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lifebit-ai / nf-rnaseq-salmon

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SUBREADFEATURE COUNTS ERROR #9

Open manu-lifebit opened 2 years ago

manu-lifebit commented 2 years ago

The pipeline run with the complete human dataset in star/hisat2 mode showed an error related to the QC step subreadfeaturecounts: Screenshot from 2022-01-27 11-21-04

This error occurs when we don't specify the human ref files. The pipeline tries to find the "gene_biotype" field in the ref gtf fle according to the config file https://github.com/lifebit-ai/nf-rnaseq-salmon/blob/sk-sahu-dsl-1-latest/assets/multiqc/biotypes_header.txt. The downloaded ref file doesn't have this field and the process shows the error. As this is part of the QC to show in the multiqc report the pipeline can continue and the final results are generated normally, so this is not a crucial error but it has to be addressed in the next pipeline iteration.

example run with error: https://cloudos.lifebit.ai/public/jobs/61f1952f8c574a01e8e035e1 https://cloudos.lifebit.ai/public/jobs/61f18d118c574a01e8e0166f

example run without error: https://cloudos.lifebit.ai/public/jobs/61f0a8f18c574a01e8deecd7 (yeast. The gtf ref file contains the tag) https://lifebit.atlassian.net/browse/DEL-5411

manu-lifebit commented 2 years ago

task created to address this https://lifebit.atlassian.net/browse/DEL-5807