Merge pull request #1 from nf-core/master

First release of nf-core Hi-C pipeline

.github/CONTRIBUTING.md

@@ -6,7 +6,9 @@ We try to manage the required tasks for nf-core/hic using GitHub issues, you pro
 
 However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;)
 
-> If you need help using or modifying nf-core/hic then the best place to go is the Gitter chatroom where you can ask us questions directly: https://gitter.im/nf-core/Lobby
+> If you need help using or modifying nf-core/hic then the best place to ask is on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).
+
+
 
 ## Contribution workflow
 If you'd like to write some code for nf-core/hic, the standard workflow
@@ -42,4 +44,4 @@ If there are any failures then the automated tests fail.
 These tests are run both with the latest available version of Nextflow and also the minimum required version that is stated in the pipeline code.
 
 ## Getting help
-For further information/help, please consult the [nf-core/hic documentation](https://github.com/nf-core/hic#documentation) and don't hesitate to get in touch on [Gitter](https://gitter.im/nf-core/Lobby)
+For further information/help, please consult the [nf-core/hic documentation](https://github.com/nf-core/hic#documentation) and don't hesitate to get in touch on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).

.github/markdownlint.yml

@@ -0,0 +1,9 @@
+# Markdownlint configuration file
+default: true,
+line-length: false
+no-multiple-blanks: 0
+blanks-around-headers: false
+blanks-around-lists: false
+header-increment: false
+no-duplicate-header:
+    siblings_only: true

.gitignore

@@ -4,3 +4,4 @@ data/
 results/
 .DS_Store
 tests/test_data
+*.pyc

.travis.yml

@@ -13,7 +13,8 @@ before_install:
   # Pull the docker image first so the test doesn't wait for this
   - docker pull nfcore/hic:dev
   # Fake the tag locally so that the pipeline runs properly
-  - docker tag nfcore/hic:dev nfcore/hic:latest
+  # Looks weird when this is :dev to :dev, but makes sense when testing code for a release (:dev to :1.0.1)
+  - docker tag nfcore/hic:dev nfcore/hic:1.0.0
 
 install:
   # Install Nextflow
@@ -25,12 +26,17 @@ install:
   - pip install nf-core
   # Reset
   - mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
+  # Install markdownlint-cli
+  - sudo apt-get install npm && npm install -g markdownlint-cli
 
 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}
+  # Lint the documentation
+  - markdownlint ${TRAVIS_BUILD_DIR} -c ${TRAVIS_BUILD_DIR}/.github/markdownlint.yml
   # Run the pipeline with the test profile
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker

CHANGELOG.md

@@ -1,15 +1,17 @@
 # nf-core/hic: Changelog
 
-## v1.0dev - 2019-04-09
-
-	First version of nf-core-hic pipeline which is a Nextflow implementation of the HiC-Pro pipeline [https://github.com/nservant/HiC-Pro].
-	Note that all HiC-Pro functionalities are not yet all implemented. The current version is designed for protocols based on restriction enzyme digestion.
-
-	In summary, this version allows :
-	* Automatic detection and generation of annotation files based on igenomes if not provided.
-	* Two-steps alignment of raw sequencing reads
-	* Reads filtering and detection of valid interaction products
-	* Generation of raw contact matrices for a set of resolutions
-	* Normalization of the contact maps using the ICE algorithm
-	* Generation of cooler file for visualization on higlass [https://higlass.io/]
-	* Quality report based on HiC-Pro MultiQC module
+## v1.0 - 2019-05-06
+
+First version of nf-core Hi-C pipeline which is a Nextflow implementation of the [HiC-Pro pipeline](https://github.com/nservant/HiC-Pro/).
+Note that all HiC-Pro functionalities are not yet all implemented.
+The current version supports most protocols including Hi-C, in situ Hi-C, DNase Hi-C, Micro-C, capture-C or HiChip data.
+
+In summary, this version allows :
+
+* Automatic detection and generation of annotation files based on igenomes if not provided.
+* Two-steps alignment of raw sequencing reads
+* Reads filtering and detection of valid interaction products
+* Generation of raw contact matrices for a set of resolutions
+* Normalization of the contact maps using the ICE algorithm
+* Generation of cooler file for visualization on [higlass](https://higlass.io/)
+* Quality report based on HiC-Pro MultiQC module

CODE_OF_CONDUCT.md

@@ -34,7 +34,7 @@ This Code of Conduct applies both within project spaces and in public spaces whe
 
 ## 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.
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on [Slack](https://nf-core-invite.herokuapp.com/). 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.
 

