Open january3 opened 9 months ago
can confirm with pattern input/{sample}/fastq/{sample}_S*_{lane}_{mate}_*
.
at least for star
and fastqc
, I think it's because there's no all_lanes
flag as (e.g.,) in rule ciri
patrick has a # TODO: case of ignored wildcards? meant for e.g. allFlowcell
in get_fastq_pairs
Fastq files were stored according to the following pattern:
input/{sample}/fastq/{sample}{lane}{mate}
seasnap-mapping with this configuration did not correctly run - the file argument was empty for fastqc and star.