Update changelog and docs

nf-core · Mar 3, 2020 · 21fbef6 · 21fbef6
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@
 * Fixes missing parameter `-p` [#351](https://github.com/nf-core/rnaseq/issues/351)
 * Fixes broken links [#357](https://github.com/nf-core/rnaseq/issues/357)
 * Fixes label name in fastQC process, Issue [#345]
+* Make publishDir mode configurable [#391](https://github.com/nf-core/rnaseq/pull/391)
 
 #### Updated Packages
 

diff --git a/docs/usage.md b/docs/usage.md
@@ -517,6 +517,9 @@ Set this parameter to your e-mail address to get a summary e-mail with details o
 ### `--email_on_fail`
 This works exactly as with `--email`, except emails are only sent if the workflow is not successful.
 
+### `--publish_dir_mode`
+Choose the publishDir mode. Default is `copy`. See https://www.nextflow.io/docs/latest/process.html#publishdir for more details. 
+
 ### `-name`
 
 Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.

diff --git a/main.nf b/main.nf
@@ -95,6 +95,7 @@ def helpMessage() {
       --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               Same as --email, except only send mail if the workflow is not successful
       --max_multiqc_email_size      Threshold 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)
+      --publish_dir_mode            Choose the publishDir mode. Default 'copy'. See https://www.nextflow.io/docs/latest/process.html#publishdir for more details. 
       -name                         Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic
 
     AWSBatch options: