name: star_align description: Align reads to a reference genome using STAR keywords: - align - fasta - genome - reference tools: - star: description: | STAR is a software package for mapping DNA sequences against a large reference genome, such as the human genome. homepage: https://github.com/alexdobin/STAR manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf doi: 10.1093/bioinformatics/bts635 input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: type: file description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - index: type: directory description: STAR genome index pattern: "star" output: - bam: type: file description: Output BAM file containing read alignments pattern: "*.{bam}" - log_final: type: file description: STAR final log file pattern: "*Log.final.out" - log_out: type: file description: STAR lot out file pattern: "*Log.out" - log_progress: type: file description: STAR log progress file pattern: "*Log.progress.out" - versions: type: file description: File containing software versions pattern: "versions.yml" - bam_sorted: type: file description: Sorted BAM file of read alignments (optional) pattern: "*sortedByCoord.out.bam" - bam_transcript: type: file description: Output BAM file of transcriptome alignment (optional) pattern: "*toTranscriptome.out.bam" - bam_unsorted: type: file description: Unsorted BAM file of read alignments (optional) pattern: "*Aligned.unsort.out.bam" - fastq: type: file description: Unmapped FastQ files (optional) pattern: "*fastq.gz" - tab: type: file description: STAR output tab file(s) (optional) pattern: "*.tab" - junction: type: file description: STAR chimeric junction output file (optional) pattern: "*.out.junction" authors: - "@kevinmenden" - "@drpatelh" - "@praveenraj2018"