Workflow: RNA-Seq alignment and transcript/gene abundance workflow

Fetched 2023-01-05 07:39:02 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs trimming_min_readlength trimming_min_readlength bam_to_trimmed_fastq_and_hisat_alignments bam to trimmed fastqs and HISAT alignments trimming_min_readlength->bam_to_trimmed_fastq_and_hisat_alignments min_readlength instrument_data_bams instrument_data_bams instrument_data_bams->bam_to_trimmed_fastq_and_hisat_alignments bam refFlat refFlat generate_qc_metrics Picard: RNA Seq Metrics refFlat->generate_qc_metrics refFlat read_group_id read_group_id read_group_id->bam_to_trimmed_fastq_and_hisat_alignments read_group_id reference_annotation reference_annotation stringtie StringTie reference_annotation->stringtie reference_annotation ribosomal_intervals ribosomal_intervals ribosomal_intervals->generate_qc_metrics ribosomal_intervals trimming_adapter_min_overlap trimming_adapter_min_overlap trimming_adapter_min_overlap->bam_to_trimmed_fastq_and_hisat_alignments adapter_min_overlap sample_name sample_name sample_name->stringtie sample_name trimming_adapter_trim_end trimming_adapter_trim_end trimming_adapter_trim_end->bam_to_trimmed_fastq_and_hisat_alignments adapter_trim_end species species strand strand strand->stringtie strand strand->generate_qc_metrics strand strand->bam_to_trimmed_fastq_and_hisat_alignments strand kallisto Kallisto: Quant strand->kallisto strand trimming_max_uncalled trimming_max_uncalled trimming_max_uncalled->bam_to_trimmed_fastq_and_hisat_alignments max_uncalled read_group_fields read_group_fields read_group_fields->bam_to_trimmed_fastq_and_hisat_alignments read_group_fields reference_index reference_index reference_index->bam_to_trimmed_fastq_and_hisat_alignments reference_index kallisto_index kallisto_index kallisto_index->kallisto kallisto_index gene_transcript_lookup_table gene_transcript_lookup_table transcript_to_gene Kallisto: TranscriptToGene gene_transcript_lookup_table->transcript_to_gene gene_transcript_lookup_table trimming_adapters trimming_adapters trimming_adapters->bam_to_trimmed_fastq_and_hisat_alignments adapters assembly assembly final_bam final_bam fusion_evidence fusion_evidence stringtie_transcript_gtf stringtie_transcript_gtf chart chart stringtie_gene_expression_tsv stringtie_gene_expression_tsv gene_abundance gene_abundance metrics metrics transcript_abundance_h5 transcript_abundance_h5 transcript_abundance_tsv transcript_abundance_tsv mark_dup Mark duplicates and Sort mark_dup->final_bam mark_dup->stringtie bam merge Sambamba: merge merge->mark_dup bam index_bam samtools index merge->index_bam bam index_bam->generate_qc_metrics bam stringtie->stringtie_transcript_gtf stringtie->stringtie_gene_expression_tsv generate_qc_metrics->chart generate_qc_metrics->metrics transcript_to_gene->gene_abundance bam_to_trimmed_fastq_and_hisat_alignments->merge bams bam_to_trimmed_fastq_and_hisat_alignments->kallisto fastqs kallisto->fusion_evidence kallisto->transcript_abundance_h5 kallisto->transcript_abundance_tsv kallisto->transcript_to_gene transcript_table_h5 default1 "coordinate" default1->mark_dup input_sort_order
Workflow as SVG
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Inputs

ID Type Title Doc
strand
refFlat File
species String

the species being analyzed, such as homo_sapiens or mus_musculus

assembly String

the assembly used, such as GRCh37/38, GRCm37/38

sample_name String
read_group_id String[]
kallisto_index File
reference_index File
read_group_fields 846b8b695ed8abedc167b8972942dc0e[]
trimming_adapters File
ribosomal_intervals File (Optional)
instrument_data_bams File[]
reference_annotation File
trimming_max_uncalled Integer
trimming_min_readlength Integer
trimming_adapter_trim_end String
gene_transcript_lookup_table File
trimming_adapter_min_overlap Integer

Steps

ID Runs Label Doc
merge
../tools/merge_bams.cwl (CommandLineTool)
Sambamba: merge
kallisto
../tools/kallisto.cwl (CommandLineTool)
Kallisto: Quant
mark_dup
../tools/mark_duplicates_and_sort.cwl (CommandLineTool)
Mark duplicates and Sort
index_bam
../tools/index_bam.cwl (CommandLineTool)
samtools index
stringtie
../tools/stringtie.cwl (CommandLineTool)
StringTie
transcript_to_gene
../tools/transcript_to_gene.cwl (CommandLineTool)
Kallisto: TranscriptToGene
generate_qc_metrics
../tools/generate_qc_metrics.cwl (CommandLineTool)
Picard: RNA Seq Metrics
bam_to_trimmed_fastq_and_hisat_alignments bam to trimmed fastqs and HISAT alignments

Outputs

ID Type Label Doc
chart File (Optional)
metrics File
final_bam File
gene_abundance File
fusion_evidence File
transcript_abundance_h5 File
stringtie_transcript_gtf File
transcript_abundance_tsv File
stringtie_gene_expression_tsv File
Permalink: https://w3id.org/cwl/view/git/06d2440d115b446c299b4ce96e8812d2f8df86ec/definitions/pipelines/rnaseq.cwl