Update template to v1.7

.github/CONTRIBUTING.md

@@ -6,7 +6,7 @@ We try to manage the required tasks for nf-core/nanodemux using GitHub issues, y
 
 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/nanodemux then the best place to ask is on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).
+> If you need help using or modifying nf-core/nanodemux then the best place to ask is on the pipeline channel on [Slack](https://nf-co.re/join/slack/).
 
 
 
@@ -32,7 +32,7 @@ Typically, pull-requests are only fully reviewed when these tests are passing, t
 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.
+The nf-core has a [set of guidelines](https://nf-co.re/developers/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.
@@ -44,4 +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/nanodemux documentation](https://github.com/nf-core/nanodemux#documentation) and don't hesitate to get in touch on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).
+For further information/help, please consult the [nf-core/nanodemux documentation](https://github.com/nf-core/nanodemux#documentation) and don't hesitate to get in touch on the [nf-core/nanodemux pipeline channel](https://nfcore.slack.com/channels/nanodemux) on [Slack](https://nf-co.re/join/slack/).

.travis.yml

@@ -9,7 +9,7 @@ matrix:
 
 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" ])'
+  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && ([ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ] || [ $TRAVIS_PULL_REQUEST_BRANCH = "patch" ]))'
   # Pull the docker image first so the test doesn't wait for this
   #- docker pull nfcore/nanodemux:dev
   # Fake the tag locally so that the pipeline runs properly

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 [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.
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on [Slack](https://nf-co.re/join/slack/). 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 +1,4 @@
-FROM nfcore/base
+FROM nfcore/base:1.7
 LABEL authors="Chelsea Sawyer" \
       description="Docker image containing all requirements for nf-core/nanodemux pipeline"
 

README.md

@@ -1,4 +1,4 @@
-# ![nfcore/nanodemux](docs/images/nfcore-nanodemux_logo.png)
+# ![nfcore/nanodemux](docs/images/nf-core-nanodemux_logo.png)
 
 [![Build Status](https://travis-ci.com/nf-core/nanodemux.svg?branch=master)](https://travis-ci.com/nf-core/nanodemux)
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.32.0-brightgreen.svg)](https://www.nextflow.io/)
@@ -21,6 +21,27 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
     * Convert `.sam` to co-ordinate sorted `.bam` and obtain mapping metrics ([`SAMtools`](http://www.htslib.org/doc/samtools.html))
 4. Present QC for alignment results ([`MultiQC`](https://multiqc.info/docs/))
 
+## Quick Start
+
+i. Install [`nextflow`](https://nf-co.re/usage/installation)
+
+ii. Install one of [`docker`](https://docs.docker.com/engine/installation/) or [`singularity`](https://www.sylabs.io/guides/3.0/user-guide/)
+
+iii. Download the pipeline and test it on a minimal dataset with a single command
+
+```bash
+nextflow run nf-core/nanodemux -profile test,<docker/singularity>
+```
+
+iv. Start running your own analysis!
+
+<!-- TODO nf-core: Update the default command above used to run the pipeline -->
+```bash
+nextflow run nf-core/nanodemux -profile <docker/singularity>
+```
+
+See [usage docs](docs/usage.md) for all of the available options when running the pipeline.
+
 ## Documentation
 
 The nf-core/nanodemux pipeline comes with documentation about the pipeline, found in the `docs/` directory:
@@ -35,13 +56,21 @@ The nf-core/nanodemux pipeline comes with documentation about the pipeline, foun
 5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
 
 ## Credits
+
 nf-core/nanodemux was originally written by [Chelsea Sawyer](https://github.com/csawye01) and [Harshil Patel](https://github.com/drpatelh) from The Bioinformatics & Biostatistics Group for use at The Francis Crick Institute, London.
 
-Many thanks to others who have helped out along the way too, including (but not limited to):  [`@crickbabs`](https://github.com/crickbabs)
+Many thanks to others who have helped out along the way too, including (but not limited to): [`@crickbabs`](https://github.com/crickbabs)
+
+## Contributions and Support
+
+If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
+
+For further information or help, don't hesitate to get in touch on [Slack](https://nfcore.slack.com/channels/nf-core/nanodemux) (you can join with [this invite](https://nf-co.re/join/slack)).
 
 ## Citation
 
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi. -->
-<!-- If you use  {{ cookiecutter.name }} for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+<!-- If you use nf-core/nanodemux for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
-Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1).
+You can cite the `nf-core` pre-print as follows:
+> Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v1).

assets/email_template.html

@@ -11,7 +11,7 @@
 <body>
 <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
-<img src="cid:nfcorenanodemuxlogo">
+<img src="cid:nfcorepipelinelogo">
 
 <h1>nf-core/nanodemux v${version}</h1>
 <h2>Run Name: $runName</h2>

assets/email_template.txt

@@ -1,6 +1,12 @@
-========================================
- nf-core/nanodemux v${version}
-========================================
+----------------------------------------------------
+                                        ,--./,-.
+        ___     __   __   __   ___     /,-._.--~\\
+  |\\ | |__  __ /  ` /  \\ |__) |__         }  {
+  | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,
+                                        `._,._,'
+  nf-core/nanodemux v${version}
+----------------------------------------------------
+
 Run Name: $runName
 
