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