@
 <html>
 <head>
+  <head>
+  <meta charset="utf-8">
+  <meta http-equiv="X-UA-Compatible" content="IE=edge">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
+
+  <meta name="description" content="nf-core/chipseq: ChIP-seq analysis using BWA and MACS2 with QC steps.">
+  <title>nf-core/chipseq Pipeline Report</title>
 </head>
 <body>
 <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
-<img src="cid:nfcorechipseqlogo">
-
-<h1>nf-core/chipseq: ChIP-Seq Best Practice v${version}</h1>
+<h1>nf-core/chipseq v${version}</h1>
 <h2>Run Name: $runName</h2>
 
-<% if (success){
-    out << """
-    <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        nf-core/chipseq execution completed successfully!
-    </div>
-    """
-} else {
+<% if (!success){
     out << """
     <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
         <h4 style="margin-top:0; color: inherit;">nf-core/chipseq execution completed unsuccessfully!</h4>
@@ -24,6 +23,12 @@ <h4 style="margin-top:0; color: inherit;">nf-core/chipseq execution completed un
         <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
     </div>
     """
+} else {
+    out << """
+    <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+        nf-core/chipseq execution completed successfully!
+    </div>
+    """
 }
 %>
 
@@ -38,14 +43,8 @@ <h3>Pipeline Configuration:</h3>
     </tbody>
 </table>
 
-<p>nf-core/chipseq is a bioinformatics best-practice analysis pipeline used for ChIP-sequencing data. It is developed at the National Genomics Infastructure at SciLifeLab Stockholm, Sweden.</p>
-<p>The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.</p>
-<p>For more information, please see the pipeline homepage: <a href="https://github.com/nf-core/chipseq">https://github.com/nf-core/chipseq</a></p>
-
-<hr style="height: 3px; padding: 0; margin: 24px 0; background-color: #e1e4e8; border: 0;">
-
-<img src="cid:scilifelablogo">
-<img src="cid:ngilogo">
+<p>nf-core/chipseq</p>
+<p><a href="https://github.com/nf-core/chipseq">https://github.com/nf-core/chipseq</a></p>
 
 </div>
 

assets/email_template.txt

@@ -1,6 +1,6 @@
-===============================================
- nf-core/chipseq: ChIP-Seq Best Practice v${version}
-===============================================
+========================================
+ nf-core/chipseq v${version}
+========================================
 Run Name: $runName
 
 <% if (success){
@@ -11,9 +11,28 @@ Run Name: $runName
 ####################################################
 The exit status of the task that caused the workflow execution to fail was: $exitStatus.
 The full error message was:
+
+${errorReport}
+"""
+} %>
+
+
+<% if (!success){
+    out << """####################################################
+## nf-core/chipseq execution completed unsuccessfully! ##
+####################################################
+The exit status of the task that caused the workflow execution to fail was: $exitStatus.
+The full error message was:
+
 ${errorReport}
 """
-} %>s
+} else {
+    out << "## nf-core/chipseq execution completed successfully! ##"
+}
+%>
+
+
+
 
 The workflow was completed at $dateComplete (duration: $duration)
 
@@ -28,6 +47,5 @@ Pipeline Configuration:
 <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %>
 
 --
-nf-core/chipseq is a bioinformatics best-practice analysis pipeline used for ChIP-sequencing data. It is developed at the National Genomics Infastructure at SciLifeLab Stockholm, Sweden.
-The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
-For more information, please see the pipeline homepage: https://github.com/nf-core/chipseq
+nf-core/chipseq
+https://github.com/nf-core/chipseq

conf/multiqc_config.yaml → assets/multiqc_config.yaml

@@ -9,7 +9,6 @@ report_comment: >
     This report has been generated by the <a href="https://github.com/nf-core/chipseq" target="_blank">nf-core/chipseq</a>
     analysis pipeline. For information about how to interpret these results, please see the
     <a href="https://github.com/nf-core/chipseq/blob/master/docs/output.md" target="_blank">documentation</a>.
-custom_data:
 report_section_order:
     nfcore-chipseq:
         order: -1000