Align reads to a reference genome using STAR
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
reads
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
meta2
Groovy Map containing reference information e.g. [ id:‘test’ ]
index
STAR genome index
star
meta3
gtf
Annotation GTF file
*.{gtf}
star_ignore_sjdbgtf
Ignore annotation GTF file
seq_platform
Sequencing platform
seq_center
Sequencing center
bam
Output BAM file containing read alignments
*.{bam}
log_final
STAR final log file
*Log.final.out
log_out
STAR lot out file
*Log.out
log_progress
STAR log progress file
*Log.progress.out
versions
File containing software versions
versions.yml
bam_sorted
Sorted BAM file of read alignments (optional)
*sortedByCoord.out.bam
bam_transcript
Output BAM file of transcriptome alignment (optional)
*toTranscriptome.out.bam
bam_unsorted
Unsorted BAM file of read alignments (optional)
*Aligned.unsort.out.bam
fastq
Unmapped FastQ files (optional)
*fastq.gz
tab
STAR output tab file(s) (optional)
*.tab
junction
STAR chimeric junction output file (optional)
*.out.junction
wig
STAR output wiggle format file(s) (optional)
*.wig
bedgraph
STAR output bedGraph format file(s) (optional)
*.bg
STAR is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
