pipelines_rnaseq_star_fusion.cwl

Documentation for rnaseq_star_fusion.cwl

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Overview

STAR-RNA-Seq alignment and transcript/gene abundance workflow

Inputs

Name	Label	Description	Type	Secondary Files
unaligned			../types/sequence_data.yml#sequence_data[]
outsam_attrrg_line			string[]
star_genome_dir			Directory
star_fusion_genome_dir			Directory
cdna_fasta			File
reference			File	['.fai', '^.dict']
gtf_file			File
trimming_adapters			File
trimming_adapter_trim_end			string
trimming_adapter_min_overlap			int
trimming_max_uncalled			int
trimming_min_readlength			int
kallisto_index			File
gene_transcript_lookup_table			File
strand			['null', {'type': 'enum', 'symbols': ['first', 'second', 'unstranded']}]
refFlat			File
ribosomal_intervals			File
sample_name			string
unzip_fastqs			boolean?

Outputs

Name	Label	Description	Type	Secondary Files
cram			File	['.crai', '^.crai']
star_fusion_out			File
star_junction_out			File
star_fusion_log			File
star_fusion_predict			File
star_fusion_abridge			File
stringtie_transcript_gtf			File
stringtie_gene_expression_tsv			File
transcript_abundance_tsv			File
transcript_abundance_h5			File
gene_abundance			File
metrics			File
chart			File
fusion_evidence			File
strand_info			File[]
bamcoverage_bigwig			File

Steps

Name	CWL Run
sequence_to_trimmed_fastq	subworkflows/sequence_to_trimmed_fastq.cwl
strandedness_check	tools/strandedness_check.cwl
star_align_fusion	tools/star_align_fusion.cwl
star_fusion_detect	tools/star_fusion_detect.cwl
kallisto	tools/kallisto.cwl
transcript_to_gene	tools/transcript_to_gene.cwl
sort_bam	tools/samtools_sort.cwl
mark_dup	tools/mark_duplicates_and_sort.cwl
index_bam	tools/index_bam.cwl
stringtie	tools/stringtie.cwl
generate_qc_metrics	tools/generate_qc_metrics.cwl
bam_to_cram	tools/bam_to_cram.cwl
index_cram	tools/index_cram.cwl
cgpbigwig_bamcoverage	tools/bam_to_bigwig.cwl