diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index a90769de..a7783031 100644 --- 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 index 85665d42..bbbae0c1 100644 --- 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 index 3679a380..bd63c010 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/scrnaseq + This report has been generated by the nf-core/scrnaseq analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. 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 index 325ed32b..5e5ec430 100644 Binary files a/assets/nf-core-scrnaseq_logo_light.png and b/assets/nf-core-scrnaseq_logo_light.png differ diff --git a/lib/WorkflowScrnaseq.groovy b/lib/WorkflowScrnaseq.groovy index e4089a57..15584b23 100755 --- 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 index 76a0d4a2..6c0cc5f4 100644 --- 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' }