reverts commits 8b199f0 and aceca71

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -44,8 +44,7 @@ body:
 
         * Executor _(eg. slurm, local, awsbatch)_
 
-        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
-        or Apptainer)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
 
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
 

.github/workflows/branch.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'sage-bionetworks-workflows/nf-dcqc'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == sage-bionetworks-workflows/nf-dcqc ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == sage-bionetworks-workflows/nf-dcqc ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets

.github/workflows/linting.yml

@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
+          python-version: "3.7"
           architecture: "x64"
 
       - name: Install dependencies

README.md

@@ -55,13 +55,12 @@ On release, automated continuous integration tests run the pipeline on a full-si
 ## Special Considerations for Running `nf-dcqc` on Nextflow Tower
 
 `nf-dcqc` leverages the reports feature when executed on Tower. This is done by pointing Tower to the generated `output.csv` file which is saved to `params.outdir` after a successful run. By default, the `outdir` for the workflow is set to a local directory called `results`. This does not work on Nextflow Tower runs, as you will not have access to the `results` directory once the job has completed. Thus, the `outdir` should be set to an S3 bucket location that the Tower workspace you are using has access to. For example, in the `pipeline parameters` for a Tower run, you can provide YAML such as:
-
 ```yaml
 outdir: s3://example-project-tower-bucket/dcqc_output
 ```
-
 From the reports tab within your workflow run, you can view and download the generated `output.csv` file.
 
+
 ## Credits
 
 sage/dcqc was originally written by Bruno Grande <[email protected]>.

lib/NfcoreSchema.groovy

@@ -2,7 +2,6 @@
 // This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template.
 //
 
-import nextflow.Nextflow
 import org.everit.json.schema.Schema
 import org.everit.json.schema.loader.SchemaLoader
 import org.everit.json.schema.ValidationException
@@ -84,7 +83,6 @@ class NfcoreSchema {
             'stub-run',
             'test',
             'w',
-            'with-apptainer',
             'with-charliecloud',
             'with-conda',
             'with-dag',
@@ -179,7 +177,7 @@ class NfcoreSchema {
         }
 
         if (has_error) {
-            Nextflow.error('Exiting!')
+            System.exit(1)
         }
     }