Add pre-run script as an option for the Tower CLI

CHANGELOG.md

@@ -1,5 +1,9 @@
 # nf-core/tower-action: Changelog
 
+## [[v2.1](https://github.com/nf-core/tower-action/releases/tag/v2.1)] - 2021-11-30
+
+Add option to pass pre-run script to Tower CLI.
+
 ## [[v2.0](https://github.com/nf-core/tower-action/releases/tag/v2.0)] - 2021-11-19
 
 A complete rewrite of the action to use the new [Nextflow Tower CLI](https://github.com/seqeralabs/tower-cli)

README.md

@@ -150,6 +150,22 @@ These should be supplied as a valid JSON object, quoted as a string in your GitH
 
 Pipeline config profiles to use. Should be comma separated without spaces.
 
+### `pre_run_script`
+
+**[Optional]** Pre-run script before launch.
+
+Pre-run script executed before pipeline launch. This would be particularly useful if you wanted to use a different version of Nextflow than the default available in Tower. You can set this in the pipeline Github Actions:
+
+```yaml
+jobs:
+  run-tower:
+    steps:
+      - uses: nf-core/tower-action@v2
+        with:
+          pre_run_script: 'export NXF_VER=21.10.3'
+          # Truncated..
+```
+
 ## Credits
 
 This GitHub Action was written by Phil Ewels ([@ewels](https://github.com/ewels)), with help from and based on earlier work by Gisela Gabernet ([@ggabernet](https://github.com/ggabernet)).

action.yml

@@ -38,6 +38,9 @@ inputs:
   profiles:
     description: Nextflow config profiles
     required: false
+  pre_run_script:
+    description: Pre-run script before launch
+    required: false
 
 runs:
   using: 'docker'
@@ -52,3 +55,4 @@ runs:
     WORKDIR: ${{ inputs.workdir }}
     PARAMETERS: ${{ toJson(fromJson(inputs.parameters)) }}
     CONFIG_PROFILES: ${{ inputs.profiles }}
+    PRE_RUN_SCRIPT: ${{ inputs.pre_run_script }}

entrypoint.sh

@@ -12,4 +12,5 @@ tw launch $PIPELINE \
     ${WORKDIR:+"--work-dir=$WORKDIR"} \
     ${TOWER_COMPUTE_ENV:+"--compute-env=$TOWER_COMPUTE_ENV"} \
     ${REVISION:+"--revision=$REVISION"} \
-    ${CONFIG_PROFILES:+"--profile=$CONFIG_PROFILES"}
+    ${CONFIG_PROFILES:+"--profile=$CONFIG_PROFILES"} \
+    ${PRE_RUN_SCRIPT:+"--pre-run=$PRE_RUN_SCRIPT"}