Merge pull request #877 from drpatelh/create

Updates to nf-core modules create command
nf-core · Mar 15, 2021 · d0b7daf · d0b7daf
2 parents 5144075 + 196acfa
commit d0b7daf
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/nf_core/module-template/{{cookiecutter.tool_name}}/software/functions.nf b/nf_core/module-template/{{cookiecutter.tool_name}}/software/functions.nf
@@ -18,6 +18,7 @@ def initOptions(Map args) {
     def Map options = [:]
     options.args          = args.args ?: ''
     options.args2         = args.args2 ?: ''
+    options.args3         = args.args3 ?: ''
     options.publish_by_id = args.publish_by_id ?: false
     options.publish_dir   = args.publish_dir ?: ''
     options.publish_files = args.publish_files

diff --git a/nf_core/module-template/{{cookiecutter.tool_name}}/software/main.nf b/nf_core/module-template/{{cookiecutter.tool_name}}/software/main.nf
@@ -18,7 +18,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
 // TODO nf-core: Optional inputs are not currently supported by Nextflow. However, "fake files" MAY be used to work around this issue.
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process {{ cookiecutter.tool_name_upper }} {
     {{ 'tag "$meta.id"' if cookiecutter.has_meta else "'$bam'" }}
@@ -30,9 +30,8 @@ process {{ cookiecutter.tool_name_upper }} {
     // TODO nf-core: List required Conda package(s).
     //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
     //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    conda (params.enable_conda ? "{{ cookiecutter.bioconda if cookiecutter.bioconda else 'YOUR-TOOL-HERE' }}" : null)
-
     // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
+    conda (params.enable_conda ? "{{ cookiecutter.bioconda if cookiecutter.bioconda else 'YOUR-TOOL-HERE' }}" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/{{ cookiecutter.container_tag if cookiecutter.container_tag else 'YOUR-TOOL-HERE' }}"
     } else {
@@ -54,7 +53,6 @@ process {{ cookiecutter.tool_name_upper }} {
     // TODO nf-core: List additional required output channels/values here
     path "*.version.txt"          , emit: version
 
-
     script:
     def software = getSoftwareName(task.process)
     {% if cookiecutter.has_meta %}
@@ -76,6 +74,7 @@ process {{ cookiecutter.tool_name_upper }} {
         -o ${prefix}.bam \\
         -T $prefix \\
         $bam
+
     echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
     """
 }