Merge branch 'master' into update_kmcp

modules/nf-core/fcs/fcsgx/main.nf

@@ -3,8 +3,8 @@ process FCS_FCSGX {
     label 'process_low'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/releases/0.2.3/fcs-gx.0.2.3.sif':
-        'docker.io/ncbi/fcs-gx:0.2.3' }"
+        'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/releases/0.4.0/fcs-gx.sif':
+        'docker.io/ncbi/fcs-gx:0.4.0' }"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
@@ -26,7 +26,7 @@ process FCS_FCSGX {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def FCSGX_VERSION = '0.2.3'
+    def FCSGX_VERSION = '0.4.0'
 
     """
     python3 /app/bin/run_gx \\
@@ -42,4 +42,20 @@ process FCS_FCSGX {
         FCS-GX: $FCSGX_VERSION
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def FCSGX_VERSION = '0.4.0'
+
+    """
+    mkdir -p out
+    touch out/${prefix}.fcs_gx_report.txt
+    touch out/${prefix}.taxonomy.rpt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python3 --version 2>&1 | sed -e "s/Python //g")
+        FCS-GX: $FCSGX_VERSION
+    END_VERSIONS
+    """
 }