Merge pull request #78 from nf-core/template_merge

drpatelh · web-flow · commit dc2f798a66d2 · 2019-05-10T16:59:03.000+01:00
Create TEMPLATE branch for automated syncing
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -6,7 +6,9 @@ We try to manage the required tasks for nf-core/chipseq 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/chipseq then the best place to ask is the nf-core `chipseq` channel on [Slack](https://nf-core-invite.herokuapp.com/).
+> If you need help using or modifying nf-core/chipseq 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/chipseq, 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/chipseq documentation](https://github.com/nf-core/chipseq#documentation) and don't hesitate to get in touch on the nf-core `chipseq` channel on [Slack](https://nf-core-invite.herokuapp.com/).
+For further information/help, please consult the [nf-core/chipseq documentation](https://github.com/nf-core/chipseq#documentation) and don't hesitate to get in touch on the pipeline channel on [Slack](https://nf-core-invite.herokuapp.com/).
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -25,7 +25,7 @@ A clear and concise description of what you expected to happen.
 #### Container engine:
  - Engine: [e.g. Conda, Docker or Singularity]
  - version: [e.g. 1.0.0]
- - Image tag: [e.g. nfcore/imcyto:1.0.0]
+ - Image tag: [e.g. nfcore/chipseq:1.0.0]
 
 #### Additional context
 Add any other context about the problem here.
diff --git a/.travis.yml b/.travis.yml
@@ -15,7 +15,7 @@ before_install:
   # Fake the tag locally so that the pipeline runs properly
   # 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/chipseq:dev nfcore/chipseq:dev
-  
+
 install:
   # Install Nextflow
   - mkdir /tmp/nextflow && cd /tmp/nextflow
diff --git a/Dockerfile b/Dockerfile
@@ -1,6 +1,6 @@
 FROM nfcore/base
-LABEL authors="phil.ewels@scilifelab.se" \
-      description="Docker image containing all requirements for the nfcore/chipseq pipeline"
+LABEL authors="Philip Ewels" \
+      description="Docker image containing all requirements for nf-core/chipseq pipeline"
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) Chuan Wang
+Copyright (c) Philip Ewels
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/assets/email_template.html b/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/chipseq: Nextflow ChIP-Seq analysis pipeline, part of the nf-core community.">
+  <meta name="description" content="nf-core/chipseq: ChIP-seq peak-calling and differential analysis pipeline.">
   <title>nf-core/chipseq Pipeline Report</title>
 </head>
 <body>
diff --git a/assets/email_template.txt b/assets/email_template.txt
@@ -16,12 +16,15 @@ ${errorReport}
 """
 } %>
 
+
 The workflow was completed at $dateComplete (duration: $duration)
 
 The command used to launch the workflow was as follows:
 
   $commandLine
 
+
+
 Pipeline Configuration:
 -----------------------
 <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %>
diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml
@@ -0,0 +1,9 @@
+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" target="_blank">documentation</a>.
+report_section_order:
+    nf-core/chipseq-software-versions:
+        order: -1000
+
+export_plots: true
diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py
@@ -48,7 +48,7 @@
         if match:
             results[k] = "v{}".format(match.group(1))
 
-# Strip HOMER
+# Remove software set to false in results
 for k in results:
     if not results[k]:
         del(results[k])
diff --git a/docs/usage.md b/docs/usage.md
@@ -2,6 +2,9 @@
 
 ## Table of contents
 
+<!-- Install Atom plugin markdown-toc-auto for this ToC to auto-update on save -->
+<!-- TOC START min:2 max:3 link:true asterisk:true update:true -->
+* [Table of contents](#table-of-contents)
 * [Introduction](#introduction)
 * [Running the pipeline](#running-the-pipeline)
   * [Updating the pipeline](#updating-the-pipeline)
@@ -51,6 +54,8 @@
   * [`--plaintext_email`](#--plaintext_email)
   * [`--monochrome_logs`](#--monochrome_logs)
   * [`--multiqc_config`](#--multiqc_config)
+<!-- TOC END -->
+
 
 ## Introduction
 Nextflow handles job submissions on SLURM or other environments, and supervises running the jobs. Thus the Nextflow process must run until the pipeline is finished. We recommend that you put the process running in the background through `screen` / `tmux` or similar tool. Alternatively you can run nextflow within a cluster job submitted your job scheduler.
@@ -93,6 +98,7 @@ First, go to the [nf-core/chipseq releases page](https://github.com/nf-core/chip
 
 This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future.
 
+
 ## Main arguments
 
 ### `-profile`
@@ -101,7 +107,7 @@ Use this parameter to choose a configuration profile. Profiles can give configur
 If `-profile` is not specified at all the pipeline will be run locally and expects all software to be installed and available on the `PATH`.
 
