nf-core · drpatelh · Apr 11, 2019 · Apr 11, 2019 · Apr 11, 2019 · Apr 11, 2019
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -6,7 +6,9 @@ We try to manage the required tasks for nf-core/atacseq 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/atacseq then the best place to ask is the nf-core `atacseq` channel on [Slack](https://nf-core-invite.herokuapp.com/).
+> If you need help using or modifying nf-core/atacseq 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/atacseq, 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/atacseq documentation](https://github.com/nf-core/atacseq#documentation) and don't hesitate to get in touch on the nf-core `atacseq` channel on [Slack](https://nf-core-invite.herokuapp.com/).
+For further information/help, please consult the [nf-core/atacseq documentation](https://github.com/nf-core/atacseq#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/atacseq:1.0.0]
 
 #### Additional context
 Add any other context about the problem here.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,4 +1,4 @@
 # nf-core/atacseq: Changelog
 
-## v1.0dev - [date]
+## v1.0.0 - [date]
 Initial release of nf-core/atacseq, created with the [nf-core](http://nf-co.re/) template.
diff --git a/Dockerfile b/Dockerfile
@@ -1,6 +1,6 @@
 FROM nfcore/base
-LABEL authors="harshil.patel@crick.ac.uk" \
-      description="Docker image containing all requirements for the nfcore/atacseq pipeline"
+LABEL authors="Harshil Patel" \
+      description="Docker image containing all requirements for nf-core/atacseq pipeline"
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a

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/atacseq" target="_blank">nf-core/atacseq</a>
+    analysis pipeline. For information about how to interpret these results, please see the
+    <a href="https://github.com/nf-core/atacseq" target="_blank">documentation</a>.
+report_section_order:
+    nf-core/atacseq-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
@@ -192,7 +192,7 @@ 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`
@@ -364,7 +364,8 @@ 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`.
@@ -388,7 +389,7 @@ unzip master.zip
 
 ## Run the pipeline
 cd /path/to/my/data
-nextflow run /path/to/atacseq_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
@@ -1775,7 +1775,6 @@ 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
@@ -1839,6 +1838,13 @@ 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/atacseq]${c_green} Pipeline completed successfully${c_reset}"
     } else {

diff --git a/nextflow.config b/nextflow.config
@@ -105,19 +105,19 @@ 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 {