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. Gzipped FastQ files are decompressed on the fly with
‘–readFilesCommand zcat’, unless ‘–readFilesCommand’ is set in ext.args.
meta2
:map
Groovy Map containing reference information
e.g. [ id:‘test’ ]
index
:directory
STAR genome index
star
meta3
:map
Groovy Map containing reference information
e.g. [ id:‘test’ ]
gtf
:file
Annotation GTF file
*.{gtf}
star_ignore_sjdbgtf
:boolean
Ignore annotation GTF file
Output
name:type
description
pattern
log_final
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*Log.final.out
:file
STAR final log file
*Log.final.out
log_out
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*Log.out
:file
STAR lot out file
*Log.out
log_progress
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*Log.progress.out
:file
STAR log progress file
*Log.progress.out
versions_star
${task.process}
:string
The name of the process
star
:string
The name of the tool
STAR --version | sed "s/STAR_//"
:eval
The expression to obtain the version of the tool
versions_samtools
${task.process}
:string
The name of the process
samtools
:string
The name of the tool
samtools --version | sed -n '1s/samtools //p'
:eval
The expression to obtain the version of the tool
versions_gawk
${task.process}
:string
The name of the process
gawk
:string
The name of the tool
gawk --version | sed -n '1s/GNU Awk \([0-9.]*\).*/\1/p'
:eval
The expression to obtain the version of the tool
bam
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*d.out.bam
:file
Output BAM file containing read alignments
*.{bam}
bam_sorted
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.sortedByCoord.out.bam
:file
Sorted BAM file of read alignments (optional)
*sortedByCoord.out.bam
bam_sorted_aligned
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.Aligned.sortedByCoord.out.bam
:file
Sorted BAM file of read alignments (optional)
*.Aligned.sortedByCoord.out.bam
bam_transcript
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*toTranscriptome.out.bam
:file
Output BAM file of transcriptome alignment (optional)
*toTranscriptome.out.bam
bam_unsorted
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*Aligned.unsort.out.bam
:file
Unsorted BAM file of read alignments (optional)
*Aligned.unsort.out.bam
fastq
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*fastq.gz
:file
Unmapped FastQ files (optional)
*fastq.gz
tab
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.tab
:file
STAR output tab file(s) (optional)
*.tab
spl_junc_tab
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.SJ.out.tab
:file
STAR output splice junction tab file
*.SJ.out.tab
read_per_gene_tab
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.ReadsPerGene.out.tab
:file
STAR output read per gene tab file
*.ReadsPerGene.out.tab
junction
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.out.junction
:file
STAR chimeric junction output file (optional)
*.out.junction
sam
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.out.sam
:file
STAR output SAM file(s) (optional)
*.out.sam
wig
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.wig
:file
STAR output wiggle format file(s) (optional)
*.wig
bedgraph
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.bg
:file
STAR output bedGraph format file(s) (optional)
*.bg
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
star
:string
The name of the tool
STAR --version | sed "s/STAR_//"
:eval
The expression to obtain the version of the tool
${task.process}
:string
The name of the process
samtools
:string
The name of the tool
samtools --version | sed -n '1s/samtools //p'
:eval
The expression to obtain the version of the tool
${task.process}
:string
The name of the process
gawk
:string
The name of the tool
gawk --version | sed -n '1s/GNU Awk \([0-9.]*\).*/\1/p'
:eval
The expression to obtain the version of the tool
Tools
star
MIT
STAR is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
