fastq_align_star
Align reads to a reference genome using bowtie2 then sort with samtools
Input
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
Structure: [ val(meta), [ path(reads) ] ]
Output
Output BAM file of transcriptome alignment (optional)
Structure: [ val(meta), path(bam) ]
Transcriptome-level BAM file ordered by samtools (optional)
Structure: [ val(meta), path(bam) ]
Transcriptome-level BAI index of the ordered BAM file (optional)
Structure: [ val(meta), path(bai) ]
Transcriptome-level file containing samtools stats output (optional)
Structure: [ val(meta), path(stats) ]
Transcriptome-level file containing samtools flagstat output (optional)
Structure: [ val(meta), path(flagstat) ]
Transcriptome-level file containing samtools idxstats output (optional)
Structure: [ val(meta), path(idxstats) ]