Merge pull request #113 from drpatelh/master

Bump version to 1.1.0

Author: drpatelh

.travis.yml

@@ -14,7 +14,7 @@ before_install:
   - docker pull nfcore/chipseq:dev
   # 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
+  - docker tag nfcore/chipseq:dev nfcore/chipseq:1.1.0
 
 install:
   # Install Nextflow
@@ -39,4 +39,4 @@ script:
   # 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
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker -ansi-log false

CHANGELOG.md

@@ -5,7 +5,7 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## [Unpublished Version / DEV]
+## [1.1.0] - 2019-11-01
 
 ### `Added`
 

Dockerfile

@@ -4,5 +4,5 @@ LABEL authors="Philip Ewels" \
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-RUN conda env export --name nf-core-chipseq-1.0.1dev > nf-core-chipseq-1.0.1dev.yml
-ENV PATH /opt/conda/envs/nf-core-chipseq-1.0.1dev/bin:$PATH
+RUN conda env export --name nf-core-chipseq-1.1.0 > nf-core-chipseq-1.1.0.yml
+ENV PATH /opt/conda/envs/nf-core-chipseq-1.1.0/bin:$PATH

environment.yml

@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-core-chipseq-1.0.1dev
+name: nf-core-chipseq-1.1.0
 channels:
   - conda-forge
   - bioconda

main.nf

@@ -1535,7 +1535,7 @@ workflow.onComplete {
     // Set up the e-mail variables
     def subject = "[nf-core/chipseq] Successful: $workflow.runName"
     if (!workflow.success) {
-      subject = "[nf-core/chipseq] FAILED: $workflow.runName"
+        subject = "[nf-core/chipseq] FAILED: $workflow.runName"
     }
     def email_fields = [:]
     email_fields['version'] = workflow.manifest.version
@@ -1601,21 +1601,21 @@ workflow.onComplete {
     // Send the HTML e-mail
     if (email_address) {
         try {
-          if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
-          // Try to send HTML e-mail using sendmail
-          [ 'sendmail', '-t' ].execute() << sendmail_html
-          log.info "[nf-core/chipseq] Sent summary e-mail to $email_address (sendmail)"
+            if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+            // Try to send HTML e-mail using sendmail
+            [ 'sendmail', '-t' ].execute() << sendmail_html
+            log.info "[nf-core/chipseq] Sent summary e-mail to $email_address (sendmail)"
         } catch (all) {
-          // Catch failures and try with plaintext
-          [ 'mail', '-s', subject, email_address ].execute() << email_txt
-          log.info "[nf-core/chipseq] Sent summary e-mail to $email_address (mail)"
+            // Catch failures and try with plaintext
+            [ 'mail', '-s', subject, email_address ].execute() << email_txt
+            log.info "[nf-core/chipseq] Sent summary e-mail to $email_address (mail)"
         }
     }
 
     // Write summary e-mail HTML to a file
     def output_d = new File("${params.outdir}/pipeline_info/")
     if (!output_d.exists()) {
-      output_d.mkdirs()
+        output_d.mkdirs()
     }
     def output_hf = new File(output_d, "pipeline_report.html")
     output_hf.withWriter { w -> w << email_html }
@@ -1628,9 +1628,9 @@ workflow.onComplete {
     c_red = params.monochrome_logs ? '' : "\033[0;31m";
 
     if (workflow.stats.ignoredCount > 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.ignoredCount} ${c_reset}"
-      log.info "${c_green}Number of successfully ran process(es) : ${workflow.stats.succeedCount} ${c_reset}"
+        log.info "${c_purple}Warning, pipeline completed, but with errored process(es) ${c_reset}"
+        log.info "${c_red}Number of ignored errored process(es) : ${workflow.stats.ignoredCount} ${c_reset}"
+        log.info "${c_green}Number of successfully ran process(es) : ${workflow.stats.succeedCount} ${c_reset}"
     }
 
     if (workflow.success) {

nextflow.config

@@ -85,7 +85,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/chipseq:dev'
+process.container = 'nfcore/chipseq:1.1.0'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -147,7 +147,7 @@ manifest {
   description = 'ChIP-seq peak-calling and differential analysis pipeline.'
   mainScript = 'main.nf'
   nextflowVersion = '>=19.04.0'
-  version = '1.0.1dev'
+  version = '1.1.0'
 }
 
 // Function to ensure that resource requirements don't go beyond