Dockerfile

@@ -2,6 +2,9 @@ FROM nfcore/base
 LABEL authors="Nicolas Servant" \
       description="Docker image containing all requirements for nf-core/hic pipeline"
 
+## Install gcc for pip iced install
+RUN apt-get update && apt-get install -y gcc g++ && apt-get clean -y
+
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-hic-1.0dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-hic-1.0.0/bin:$PATH

README.md

@@ -1,8 +1,8 @@
 # ![nf-core/hic](docs/images/nfcore-hic_logo.png)
 
-**Analysis of Chromosome Conformation Capture data (Hi-C)**
+**Analysis of Chromosome Conformation Capture data (Hi-C)**.
 
-[![Build Status](https://travis-ci.org/nf-core/hic.svg?branch=master)](https://travis-ci.org/nf-core/hic)
+[![Build Status](https://travis-ci.com/nf-core/hic.svg?branch=master)](https://travis-ci.com/nf-core/hic)
 [![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/)
@@ -12,8 +12,9 @@ https://img.shields.io/badge/singularity-available-7E4C74.svg)
 
 ### Introduction
 This pipeline is based on the [HiC-Pro workflow](https://github.com/nservant/HiC-Pro).
-It was designed to process Hi-C data from raw fastq files (paired-end Illumina data) to normalized contact maps. The current version supports digestion protocols.
-Support for other protocols is ongoing.
+It was designed to process Hi-C data from raw fastq files (paired-end Illumina data) to normalized contact maps.
+The current version supports most protocols, including digestion protocols as well as protocols that do not require restriction enzymes such as DNase Hi-C.
+In practice, this workflow was successfully applied to many data-sets including dilution Hi-C, in situ Hi-C, DNase Hi-C, Micro-C, capture-C, capture Hi-C or HiChip data.
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
 

assets/email_template.txt

@@ -17,23 +17,6 @@ ${errorReport}
 } %>
 
 
-<% if (!success){
-    out << """####################################################
-## nf-core/hic execution completed unsuccessfully! ##
-####################################################
-The exit status of the task that caused the workflow execution to fail was: $exitStatus.
-The full error message was:
-
-${errorReport}
-"""
-} else {
-    out << "## nf-core/hic execution completed successfully! ##"
-}
-%>
-
-
-
-
 The workflow was completed at $dateComplete (duration: $duration)
 
 The command used to launch the workflow was as follows:

assets/multiqc_config.yaml

@@ -0,0 +1,9 @@
+report_comment: >
+    This report has been generated by the <a href="https://github.com/nf-core/hic" target="_blank">nf-core/hic</a>
+    analysis pipeline. For information about how to interpret these results, please see the
+    <a href="https://github.com/nf-core/hic" target="_blank">documentation</a>.
+report_section_order:
+    nf-core/hic-software-versions:
+        order: -1000
+
+export_plots: true

assets/sendmail_template.txt

@@ -1,11 +1,36 @@
 To: $email
 Subject: $subject
 Mime-Version: 1.0
-Content-Type: multipart/related;boundary="nfmimeboundary"
+Content-Type: multipart/related;boundary="nfcoremimeboundary"
 
---nfmimeboundary
+--nfcoremimeboundary
 Content-Type: text/html; charset=utf-8
 
 $email_html
 
---nfmimeboundary--
+<%
+if (mqcFile){
+def mqcFileObj = new File("$mqcFile")
+if (mqcFileObj.length() < mqcMaxSize){
+out << """
+--nfcoremimeboundary
+Content-Type: text/html; name=\"multiqc_report\"
+Content-Transfer-Encoding: base64
+Content-ID: <mqcreport>
+Content-Disposition: attachment; filename=\"${mqcFileObj.getName()}\"
+
+${mqcFileObj.
+  bytes.
+  encodeBase64().
+  toString().
+  tokenize( '\n' )*.
+  toList()*.
+  collate( 76 )*.
+  collect { it.join() }.
+  flatten().
+  join( '\n' )}
+"""
+}}
+%>
+
+--nfcoremimeboundary--