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Alignment subworkflows #20

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mirpedrol opened this issue Mar 10, 2023 · 0 comments

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enhancement good-first-issue

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mirpedrol commented Mar 10, 2023 •

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Description of feature

Instead of using modules for the alignment step, use the nf-core subworkflows.

Use fastq_align_bwa for BWA alignment
Use fastq_align_bowtie2 for bowtie2 alignemnt
Create and use a new subworkflow for minimap2 alignment
Once we have Samtools stats we can also add these to the MultiQC report

** Consider creating a subworkflow with indexing + the respective alignment subworkflows

mirpedrol added enhancement good-first-issue labels

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