nf-core · drpatelh · Mar 9, 2022 · Mar 7, 2022 · Mar 8, 2022 · Mar 8, 2022
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
@@ -47,7 +47,7 @@ jobs:
       - name: Run nf-core/tools
         run: |
           nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
-          nextflow run nf-core-testpipeline -profile test,docker
+          nextflow run nf-core-testpipeline -profile test,docker --outdir ./results
 
       - name: Upload log file artifact
         if: ${{ always() }}

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,6 +15,7 @@
 * Add `.yamllint.yml` to avoid line length and document start errors ([#1407](https://github.com/nf-core/tools/issues/1407))
 * Add `--publish_dir_mode` back into the pipeline template ([nf-core/rnaseq#752](https://github.com/nf-core/rnaseq/issues/752#issuecomment-1039451607))
 * Add optional loading of of pipeline-specific institutional configs to `nextflow.config`
+* Make `--outdir` a mandatory parameter ([nf-core/tools#1415](https://github.com/nf-core/tools/issues/1415))
 
 ## General
 

diff --git a/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md b/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md
@@ -19,7 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/{{ name }}/t
     - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/{{ name }}/tree/master/.github/CONTRIBUTING.md)
     - [ ] If necessary, also make a PR on the {{ name }} _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker` --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -23,6 +23,8 @@ jobs:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          pipeline: ${{ github.repository }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %}
           parameters: |
             {

diff --git a/nf_core/pipeline-template/.github/workflows/awstest.yml b/nf_core/pipeline-template/.github/workflows/awstest.yml
@@ -17,6 +17,8 @@ jobs:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          pipeline: ${{ github.repository }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %}
           parameters: |
             {

diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml
@@ -14,7 +14,7 @@ env:
 
 jobs:
   test:
-    name: Run workflow tests
+    name: Run pipeline with test data
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: {% raw %}${{{% endraw %} github.event_name != 'push' || (github.event_name == 'push' && github.repository == '{{ name }}') {% raw %}}}{% endraw %}
     runs-on: ubuntu-latest
@@ -49,4 +49,4 @@ jobs:
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
@@ -40,7 +40,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
     ```console
-    nextflow run {{ name }} -profile test,YOURPROFILE
+    nextflow run {{ name }} -profile test,YOURPROFILE --outdir <OUTDIR>
     ```
 
     Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
@@ -55,7 +55,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
     <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
 
     ```console
-    nextflow run {{ name }} -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.csv --genome GRCh37
+    nextflow run {{ name }} --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
     ```
 
 ## Documentation

diff --git a/nf_core/pipeline-template/conf/modules.config b/nf_core/pipeline-template/conf/modules.config
@@ -3,10 +3,10 @@
     Config file for defining DSL2 per module options and publishing paths
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Available keys to override module options:
-        ext.args            = Additional arguments appended to command in module.
-        ext.args2           = Second set of arguments appended to command in module (multi-tool modules).
-        ext.args3           = Third set of arguments appended to command in module (multi-tool modules).
-        ext.prefix          = File name prefix for output files.
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
 ----------------------------------------------------------------------------------------
 */
 

diff --git a/nf_core/pipeline-template/conf/test.config b/nf_core/pipeline-template/conf/test.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run {{ name }} -profile test,<docker/singularity>
+        nextflow run {{ name }} -profile test,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/nf_core/pipeline-template/conf/test_full.config b/nf_core/pipeline-template/conf/test_full.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a full size pipeline test.
 
     Use as follows:
-        nextflow run {{ name }} -profile test_full,<docker/singularity>
+        nextflow run {{ name }} -profile test_full,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md
@@ -57,7 +57,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
 The typical command for running the pipeline is as follows:
 
 ```console
-nextflow run {{ name }} --input samplesheet.csv --genome GRCh37 -profile docker
+nextflow run {{ name }} --input samplesheet.csv  --outdir <OUTDIR> --genome GRCh37 -profile docker
 ```
 
 This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
@@ -24,7 +24,7 @@ params {
     max_multiqc_email_size     = '25.MB'
 
     // Boilerplate options
-    outdir                     = './results'
+    outdir                     = null
     tracedir                   = "${params.outdir}/pipeline_info"
     publish_dir_mode           = 'copy'
     email                      = null
@@ -63,7 +63,7 @@ try {
     System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
 }
 
-// Load {{ name }} custom profiles from different institutions. 
+// Load {{ name }} custom profiles from different institutions.
 // Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
 // try {
 //   includeConfig "${params.custom_config_base}/pipeline/{{ short_name }}.config"

diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
@@ -11,7 +11,8 @@
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
             "required": [
-                "input"
+                "input",
+                "outdir"
             ],
             "properties": {
                 "input": {
@@ -26,8 +27,8 @@
                 },
                 "outdir": {
                     "type": "string",
-                    "description": "Path to the output directory where the results will be saved.",
-                    "default": "./results",
+                    "format": "directory-path",
+                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                     "fa_icon": "fas fa-folder-open"
                 },
                 "email": {