pipelines_rnaseq.cwl

Documentation for rnaseq.cwl

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Overview

RNA-Seq alignment and transcript/gene abundance workflow

Inputs

Name	Label	Description	Type	Secondary Files
reference			['string', 'File']	['.fai', '^.dict']
reference_index			File	['.1.ht2', '.2.ht2', '.3.ht2', '.4.ht2', '.5.ht2', '.6.ht2', '.7.ht2', '.8.ht2']
reference_annotation			File
rna_sequence			../types/sequence_data.yml#sequence_data[]
read_group_id			string[]
read_group_fields			{'type': 'array', 'items': {'type': 'array', 'items': 'string'}}
sample_name			string
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?
species		the species being analyzed, such as homo_sapiens or mus_musculus	string
assembly		the assembly used, such as GRCh37/38, GRCm37/38	string

Outputs

Name	Label	Description	Type	Secondary Files
final_bam			File	['.bai']
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
bamcoverage_bigwig			File

Steps

Name	CWL Run
sequence_to_trimmed_fastq_and_hisat_alignments	subworkflows/sequence_to_trimmed_fastq_and_hisat_alignments.cwl
kallisto	tools/kallisto.cwl
transcript_to_gene	tools/transcript_to_gene.cwl
merge	tools/merge_bams.cwl
position_sort	tools/samtools_sort.cwl
index_bam	tools/index_bam.cwl
mark_dup	tools/mark_duplicates_and_sort.cwl
stringtie	tools/stringtie.cwl
generate_qc_metrics	tools/generate_qc_metrics.cwl
cgpbigwig_bamcoverage	tools/bam_to_bigwig.cwl