Merge pull request #38 from nf-core/dev

Major changes towards release

.github/CONTRIBUTING.md

@@ -6,7 +6,7 @@ We try to manage the required tasks for nf-core/bcellmagic using GitHub issues,
 
 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/bcellmagic 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/bcellmagic 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/bcellmagic, the standard workflow
@@ -22,7 +22,6 @@ is as follows:
 
 If you're not used to this workflow with git, you can start with some [basic docs from GitHub](https://help.github.com/articles/fork-a-repo/) or even their [excellent interactive tutorial](https://try.github.io/).
 
-
 ## Tests
 When you create a pull request with changes, [Travis CI](https://travis-ci.org/) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
@@ -42,4 +41,4 @@ 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/bcellmagic documentation](https://github.com/nf-core/bcellmagic#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/bcellmagic documentation](https://github.com/nf-core/bcellmagic#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

@@ -5,4 +5,7 @@ results/
 .DS_Store
 tests/test_data
 runBcellmagic.sh
-.idea/
+.idea/
+*.pyc
+node_modules/
+package-lock.json

.travis.yml

@@ -11,20 +11,23 @@ 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/bcellmagic
+  - docker pull nfcore/bcellmagic:dev
   # Fake the tag locally so that the pipeline runs properly
-  - docker tag nfcore/bcellmagic nfcore/bcellmagic: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/bcellmagic:dev nfcore/bcellmagic:1.0.0
 
 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 
+  - pip install --upgrade pip
   - 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
@@ -33,5 +36,7 @@ env:
 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

@@ -1,4 +1,5 @@
 # nf-core/bcellmagic: Changelog
 
-## v1.0dev - <date>
+## v1.0.0 - 2019-04-16 - "Alohomora"
+
 Initial release of nf-core/bcellmagic, created with the [nf-core](http://nf-co.re/) template.

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

@@ -1,4 +1,8 @@
-FROM kleinstein/immcantation:2.6.0
-LABEL authors="Gisela Gabernet" \
+FROM nfcore/base
+LABEL authors="Gisela Gabernet, Simon Heumos, Alexander Peltzer" \
       description="Docker image containing all requirements for nf-core/bcellmagic pipeline"
-RUN sudo dnf install -y bash
+
+COPY environment.yml /
+RUN conda env create -f /environment.yml && conda clean -a
+ENV PATH /opt/conda/envs/nf-core-bcellmagic-1.0.0/bin:$PATH
+RUN ln -s /opt/conda/envs/nf-core-bcellmagic-1.0.0/bin/vsearch /opt/conda/envs/nf-core-bcellmagic-1.0.0/bin/usearch

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) Gisela Gabernet
+Copyright (c) Gisela Gabernet, Simon Heumos, Alexander Peltzer
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,6 +1,6 @@
 # nf-core/bcellmagic
 
-A pipeline to analyze B-cell repertoires based on [Immcantation 2.5.0](https://immcantation.readthedocs.io/en/version-2.5.0/).
+A pipeline to analyze B-cell repertoires.
 
 [![Build Status](https://travis-ci.org/nf-core/bcellmagic.svg?branch=master)](https://travis-ci.org/nf-core/bcellmagic)
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.32.0-brightgreen.svg)](https://www.nextflow.io/)
@@ -11,33 +11,22 @@ A pipeline to analyze B-cell repertoires based on [Immcantation 2.5.0](https://i
 https://img.shields.io/badge/singularity-available-7E4C74.svg)
 
 ### Introduction
-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.
 
+The nf-core/bcellmagic pipeline is built to analyze B-cell repertoire sequencing data from targeted amplification experiments. It makes use of the [Immcantation 2.5.0](https://immcantation.readthedocs.io/en/version-2.5.0/) toolset for the analysis of B-cell repertoires.
+
+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.
 
-### Documentation
+## Documentation
 The nf-core/bcellmagic pipeline comes with documentation about the pipeline, found in the `docs/` directory:
 
-1. [Installation](docs/installation.md)
+1. [Installation](https://nf-co.re/usage/installation)
 2. Pipeline configuration
-    * [Local installation](docs/configuration/local.md)
-    * [Adding your own system](docs/configuration/adding_your_own.md)
+    * [Local installation](https://nf-co.re/usage/local_installation)
+    * [Adding your own system config](https://nf-co.re/usage/adding_own_config)
+    * [Reference genomes](https://nf-co.re/usage/reference_genomes)
 3. [Running the pipeline](docs/usage.md)
 4. [Output and how to interpret the results](docs/output.md)
-5. [Troubleshooting](docs/troubleshooting.md)
-
-Input needs to be a TSV file following this format in general:
-
-```
-ID	Source	Treatment	Extraction_time	Population	R1	R2	I1
-QMKMK072AD	Patient 2	Terifluomid	baseline	p	sample_S8_L001_R1_001.fastq.gz	sample_S8_L001_R2_001.fastq.gz	sample_S8_L001_I1_001.fastq.gz
-```
-Attention, the R1/R2 and I1 naming patterns are crucial!
-
-An example call of the pipeline could be then:
-
-```
-nextflow run ggabernet/bcellmagic -profile standard,docker --metadata metasheet_test.tsv --cprimers CPrimers_IG.fasta --vprimers VPrimers.fasta --max_memory 8.GB --max_cpus 8 -resume 
-```
+5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
 
-### Credits
-nf-core/bcellmagic was originally written by Gisela Gabernet, Simon Heumos and Alexander Peltzer.
+## Credits
+nf-core/bcellmagic was originally written by Gisela Gabernet, Simon Heumos, Alexander Peltzer.

assets/email_template.html

@@ -5,7 +5,7 @@
   <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/bcellmagic: Well, its magic? ">
+  <meta name="description" content="nf-core/bcellmagic: B/T cell repertoire analysis pipeline with immcantation framework. WIP, currently requires a bunch of changes first.">
   <title>nf-core/bcellmagic Pipeline Report</title>
 </head>
 <body>

assets/multiqc_config.yaml

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

bin/alakazam.R

@@ -15,17 +15,17 @@ inputtable = args[1]
 
 output_folder = dirname(inputtable)
 
-db <- readChangeoDb(inputtable)
+#db <- readChangeoDb(inputtable)
 
-dbsubset <- subset(db, C_PRIMER %in% c("IgG", "IgA", "IgM"))
+#dbsubset <- subset(db, C_PRIMER %in% c("IgG", "IgA", "IgM"))
 
 # Calculate and plot rank abundance curve
-a <- estimateAbundance(dbsubset, group="C_PRIMER")
-ggsave(paste(output_folder,"abundance.pdf",sep="/"), plotAbundanceCurve(a,silent=T))
+#a <- estimateAbundance(dbsubset, group="C_PRIMER")
+#ggsave(paste(output_folder,"abundance.pdf",sep="/"), plotAbundanceCurve(a,silent=T))
 
 # Generate Hill diversity curve
-d <- rarefyDiversity(dbsubset, group="C_PRIMER")
-ggsave(paste(output_folder,"diversity.pdf",sep="/"), plotDiversityCurve(d,silent=T))
+#d <- rarefyDiversity(dbsubset, group="C_PRIMER")
+#ggsave(paste(output_folder,"diversity.pdf",sep="/"), plotDiversityCurve(d,silent=T))
 
 # # Calculate CD3 amino acid properties
 # p <- aminoAcidProperties(dbsubset, seq="JUNCTION", nt = T, trim=T, label="CDR3")