Add publish_dir_mode param to pipeline template

CHANGELOG.md

@@ -2,6 +2,10 @@
 
 ## v1.10dev
 
+### Template
+
+* Add `--publish_dir_mode` parameter [#585](https://github.com/nf-core/tools/issues/585)
+
 ### Linting
 
 * Refactored PR branch tests to be a little clearer.

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/usage.md

@@ -24,6 +24,7 @@
   * [`--awscli`](#--awscli)
 * [Other command line parameters](#other-command-line-parameters)
   * [`--outdir`](#--outdir)
+  * [`--publish_dir_mode`](#--publish_dir_mode)
   * [`--email`](#--email)
   * [`--email_on_fail`](#--email_on_fail)
   * [`--max_multiqc_email_size`](#--max_multiqc_email_size)
@@ -237,6 +238,10 @@ Please make sure to also set the `-w/--work-dir` and `--outdir` parameters to a
 
 The output directory where the results will be saved.
 
+### `--publish_dir_mode`
+
+Value passed to Nextflow [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir) directive for publishing results in the output directory. Available: 'symlink', 'rellink', 'link', 'copy', 'copyNoFollow' and 'move' (Default: 'copy').
+
 ### `--email`
 
 Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/main.nf

@@ -34,6 +34,7 @@ def helpMessage() {
 
     Other options:
       --outdir [file]                 The output directory where the results will be saved
+      --publish_dir_mode [str]        Mode for publishing results in the output directory. Available: symlink, rellink, link, copy, copyNoFollow, move (Default: copy)
       --email [email]                 Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits
       --email_on_fail [email]         Same as --email, except only send mail if the workflow is not successful
       --max_multiqc_email_size [str]  Theshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached (Default: 25MB)
@@ -73,12 +74,13 @@ params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false :
 if (params.fasta) { ch_fasta = file(params.fasta, checkIfExists: true) }
 
 // Has the run name been specified by the user?
-//  this has the bonus effect of catching both -name and --name
+// this has the bonus effect of catching both -name and --name
 custom_runName = params.name
 if (!(workflow.runName ==~ /[a-z]+_[a-z]+/)) {
     custom_runName = workflow.runName
 }
 
+// AWS batch settings
 if (workflow.profile.contains('awsbatch')) {
     // AWSBatch sanity checking
     if (!params.awsqueue || !params.awsregion) exit 1, "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
@@ -174,7 +176,7 @@ Channel.from(summary.collect{ [it.key, it.value] })
  * Parse software version numbers
  */
 process get_software_versions {
-    publishDir "${params.outdir}/pipeline_info", mode: 'copy',
+    publishDir "${params.outdir}/pipeline_info", mode: params.publish_dir_mode,
         saveAs: { filename ->
                       if (filename.indexOf(".csv") > 0) filename
                       else null
@@ -201,7 +203,7 @@ process get_software_versions {
 process fastqc {
     tag "$name"
     label 'process_medium'
-    publishDir "${params.outdir}/fastqc", mode: 'copy',
+    publishDir "${params.outdir}/fastqc", mode: params.publish_dir_mode,
         saveAs: { filename ->
                       filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"
                 }
@@ -222,7 +224,7 @@ process fastqc {
  * STEP 2 - MultiQC
  */
 process multiqc {
-    publishDir "${params.outdir}/MultiQC", mode: 'copy'
+    publishDir "${params.outdir}/MultiQC", mode: params.publish_dir_mode
 
     input:
     file (multiqc_config) from ch_multiqc_config
@@ -251,7 +253,7 @@ process multiqc {
  * STEP 3 - Output Description HTML
  */
 process output_documentation {
-    publishDir "${params.outdir}/pipeline_info", mode: 'copy'
+    publishDir "${params.outdir}/pipeline_info", mode: params.publish_dir_mode
 
     input:
     file output_docs from ch_output_docs

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config

@@ -14,6 +14,7 @@ params {
   reads = "data/*{1,2}.fastq.gz"
   single_end = false
   outdir = './results'
+  publish_dir_mode = 'copy'
 
   // Boilerplate options
   name = false