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bihealth / seasnap-pipeline

SeA-SnaP: (Se)q (A)nalysis (Sna)kemake (P)ipeline
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seasnap-mapping does not run for some in path configurations #29

Open january3 opened 9 months ago

january3 commented 9 months ago

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.

bobermayer commented 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