Workflow: TOPMed_RNA-seq

Fetched 2021-01-14 13:11:30 GMT

TOPMed RNA-seq CWL workflow. Documentation on the workflow can be found [here](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/README.md). Example input files: [Dockstore.json](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/Dockstore.json) and [rnaseq_pipeline_fastq-example.yml](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/rnaseq_pipeline_fastq-example.yml). Quickstart instructions are [here](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/README.md#Quick Start). [GitHub Repo](https://github.com/heliumdatacommons/cwl_workflows) Pipeline steps: 1. Align RNA-seq reads with [STAR v2.5.3a](https://github.com/alexdobin/STAR). 2. Run [Picard](https://github.com/broadinstitute/picard) [MarkDuplicates](https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates). 2a. Create BAM index for MarkDuplicates BAM with [Samtools 1.6](https://github.com/samtools/samtools/releases) index. 3. Transcript quantification with [RSEM 1.3.0](https://deweylab.github.io/RSEM/) 4. Gene quantification and quality control with [RNA-SeQC 1.1.9](https://github.com/francois-a/rnaseqc)

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Inputs

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

Steps

ID Runs Label Doc
index_bam
indexbam.cwl (CommandLineTool)
run-index-bam

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

run_star
star.cwl (CommandLineTool)
run-star

A CWL wrapper for [run_STAR.py](https://github.com/broadinstitute/gtex-pipeline/blob/master/rnaseq/src/run_STAR.py)

Runs [STAR v2.5.3a](https://github.com/alexdobin/STAR)

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

[GitHub Repo](https://github.com/heliumdatacommons/cwl_workflows)

run_index_markduplicates_bam
indexbam.cwl (CommandLineTool)
run-index-bam

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

run_rsem
rsem.cwl (CommandLineTool)
run-rsem

A CWL wrapper for [run_RSEM.py](https://github.com/broadinstitute/gtex-pipeline/blob/master/rnaseq/src/run_RSEM.py)

Runs [RSEM 1.3.0](https://deweylab.github.io/RSEM/)

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

run_markduplicates
markduplicates.cwl (CommandLineTool)
run-MarkDuplicates

A CWL wrapper for [run_MarkDuplicates.py](https://github.com/broadinstitute/gtex-pipeline/blob/master/rnaseq/src/run_MarkDuplicates.py)

Runs [Picard](https://github.com/broadinstitute/picard) [MarkDuplicates](https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates)

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

[GitHub Repo](https://github.com/heliumdatacommons/cwl_workflows)

run_rna-seqc
rna_seqc.cwl (CommandLineTool)
run-seqc

A CWL wrapper for [run_rnaseqc.py](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/src/run_rnaseqc.py) duplicated from [run_rnaseqc.py](https://github.com/broadinstitute/gtex-pipeline/blob/master/rnaseq/src/run_rnaseqc.py) with minor modifications.

Runs [RNA-SeQC 1.1.9](https://github.com/francois-a/rnaseqc)

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

[GitHub Repo](https://github.com/heliumdatacommons/cwl_workflows)

sort_bam
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.

Outputs

ID Type Label Doc
rna-seqc_output_count_metrics File
markduplicates_output_bam File
markduplicates_bam_index File
rsem_output_isoforms_results File
rna-seqc_output_gene_rpkm File
markduplicates_output_metrics File
rsem_output_gene_results File
rna-seqc_output_count_outputs File
star_output_transcriptome_bam File
star_output_junctions_pass1 File
star_output_read_counts File
star_output_junctions File
star_output_chimeric_junctions File
star_output_bam_index File
star_output_logs File[]
star_output_bam File
rna-seqc_output_gene_counts File
rna-seqc_output_exon_counts File
Permalink: https://w3id.org/cwl/view/git/018d344b12e9e1b888e21e0819096f9b337d371d/topmed-workflows/TOPMed_RNAseq_pipeline/rnaseq_pipeline_fastq.cwl