From fe5c1c996a273cf59a98dfab3704c40b10e9cd05 Mon Sep 17 00:00:00 2001 From: subwaystation Date: Tue, 20 Feb 2024 16:09:06 +0100 Subject: [PATCH] fix delim bug --- conf/modules.config | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index f83fd98..f9bd285 100644 --- 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}",