Merge pull request #2 from nf-core/dev

PR for 1.0.0

.github/CONTRIBUTING.md

@@ -6,9 +6,10 @@ We try to manage the required tasks for nf-core/bacass using GitHub issues, you
 
 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/bacass 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/bacass 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/bacass, the standard workflow
 is as follows:
 
@@ -22,24 +23,27 @@ 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.
 
 There are typically two types of tests that run:
 
 ### Lint Tests
+
 The nf-core has a [set of guidelines](http://nf-co.re/guidelines) which all pipelines must adhere to.
 To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
 
 ### Pipeline Tests
+
 Each nf-core pipeline should be set up with a minimal set of test-data.
 Travis CI then runs the pipeline on this data to ensure that it exists successfully.
 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/bacass documentation](https://github.com/nf-core/bacass#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/bacass documentation](https://github.com/nf-core/bacass#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

@@ -9,3 +9,4 @@ tests/test_data
 nohup.out
 tmp/
 ._.DS_Store
+*.pyc

.travis.yml

@@ -11,10 +11,10 @@ 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/bacass:dev
-  - docker pull andreaswilm/bacass:dev
+  - docker pull nfcore/bacass:dev
   # Fake the tag locally so that the pipeline runs properly
-  - docker tag andreaswilm/bacass:dev andreaswilm/bacass: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/bacass:dev nfcore/bacass:1.0.0
 
 install:
   # Install Nextflow
@@ -24,6 +24,8 @@ install:
   # Install nf-core/tools
   - pip install --upgrade pip
   - pip install nf-core
+  # Install markdownlint-cli
+  - sudo apt-get install npm && npm install -g markdownlint-cli
   # Reset
   - mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
 
@@ -34,8 +36,8 @@ env:
 script:
   # Lint the pipeline code
   - nf-core lint ${TRAVIS_BUILD_DIR}
-  # poor man's syntax check
-  - nextflow run ${TRAVIS_BUILD_DIR} -test
+  # 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 +1,9 @@
 # nf-core/bacass: Changelog
 
-## v1.0dev - <date>
+## v1.0.0 nf-core/bacass: "Green Tin Ant"
+
 Initial release of nf-core/bacass, created with the [nf-core](http://nf-co.re/) template.
+
+This pipeline is for bacterial assembly of next-generation sequencing reads. It can be used to quality trim your reads using [Skewer](https://github.com/relipmoc/skewer) and performs basic QC using [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Afterwards, the pipeline performs read assembly using [Unicycler](https://github.com/rrwick/Unicycler) and assesses assembly quality using [QUAST](http://bioinf.spbau.ru/quast). Contamination of the assembly is checked using [Kraken2](https://ccb.jhu.edu/software/kraken2/) to verify sample purity. The resulting bacterial assembly is annotated using [Prokka](https://github.com/tseemann/prokka).
+
+Furthermore, the pipeline creates various reports in the `results` directory specified, including a [MultiQC](https://multiqc.info) report summarizing some of the findings and software versions.

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

@@ -6,4 +6,4 @@ COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
 # for bandage :/ otherwise it complains about missing libGL.so.1
 RUN apt-get install -y libgl1-mesa-glx && apt-get clean -y
-ENV PATH /opt/conda/envs/nf-core-bacass-latest/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-bacass-1.0.0/bin:$PATH

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) Andreas Wilm <[email protected]>
+Copyright (c) Andreas Wilm
 
 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

@@ -1,36 +1,35 @@
-# nf-core/bacass
-**Simple bacterial assembly and annotation pipeline**
+# ![nf-core/bacass](docs/images/nfcore-bacass_logo.png)
 
-[![Build Status](https://travis-ci.org/nf-core/bacass.svg?branch=master)](https://travis-ci.org/nf-core/bacass)
+A simple bacterial assembly and annotation pipeline
+
+[![Build Status](https://travis-ci.com/nf-core/bacass.svg?branch=master)](https://travis-ci.com/nf-core/bacass)
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A518.10.1-brightgreen.svg)](https://www.nextflow.io/)
 
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
 [![Docker](https://img.shields.io/docker/automated/nfcore/bacass.svg)](https://hub.docker.com/r/nfcore/bacass)
-![Singularity Container available](
-https://img.shields.io/badge/singularity-available-7E4C74.svg)
 
-### Introduction
+## Introduction
 
+This pipeline is for bacterial assembly of next-generation sequencing reads. It can be used to quality trim your reads using [Skewer](https://github.com/relipmoc/skewer) and performs basic QC using [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Afterwards, the pipeline performs read assembly using [Unicycler](https://github.com/rrwick/Unicycler) and assesses assembly quality using [QUAST](http://bioinf.spbau.ru/quast). Contamination of the assembly is checked using [Kraken2](https://ccb.jhu.edu/software/kraken2/) to verify sample purity. The resulting bacterial assembly is annotated using [Prokka](https://github.com/tseemann/prokka).
 
