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nf-core / demultiplex

Demultiplexing pipeline for sequencing data
https://nf-co.re/demultiplex
MIT License
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checkqc doesn't run for bclconvert #226

Closed grst closed 1 month ago

grst commented 1 month ago

Description of the bug

I'm running the exact same flowcell, once with bcl2fastq and once with bclconvert. CheckQC only runs when bcl2fastq is selected as demultiplexer.

I'd expect checkQC to run in all cases (at least with Illumina's bcl2fastq/bclconvert, but I don't think there would be any reason not to run it with the other demultiplexers as well?)

CC @apeltzer

Command used and terminal output

No response

Relevant files

BCL2FASTQ image

Bclconvert image

System information

No response

apeltzer commented 1 month ago

IIRC; checkqc is not compatible with bclconvert output.

apeltzer commented 1 month ago

Not entirely sure this is (still?) valid, please try to set it up for bclconvert, i will also ask one of the authors.

atrigila commented 1 month ago

I think it still does not support bclconvert. I did a quick test with the output from this demultiplexer and got the following:

ERROR    Could not identify a Stats.json file at: checkqc_dir/Data/Intensities/BaseCalls/Stats/Stats.json. This file is created by bcl2fastq, please ensure that you have run bcl2fastq on this runfolder before running checkqc.If this file is not located under <RUNFOLDER>/Data/Intensities/BaseCalls/Stats/Stats.json which is the default option for bcl2fastq, you can specify where the 'Stats' directory is located by changing the 'bcl2fastq_output_path' in the 'StatsJsonParser' part of the checkqc configuration file.
ERROR    Could not find a Stats.json file at: checkqc_dir/Data/Intensities/BaseCalls/Stats/Stats.json
grst commented 1 month ago

Thanks for checking! Then I'll close this issue!