Nextflow code for read-to-genome alignment

Identify nextflow code to carry out the read-to-genome alignment. This workflow probably exists, if not, it should be written.

Input: fasta file of reads

Output: bam file with read-to-genome alignments

Process:

• Index reference transcriptome
• Align transcript (fasta or fastq) files to indexed transcriptome
• Convert resulting sam file to bam file