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.

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)

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.

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

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 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.

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

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)

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