-This pipeline is for bacterial assembly of next-gen sequencing reads. It quality-trims your reads, runs QC, including a
-metagenomics classifier on your reads to check for purity, assembles the reads with
-Unicycler, annotates the assembly with Prokka and runs Quast on the assembly for quality check.
+Furthermore, the pipeline creates various reports in the `results` directory specified, including a [MultiQC](https://multiqc.info) report summarizing some of the findings and software versions.
 
-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 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 containers making installation trivial and results highly reproducible.
 
+## Documentation
 
-### Documentation
 The nf-core/bacass 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)
-    * [Reference genomes](docs/configuration/reference_genomes.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)
+5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
+
 
+## Credits
 
-### Credits
-nf-core/bacass was originally written by Andreas Wilm.
+nf-core/bacass was originally written by [Andreas Wilm](https://github.com/andreas-wilm) and is currently maintained by [Alexander Peltzer](https://github.com/apeltzer).

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/bacass: Simple bacterial assembly and annotation pipeline">
+  <meta name="description" content="nf-core/bacass: Simple bacterial assembly and annotation pipeline.">
   <title>nf-core/bacass Pipeline Report</title>
 </head>
 <body>

assets/email_template.txt

@@ -17,23 +17,6 @@ ${errorReport}
 } %>
 
 
-<% if (!success){
-    out << """####################################################
-## nf-core/bacass 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/bacass execution completed successfully! ##"
-}
-%>
-
-
-
-
 The workflow was completed at $dateComplete (duration: $duration)
 
 The command used to launch the workflow was as follows:

conf/multiqc_config.yaml → assets/multiqc_config.yaml

@@ -5,3 +5,5 @@ report_comment: >
 report_section_order:
     nf-core/bacass-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/scrape_software_versions.py

@@ -3,18 +3,28 @@
 from collections import OrderedDict
 import re
 
-# TODO nf-core: Add additional regexes for new tools in process get_software_versions
 regexes = {
     'nf-core/bacass': ['v_pipeline.txt', r"(\S+)"],
     'Nextflow': ['v_nextflow.txt', r"(\S+)"],
     'FastQC': ['v_fastqc.txt', r"FastQC v(\S+)"],
     'MultiQC': ['v_multiqc.txt', r"multiqc, version (\S+)"],
+    'Skewer': ['v_skewer.txt', r"version: (\S+)"],
+    'Kraken2': ['v_kraken2.txt', r"([\d\.]+)-beta"],
+    'Quast': ['v_quast.txt', r"QUAST v(\S+)"],
+    'Prokka': ['v_prokka.txt', r"prokka (\S+)"],
+    'Bandage': ['v_bandage.txt', r"Version: (\S+)"],    
 }
+
 results = OrderedDict()
 results['nf-core/bacass'] = '<span style="color:#999999;\">N/A</span>'
 results['Nextflow'] = '<span style="color:#999999;\">N/A</span>'
 results['FastQC'] = '<span style="color:#999999;\">N/A</span>'
 results['MultiQC'] = '<span style="color:#999999;\">N/A</span>'
+results['Skewer'] = '<span style="color:#999999;\">N/A</span>'
+results['Kraken2'] = '<span style="color:#999999;\">N/A</span>'
+results['Quast'] = '<span style="color:#999999;\">N/A</span>'
+results['Prokka'] = '<span style="color:#999999;\">N/A</span>'
+results['Bandage'] = '<span style="color:#999999;\">N/A</span>'
 
 # Search each file using its regex
 for k, v in regexes.items():
@@ -24,9 +34,14 @@
         if match:
             results[k] = "v{}".format(match.group(1))
 
+# Remove software set to false in results
+for k in results:
+    if not results[k]:
+        del(results[k])
+
 # Dump to YAML
 print ('''
-id: 'nf-core/bacass-software-versions'
+id: 'software_versions'
 section_name: 'nf-core/bacass Software Versions'
 section_href: 'https://github.com/nf-core/bacass'
 plot_type: 'html'
@@ -35,5 +50,10 @@
     <dl class="dl-horizontal">
 ''')
 for k,v in results.items():
-    print("        <dt>{}</dt><dd>{}</dd>".format(k,v))
+    print("        <dt>{}</dt><dd><samp>{}</samp></dd>".format(k,v))
 print ("    </dl>")
+
+# Write out regexes as csv file:
+with open('software_versions.csv', 'w') as f:
+    for k,v in results.items():
+        f.write("{}\t{}\n".format(k,v))

conf/awsbatch.config

@@ -1,10 +1,15 @@
 /*
  * -------------------------------------------------
- *  Nextflow config file for AWS Batch
+ *  Nextflow config file for running on AWS batch
  * -------------------------------------------------
- * Imported under the 'awsbatch' Nextflow profile in nextflow.config
- * Uses docker for software depedencies automagically, so not specified here.
+ * Base config needed for running with -profile awsbatch
  */
+params {
+  config_profile_name = 'AWSBATCH'
+  config_profile_description = 'AWSBATCH Cloud Profile'
+  config_profile_contact = 'Alexander Peltzer (@apeltzer)'
+  config_profile_url = 'https://aws.amazon.com/de/batch/'
+}
 
 aws.region = params.awsregion
 process.executor = 'awsbatch'