Merge pull request #170 from nf-core/fix_wfmash_exclude_delim

fix delim bug
nf-core · Feb 21, 2024 · 400ed3e · 400ed3e
2 parents c8cad90 + fe5c1c9
commit 400ed3e
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -106,7 +106,7 @@ process {
                 "-s ${parse_int(params.wfmash_segment_length)}",
                 "-p ${params.wfmash_map_pct_id}",
                 params.wfmash_merge_segments   ? "-M"                                : "",
-                params.wfmash_exclude_delim    ? "-Y ${params.wfmash_exclude_delim}" : "-X",
+                params.wfmash_exclude_delim    ? "-Y \"${params.wfmash_exclude_delim}\"" : "-X",
                 params.wfmash_no_splits        ? "-N"                                : "",
                 params.wfmash_block_length     ? "-l ${parse_int(params.wfmash_block_length)}"  : "-l ${parse_int(params.wfmash_segment_length) * 5}",
                 "-k ${params.wfmash_mash_kmer}",
@@ -129,7 +129,7 @@ process {
                 "-s ${parse_int(params.wfmash_segment_length)}",
                 "-p ${params.wfmash_map_pct_id}",
                 params.wfmash_merge_segments   ? "-M"                                : "",
-                params.wfmash_exclude_delim    ? "-Y ${params.wfmash_exclude_delim}" : "-X",
+                params.wfmash_exclude_delim    ? "-Y \"${params.wfmash_exclude_delim}\"" : "-X",
                 params.wfmash_no_splits        ? "-N"                                : "",
                 params.wfmash_block_length     ? "-l ${parse_int(params.wfmash_block_length)}"  : "-l ${parse_int(params.wfmash_segment_length) * 5}",
                 "-k ${params.wfmash_mash_kmer}",
@@ -153,7 +153,7 @@ process {
                 "-s ${parse_int(params.wfmash_segment_length)}",
                 "-p ${params.wfmash_map_pct_id}",
                 params.wfmash_merge_segments   ? "-M"                                : "",
-                params.wfmash_exclude_delim    ? "-Y ${params.wfmash_exclude_delim}" : "-X",
+                params.wfmash_exclude_delim    ? "-Y \"${params.wfmash_exclude_delim}\"" : "-X",
                 params.wfmash_no_splits        ? "-N"                                : "",
                 params.wfmash_block_length     ? "-l ${parse_int(params.wfmash_block_length)}"  : "-l ${parse_int(params.wfmash_segment_length) * 5}",
                 "-k ${params.wfmash_mash_kmer}",
@@ -186,7 +186,7 @@ process {
                 "-s ${parse_int(params.wfmash_segment_length)}",
                 "-p ${params.wfmash_map_pct_id}",
                 params.wfmash_merge_segments   ? "-M"                                : "",
-                params.wfmash_exclude_delim    ? "-Y ${params.wfmash_exclude_delim}" : "-X",
+                params.wfmash_exclude_delim    ? "-Y \"${params.wfmash_exclude_delim}\"" : "-X",
                 params.wfmash_no_splits        ? "-N"                                : "",
                 params.wfmash_block_length     ? "-l ${parse_int(params.wfmash_block_length)}"  : "-l ${parse_int(params.wfmash_segment_length) * 5}",
                 "-k ${params.wfmash_mash_kmer}",