 * `awsbatch`
-  * A generic configuration profile to be used with AWS Batch
+  * A generic configuration profile to be used with AWS Batch.
 * `conda`
   * A generic configuration profile to be used with [conda](https://conda.io/docs/)
   * Pulls most software from [Bioconda](https://bioconda.github.io/)
@@ -110,7 +116,7 @@ If `-profile` is not specified at all the pipeline will be run locally and expec
   * Pulls software from dockerhub: [`nfcore/chipseq`](http://hub.docker.com/r/nfcore/chipseq/)
 * `singularity`
   * A generic configuration profile to be used with [Singularity](http://singularity.lbl.gov/)
-  * Pulls software from dockerhub: [`nfcore/chipseq`](http://hub.docker.com/r/nfcore/chipseq/)
+  * Pulls software from DockerHub: [`nfcore/chipseq`](http://hub.docker.com/r/nfcore/chipseq/)
 * `test`
   * A profile with a complete configuration for automated testing
   * Includes links to test data so needs no other parameters
@@ -191,7 +197,7 @@ The pipeline config files come bundled with paths to the illumina iGenomes refer
 ### `--genome` (using iGenomes)
 There are 31 different species supported in the iGenomes references. To run the pipeline, you must specify which to use with the `--genome` flag.
 
-You can find the keys to specify the genomes in the [`iGenomes config file`](../conf/igenomes.config). Common genomes that are supported are:
+You can find the keys to specify the genomes in the [iGenomes config file](../conf/igenomes.config). Common genomes that are supported are:
 
 * Human
   * `--genome GRCh37`
@@ -200,7 +206,7 @@ You can find the keys to specify the genomes in the [`iGenomes config file`](../
 * _Drosophila_
   * `--genome BDGP6`
 * _S. cerevisiae_
-  * `--genome R64-1-1`
+  * `--genome 'R64-1-1'`
 
 > There are numerous others - check the config file for more.
 
@@ -350,7 +356,8 @@ You can also supply a run name to resume a specific run: `-resume [run-name]`. U
 Specify the path to a specific config file (this is a core NextFlow command).
 
 **NB:** Single hyphen (core Nextflow option)
-**NB:** You can use this config to override pipeline defaults.
+
+Note - you can use this to override pipeline defaults.
 
 ### `--custom_config_version`
 Provide git commit id for custom Institutional configs hosted at `nf-core/configs`. This was implemented for reproducibility purposes. Default is set to `master`.
@@ -374,7 +381,7 @@ unzip master.zip
 
 ## Run the pipeline
 cd /path/to/my/data
-nextflow run /path/to/chipseq_pipeline/ --custom_config_base /path/to/my/configs/configs-master/
+nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
 ```
 
 > Note that the nf-core/tools helper package has a `download` command to download all required pipeline
diff --git a/main.nf b/main.nf
@@ -1405,6 +1405,8 @@ process output_documentation {
     """
 }
 
+
+
 /*
  * Completion e-mail notification
  */
@@ -1435,7 +1437,6 @@ workflow.onComplete {
     if(workflow.commitId) email_fields['summary']['Pipeline repository Git Commit'] = workflow.commitId
     if(workflow.revision) email_fields['summary']['Pipeline Git branch/tag'] = workflow.revision
     if(workflow.container) email_fields['summary']['Docker image'] = workflow.container
-    email_fields['skipped_poor_alignment'] = skipped_poor_alignment
     email_fields['summary']['Nextflow Version'] = workflow.nextflow.version
     email_fields['summary']['Nextflow Build'] = workflow.nextflow.build
     email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
@@ -1499,6 +1500,13 @@ workflow.onComplete {
     c_purple = params.monochrome_logs ? '' : "\033[0;35m";
     c_green = params.monochrome_logs ? '' : "\033[0;32m";
     c_red = params.monochrome_logs ? '' : "\033[0;31m";
+
+    if (workflow.stats.ignoredCountFmt > 0 && workflow.success) {
+      log.info "${c_purple}Warning, pipeline completed, but with errored process(es) ${c_reset}"
+      log.info "${c_red}Number of ignored errored process(es) : ${workflow.stats.ignoredCountFmt} ${c_reset}"
+      log.info "${c_green}Number of successfully ran process(es) : ${workflow.stats.succeedCountFmt} ${c_reset}"
+    }
+
     if(workflow.success){
         log.info "${c_purple}[nf-core/chipseq]${c_green} Pipeline completed successfully${c_reset}"
     } else {
diff --git a/nextflow.config b/nextflow.config
@@ -3,9 +3,6 @@
  *  nf-core/chipseq Nextflow config file
  * -------------------------------------------------
  * Default config options for all environments.
- * Cluster-specific config options should be saved
- * in the conf folder and imported under a profile
- * name here.
  */
 
 // Global default params, used in configs
@@ -111,19 +108,19 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']
 
 timeline {
   enabled = true
-  file = "${params.tracedir}/nf-core/execution_timeline.html"
+  file = "${params.tracedir}/execution_timeline.html"
 }
 report {
   enabled = true
-  file = "${params.tracedir}/nf-core/execution_report.html"
+  file = "${params.tracedir}/execution_report.html"
 }
 trace {
   enabled = true
-  file = "${params.tracedir}/nf-core/execution_trace.txt"
+  file = "${params.tracedir}/execution_trace.txt"
 }
 dag {
   enabled = true
-  file = "${params.tracedir}/nf-core/pipeline_dag.svg"
+  file = "${params.tracedir}/pipeline_dag.svg"
 }
 
 manifest {
