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nf-core/parabricks/rnafq2bam @ 0.0.0-0c7146d

This tool is the equivalent of fq2bam for RNA-Seq samples, receiving inputs in FASTQ format, performing alignment with the splice-aware STAR algorithm, optionally marking of duplicate reads, and outputting an aligned BAM file ready for variant and fusion calling.

align star rna
Latest version: 0.0.0-0c7146d
Total downloads: 2
Source: nf-core/modules
Authors: @gburnett-nvidia
Maintainers: @gburnett-nvidia

Summary

This tool is the equivalent of fq2bam for RNA-Seq samples, receiving inputs in FASTQ format, performing alignment with the splice-aware STAR algorithm, optionally marking of duplicate reads, and outputting an aligned BAM file ready for variant and fusion calling.

Get started

Add the following snippet to your workflow script to include this module.

include { PARABRICKS_RNAFQ2BAM } from 'nf-core/parabricks/rnafq2bam'

License

MIT License

Process
Name PARABRICKS_RNAFQ2BAM
Input 5 channels
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
reads file

fastq.gz files

 *.fastq.gz
#2 tuple
meta2 map

Groovy Map containing fasta information
fasta file

reference fasta file - must be unzipped

 *.fasta
#3 tuple
meta3 map

Groovy Map containing genome lib dir information
index directory

Path to a genome resource library directory. The indexing required to run STAR should be completed by the user beforehand.

 *
qc_metrics boolean

Optionally report QC metrics
mark_duplicates boolean

Optionally mark duplicates
Output 20 channels
#1 bai tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}.bam.bai file

Output BAM index file

 *.{bam}.{bai}
#2 bam tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}.bam file

Output BAM file containing read alignments

 *.{bam}
#3 sam tuple
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
#4 tab tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.tab file

STAR output tab file(s) (optional)

 *.tab
#5 wig tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.wig file

STAR output wiggle format file(s) (optional)

 *.wig
#6 fastq tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*fastq.gz file

Unmapped FastQ files (optional)

 *fastq.gz
#7 log_out tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
${prefix}.Log.out file

STAR log out file

 *Log.out
#8 bedgraph tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.bg file

STAR output bedGraph format file(s) (optional)

 *.bg
#9 junction tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]