Fix formatting of module and version

nextflow-modules/modules/sccmec/main.nf

@@ -1,39 +1,39 @@
 process sccmec {
-  tag "${sampleID}"
+  tag "${sample_id}"
   scratch params.scratch
 
   input:
-    tuple val(sampleID), path(assembly)
+    tuple val(sample_id), path(assembly)
 
   output:
-    tuple val(sampleID), path(output), emit: tsv 
-    path "*versions.yml"             , emit: versions
+    tuple val(sample_id), path(output), emit: tsv 
+    path "*versions.yml"              , emit: versions
 
   script:
     def args = task.ext.args ?: ''
-    output = "${sampleID}_sccmec.tsv"
+    output = "${sample_id}_sccmec.tsv"
     outputDir = "sccmec_outdir"
     """
-    sccmec --input $assembly --prefix ${sampleID}_sccmec -o $outputDir $args
-    cp $outputDir/${sampleID}_sccmec.tsv $output
+    sccmec --input ${assembly} --prefix ${sample_id}_sccmec -o ${outputDir} ${args}
+    cp ${outputDir}/${sample_id}_sccmec.tsv ${output}
 
-    cat <<-END_VERSIONS > ${sampleID}_${task.process}_versions.yml
+    cat <<-END_VERSIONS > ${sample_id}_${task.process}_versions.yml
     ${task.process}:
      sccmec:
-      version: \$(echo \$(sccmec --version 2>&1) | tr '\n' ';')
+      version: \$(echo \$(sccmec --version 2>&1) | sed -n 's/.*sccmec_targets, version //p')
       container: ${task.container}
     END_VERSIONS
     """
 
   stub:
-    output = "${sampleID}_sccmec.tsv"
+    output = "${sample_id}_sccmec.tsv"
     """
-    touch $output
+    touch ${output}
 
-    cat <<-END_VERSIONS > ${sampleID}_${task.process}_versions.yml
+    cat <<-END_VERSIONS > ${sample_id}_${task.process}_versions.yml
     ${task.process}:
      sccmec:
-      version: \$(echo \$(sccmec --version 2>&1) | tr '\n' ';')
+      version: \$(echo \$(sccmec --version 2>&1) | sed -n 's/.*sccmec_targets, version //p')
       container: ${task.container}
     END_VERSIONS
     """