diff 0.2.0/modules/rmlst/main.nf @ 11:a5f31c44f8c9

planemo upload
author kkonganti
date Mon, 15 Jul 2024 16:11:44 -0400
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.2.0/modules/rmlst/main.nf	Mon Jul 15 16:11:44 2024 -0400
@@ -0,0 +1,37 @@
+process RMLST_POST {
+    tag "${meta.id}"
+    label "process_pico"
+    maxForks 3
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
+    conda (params.enable_conda ? "conda-forge::python=3.10 conda-forge::requests" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/requests:2.26.0' :
+        'quay.io/biocontainers/requests:2.26.0' }"
+
+    input:
+        tuple val(meta), path(genome)
+
+    output:
+        tuple val(meta), path('*.tsv')     , emit: tsv, optional: true
+        tuple val(meta), path('*.log.json'), emit: log, optional: true
+        path 'versions.yml'                , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def prefix = (task.ext.prefix ?: meta.id)
+
+        """
+        rmlst_post.py \\
+            -fasta $genome \\
+            -prefix $prefix \\
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            python: \$( python --version | sed 's/Python //g' )
+            requests: \$( python -c "import requests; print (requests.__version__)" )
+        END_VERSIONS
+        """
+}
\ No newline at end of file