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sjanssen2 / spike

NGS pipeline for SNV detection in tumor context
BSD 3-Clause "New" or "Revised" License
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Fastqc multiqc #235

Open deyazoubi opened 4 years ago

deyazoubi commented 4 years ago

add new rule

two issues have to solve

  1. lines https://github.com/sjanssen2/spike/blob/7e939e2f2bb9bffe6ec357524f877d754b3dd170/rules/fastqc/Snakefile#L17 and https://github.com/sjanssen2/spike/blob/7e939e2f2bb9bffe6ec357524f877d754b3dd170/rules/fastqc/Snakefile#L40 Sample_Project must be variable for different project

  2. after solve the point 1, for AG_remke the new rule will not work the reason is https://github.com/sjanssen2/spike/blob/7e939e2f2bb9bffe6ec357524f877d754b3dd170/scripts/parse_samplesheet.py#L559
    in this function # "only consider samples that have some spike_entity_role defined" and this not the case for AG_remke one solutions is https://github.com/sjanssen2/spike/blob/9f7e583329e595bf07ad1770b6122e58c950fdc6/scripts/parse_samplesheet.py#L571

sjanssen2 commented 4 years ago

please ping me when the tests are passing