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