Workflow: TOPMed_RNA-seq

Fetched 2023-01-12 02:05:51 GMT

TOPMed RNA-seq CWL workflow. Documentation on the workflow can be found [here]( Example input files: [Dockstore.json]( and [rnaseq_pipeline_fastq-example.yml]( Quickstart instructions are [here]( Start). [GitHub Repo]( Pipeline steps: 1. Align RNA-seq reads with [STAR v2.5.3a]( 2. Run [Picard]( [MarkDuplicates]( 2a. Create BAM index for MarkDuplicates BAM with [Samtools 1.6]( index. 3. Transcript quantification with [RSEM 1.3.0]( 4. Gene quantification and quality control with [RNA-SeQC 1.1.9](

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ID Type Title Doc
fastqs File[]
genes_gtf File
paired_end Boolean
prefix_str String
star_index Directory
is_stranded Boolean
genome_fasta File
max_frag_len Integer
rsem_ref_dir Directory
estimate_rspd Boolean
rnaseqc_flags String[]


ID Runs Label Doc
rsem.cwl (CommandLineTool)

A CWL wrapper for [](

Runs [RSEM 1.3.0](

This CWL Tool was developed as step 3 of the TOPMed RNA-seq workflow.

star.cwl (CommandLineTool)

A CWL wrapper for [](

Runs [STAR v2.5.3a](

This CWL Tool was developed as step 1 of the TOPMed RNA-seq workflow.

[GitHub Repo](

samtools-sort.cwl (CommandLineTool)

Sort alignments by leftmost coordinates, or by read name when -n is used. An appropriate @HD-SO sort order header tag will be added or an existing one updated if necessary.

Usage: samtools sort [-l level] [-m maxMem] [-o out.bam] [-O format] [-n] -T out.prefix [-@ threads] [in.bam]

Options: -l INT Set the desired compression level for the final output file, ranging from 0 (uncompressed) or 1 (fastest but minimal compression) to 9 (best compression but slowest to write), similarly to gzip(1)'s compression level setting.

If -l is not used, the default compression level will apply.

-n Sort by read names (i.e., the QNAME field) rather than by chromosomal coordinates.

-o FILE Write the final sorted output to FILE, rather than to standard output.

-O FORMAT Write the final output as sam, bam, or cram.

By default, samtools tries to select a format based on the -o filename extension; if output is to standard output or no format can be deduced, -O must be used.

-T PREFIX Write temporary files to PREFIX.nnnn.bam. This option is required.

indexbam.cwl (CommandLineTool)

A wrapper for running `samtools index <bam>`.

rna_seqc.cwl (CommandLineTool)

A CWL wrapper for []( duplicated from []( with minor modifications.

Runs [RNA-SeQC 1.1.9](

This CWL Tool was developed as step 4 of the TOPMed RNA-seq workflow.

[GitHub Repo](

markduplicates.cwl (CommandLineTool)

A CWL wrapper for [](

Runs [Picard]( [MarkDuplicates](

This CWL Tool was developed as step 2 of the TOPMed RNA-seq workflow.

[GitHub Repo](

indexbam.cwl (CommandLineTool)

A wrapper for running `samtools index <bam>`.


ID Type Label Doc
star_output_bam File
star_output_logs File[]
star_output_bam_index File
star_output_junctions File
star_output_read_counts File
markduplicates_bam_index File
rsem_output_gene_results File
markduplicates_output_bam File
rna-seqc_output_gene_rpkm File
rna-seqc_output_exon_counts File
rna-seqc_output_gene_counts File
star_output_junctions_pass1 File
rsem_output_isoforms_results File
markduplicates_output_metrics File
rna-seqc_output_count_metrics File
rna-seqc_output_count_outputs File
star_output_transcriptome_bam File
star_output_chimeric_junctions File