 <% if (success){

assets/sendmail_template.txt

@@ -9,12 +9,12 @@ Content-Type: text/html; charset=utf-8
 $email_html
 
 --nfcoremimeboundary
-Content-Type: image/png;name="nfcore-nanodemux_logo.png"
+Content-Type: image/png;name="nf-core-nanodemux_logo.png"
 Content-Transfer-Encoding: base64
-Content-ID: <nfcorenanodemuxlogo>
-Content-Disposition: inline; filename="nfcore-nanodemux_logo.png"
+Content-ID: <nfcorepipelinelogo>
+Content-Disposition: inline; filename="nf-core-nanodemux_logo.png"
 
-<% out << new File("$baseDir/assets/nfcore-nanodemux_logo.png").
+<% out << new File("$baseDir/assets/nf-core-nanodemux_logo.png").
   bytes.
   encodeBase64().
   toString().

bin/scrape_software_versions.py

@@ -2,7 +2,6 @@
 from __future__ import print_function
 from collections import OrderedDict
 import re
-import os
 
 # TODO nf-core: Add additional regexes for new tools in process get_software_versions
 regexes = {
@@ -31,13 +30,13 @@
 
 # Search each file using its regex
 for k, v in regexes.items():
-    if os.path.exists(v[0]):
+    try:
         with open(v[0]) as x:
             versions = x.read()
             match = re.search(v[1], versions)
             if match:
                 results[k] = "v{}".format(match.group(1))
-    else:
+    except IOError:
         results[k] = False
 
 # Remove software set to false in results

conf/base.config

@@ -13,7 +13,7 @@ process {
 
   // TODO nf-core: Check the defaults for all processes
   cpus = { check_max( 1 * task.attempt, 'cpus' ) }
-  memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+  memory = { check_max( 7.GB * task.attempt, 'memory' ) }
   time = { check_max( 4.h * task.attempt, 'time' ) }
 
   errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
@@ -22,23 +22,26 @@ process {
 
   // Process-specific resource requirements
   withLabel:process_low {
-    cpus = { check_max( 4 * task.attempt, 'cpus' ) }
-    memory = { check_max( 32.GB * task.attempt, 'memory' ) }
-    time = { check_max( 8.h * task.attempt, 'time' ) }
+    cpus = { check_max( 2 * task.attempt, 'cpus' ) }
+    memory = { check_max( 14.GB * task.attempt, 'memory' ) }
+    time = { check_max( 6.h * task.attempt, 'time' ) }
   }
   withLabel:process_medium {
-    cpus = { check_max( 8 * task.attempt, 'cpus' ) }
-    memory = { check_max( 64.GB * task.attempt, 'memory' ) }
-    time = { check_max( 16.h * task.attempt, 'time' ) }
+    cpus = { check_max( 6 * task.attempt, 'cpus' ) }
+    memory = { check_max( 42.GB * task.attempt, 'memory' ) }
+    time = { check_max( 8.h * task.attempt, 'time' ) }
   }
   withLabel:process_high {
-    cpus = { check_max( 16 * task.attempt, 'cpus' ) }
-    memory = { check_max( 128.GB * task.attempt, 'memory' ) }
+    cpus = { check_max( 12 * task.attempt, 'cpus' ) }
+    memory = { check_max( 84.GB * task.attempt, 'memory' ) }
     time = { check_max( 72.h * task.attempt, 'time' ) }
   }
+  withLabel:process_long {
+    time = { check_max( 20.h * task.attempt, 'time' ) }
+  }
 
   // Process-specific containers
-  withName:checkSampleSheet {
+  withName:CheckSampleSheet {
     container = 'quay.io/biocontainers/pysam:0.15.3--py27hda2845c_1'
   }
   withName:Guppy {
@@ -48,22 +51,22 @@ process {
       container = 'genomicpariscentre/guppy:3.2.2'
     }
   }
-  withName:pycoQC {
+  withName:PycoQC {
     container = 'quay.io/biocontainers/pycoqc:2.2.4--py_0'
   }
-  withName:NanoPlot_summary {
+  withName:NanoPlotSummary {
     container = 'quay.io/biocontainers/nanoplot:1.26.3--py_0'
   }
-  withName:NanoPlot_fastq {
+  withName:NanoPlotFastQ {
     container = 'quay.io/biocontainers/nanoplot:1.26.3--py_0'
   }
   withName:GraphMap {
     container = 'quay.io/biocontainers/graphmap:0.5.2--he941832_2'
   }
-  withName:minimap2 {
+  withName:MiniMap2 {
     container = 'quay.io/biocontainers/minimap2:2.17--h84994c4_0'
   }
-  withName:sortBAM {
+  withName:SortBAM {
     container = 'quay.io/biocontainers/samtools:1.9--h8571acd_11'
   }
   withName:output_documentation {
@@ -73,7 +76,7 @@ process {
     cache = false
     container = 'quay.io/biocontainers/pysam:0.15.3--py27hda2845c_1'
   }
-  withName:multiqc {
+  withName:MultiQC {
     container = 'quay.io/biocontainers/multiqc:1.7--py_4'
   }
 }