Outputs

Separate BWA-MEM2, minibwa, and HISAT2 folders are created for the selected aligners, while a base folder stores overall Nextflow information.

Output	Description	Folder
.bam	Aligned, sorted, filtered and if needed, merged, BAM file(s)	align-DNA-DATE/ALIGNER
.bam.bai	Index file for each BAM file	align-DNA-DATE/ALIGNER
.bam files and metrics files	Intermediate outputs for each scientific tool (OPTIONAL)	align-DNA-DATE/ALIGNER
report.html, timeline.html and trace.txt	A Nextflowreport, timeline and trace files	align-DNA-DATE/log
log.command.*	Process specific logging files created by Nextflow.	align-DNA-DATE

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