Fix linting part 1

nf-core · Aug 16, 2023 · bfec9ce · bfec9ce
1 parent b39bc2d
commit bfec9ce
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Showing 6 changed files with 5 additions and 7 deletions.
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -116,4 +116,3 @@ To get started:
 Devcontainer specs:
 
 - [DevContainer config](.devcontainer/devcontainer.json)
-- [Dockerfile](.devcontainer/Dockerfile)
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -42,7 +42,7 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 22.10.1)_
+        * Nextflow version _(eg. 23.04.0)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/scrnaseq" target="_blank">nf-core/scrnaseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/scrnaseq/2.4.0dev" target="_blank">nf-core/scrnaseq</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/scrnaseq" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/scrnaseq/2.4.0dev/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-scrnaseq-methods-description":
     order: -1000

diff --git a/assets/nf-core-scrnaseq_logo_light.png b/assets/nf-core-scrnaseq_logo_light.png
diff --git a/lib/WorkflowScrnaseq.groovy b/lib/WorkflowScrnaseq.groovy
@@ -14,8 +14,7 @@ class WorkflowScrnaseq {
         genomeExists(params, log)
 
         if (!params.input) {
-            log.error "Please provide an input samplesheet with --input"
-            System.exit(1)
+            Nextflow.error "Please provide an input samplesheet with --input"
         }
 
         if (!params.fasta) {

diff --git a/nextflow.config b/nextflow.config
@@ -257,7 +257,7 @@ manifest {
     description     = """Pipeline for processing 10x Genomics single cell rnaseq data"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '2.3.2'
+    version         = '2.4.0dev'
     doi             = '10.5281/zenodo.3568187'
 }
Original file line number	Diff line number	Diff line change
Expand Up		@@ -116,4 +116,3 @@ To get started:
		Devcontainer specs:

		- [DevContainer config](.devcontainer/devcontainer.json)
		- [Dockerfile](.devcontainer/Dockerfile)