Fixed description for readFilesManifest in parametersDefault.
@@ -140,7 +140,9 @@ readFilesIn Read1 Read2
string(s): paths to files that contain input read1 (and, if needed, read2)
readFilesManifest -
- string: file with the names of read files, one set of files per line, with two/three columns for SE/PE reads, formatted as: read1_file_name \tab read2_file_name \tab read_group_line.
+ string: file with the names of read files, formatted as:
+ Paired-End reads: read1_file_name \tab read2_file_name \tab read_group_line.
+ Single-End reads: read1_file_name \tab - \tab read_group_line.
Spaces, but not tabs are allowed in file names.
If read_group_line does not start with ID:, it can only contain one ID field, and ID: will be added to it.
If read_group_line starts with ID:, it can contain several fields separated by \tab, and all fields will be be copied verbatim into SAM @RG header line.
