Update Shigapass main.nf

Change shigapass module output delimiter to tab from semicolon

modules/nf-core/shigapass/main.nf

@@ -11,8 +11,8 @@ process SHIGAPASS {
     tuple val(meta), path(fasta)
 
     output:
-    tuple val(meta), path("*_ShigaPass_summary.csv"), emit: report
-    tuple val(meta), path("*_ShigaPass_Flex_summary.csv"), optional: true, emit: flex_csv
+    tuple val(meta), path("${prefix}.tsv"), emit: report
+    tuple val(meta), path("*_ShigaPass_Flex_summary.tsv"), optional: true, emit: flex_tsv
     path "versions.yml"           , emit: versions
 
     when:
@@ -43,13 +43,11 @@ process SHIGAPASS {
     # Remove the temporary file from above
     rm ${fasta_name}_tmp.txt
 
-    # Delete the directory generated by ShigaPass
-    mv ${prefix}/ShigaPass_summary.csv ${prefix}_ShigaPass_summary.csv
+    # Convert to tab delimited and move to the pwd
+    sed 's/;/\t/g' ${prefix}/ShigaPass_summary.csv > ${prefix}.tsv
 
-    # Delete the directory generated by ShigaPass
-    [ ! -f ${prefix}/ShigaPass_Flex_summary.csv ] || mv ${prefix}/ShigaPass_Flex_summary.csv ${prefix}_ShigaPass_Flex_summary.csv
-
-    rmdir ${prefix}
+    # Convert to tab delimited and move to the pwd
+    [ ! -f ${prefix}/ShigaPass_Flex_summary.csv ] || sed 's/;/\t/g' ${prefix}/ShigaPass_Flex_summary.csv > ${prefix}_Flex_summary.tsv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -61,7 +59,7 @@ process SHIGAPASS {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.csv
+    touch ${prefix}.tsv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":