Align reads to a reference genome using STAR
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads:file
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
meta2:map
Groovy Map containing reference information e.g. [ id:‘test’ ]
index:directory
STAR genome index
star
meta3:map
gtf:file
Annotation GTF file
*.{gtf}
star_ignore_sjdbgtf:boolean
Ignore annotation GTF file
seq_platform:string
Sequencing platform
seq_center:string
Sequencing center
log_final
*Log.final.out:file
STAR final log file
*Log.final.out
log_out
*Log.out:file
STAR lot out file
*Log.out
log_progress
*Log.progress.out:file
STAR log progress file
*Log.progress.out
versions
versions.yml:file
File containing software versions
versions.yml
bam
*d.out.bam:file
Output BAM file containing read alignments
*.{bam}
bam_sorted
${prefix}.sortedByCoord.out.bam:file
Sorted BAM file of read alignments (optional)
*sortedByCoord.out.bam
bam_sorted_aligned
${prefix}.Aligned.sortedByCoord.out.bam:file
*.Aligned.sortedByCoord.out.bam
bam_transcript
*toTranscriptome.out.bam:file
Output BAM file of transcriptome alignment (optional)
*toTranscriptome.out.bam
bam_unsorted
*Aligned.unsort.out.bam:file
Unsorted BAM file of read alignments (optional)
*Aligned.unsort.out.bam
fastq
*fastq.gz:file
Unmapped FastQ files (optional)
*fastq.gz
tab
*.tab:file
STAR output tab file(s) (optional)
*.tab
spl_junc_tab
*.SJ.out.tab:file
STAR output splice junction tab file
*.SJ.out.tab
read_per_gene_tab
*.ReadsPerGene.out.tab:file
STAR output read per gene tab file
*.ReadsPerGene.out.tab
junction
*.out.junction:file
STAR chimeric junction output file (optional)
*.out.junction
sam
*.out.sam
*.out.sam:file
STAR output SAM file(s) (optional)
wig
*.wig:file
STAR output wiggle format file(s) (optional)
*.wig
bedgraph
*.bg:file
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.
