| _version_ | 1866902188612124672 |
|---|---|
| author | broadinstitute |
| author_facet | broadinstitute |
| contents | <p><a href="https://github.com/broadinstitute/viral-pipelines/actions/workflows/build.yml"></a> <a href="http://viral-pipelines.readthedocs.io/en/latest/?badge=latest"></a></p> <h1>viral-pipelines</h1> <p>A set of scripts and tools for the analysis of viral NGS data.</p> <p>Workflows are written in <a href="https://github.com/openwdl/wdl">WDL</a> format. This is a portable workflow language that allows for easy execution on a wide variety of platforms:</p> <ul> <li>on individual machines (using <a href="https://github.com/chanzuckerberg/miniwdl">miniWDL</a> or <a href="https://github.com/broadinstitute/cromwell">Cromwell</a> to execute)</li> <li>on commercial cloud platforms like GCP, AWS, or Azure (using <a href="https://github.com/broadinstitute/cromwell">Cromwell</a> or <a href="https://github.com/microsoft/CromwellOnAzure">CromwellOnAzure</a>)</li> <li>on institutional HPC systems (using <a href="https://github.com/broadinstitute/cromwell">Cromwell</a>)</li> <li>on commercial platform as a service vendors (like <a href="https://dnanexus.com/">DNAnexus</a>)</li> <li>on academic cloud platforms (like <a href="https://app.terra.bio/">Terra</a>)</li> </ul> <h2>Obtaining the latest WDL workflows</h2> <p>Workflows from this repository are continuously deployed to <a href="https://dockstore.org/organizations/BroadInstitute/collections/pgs">Dockstore</a>, a GA4GH Tool Registry Service. They can then be easily imported to any bioinformatic compute platform that utilizes the TRS API and understands WDL (this includes Terra, DNAnexus, DNAstack, etc).</p> <p>Workflows are also available in the <a href="https://app.terra.bio/#workspaces/pathogen-genomic-surveillance/COVID-19">Terra featured workspace</a>.</p> <p>Workflows are continuously deployed to a <a href="https://platform.dnanexus.com/projects/F8PQ6380xf5bK0Qk0YPjB17P">DNAnexus CI project</a>.</p> <h2>Basic execution</h2> <p>The easiest way to get started is on a single, Python & Docker-capable machine (your laptop, shared workstation, or virtual machine) using <a href="https://github.com/chanzuckerberg/miniwdl">miniWDL</a> as shown above. MiniWDL can be installed either via <code>pip</code> or <code>conda</code> (via conda-forge). After confirming that it works (<code>miniwdl run_self_test</code>, you can use <a href="https://miniwdl.readthedocs.io/en/latest/getting_started.html">miniwdl run</a> to invoke WDL workflows from this repository.</p> <p>For example, to list the inputs for the assemble_refbased workflow:</p> <pre><code>miniwdl run https://raw.githubusercontent.com/broadinstitute/viral-pipelines/v2.1.8.0/pipes/WDL/workflows/assemble_refbased.wdl </code></pre> <p>This will emit:</p> <pre><code>missing required inputs for assemble_refbased: reads_unmapped_bams, reference_fasta required inputs: Array[File]+ reads_unmapped_bams File reference_fasta optional inputs: <really long list> outputs: <really long list> </code></pre> <p>To then execute this workflow on your local machine, invoke it with like this:</p> <pre><code>miniwdl run \ https://raw.githubusercontent.com/broadinstitute/viral-ngs-staging/master/pipes/WDL/workflows/assemble_refbased.wdl \ reads_unmapped_bams=PatientA_library1.bam \ reads_unmapped_bams=PatientA_library2.bam \ reference_fasta=/refs/NC_045512.2.fasta \ trim_coords_bed=/refs/NC_045512.2-artic_primers-3.bed \ sample_name=PatientA </code></pre> <p>In the above example, reads from two sequencing runs are aligned and merged together before consensus calling. The optional bed file provided turns on primer trimming at the given coordinates.</p> <h2>Available workflows</h2> <p>The workflows provided here are more fully documented at our <a href="https://viral-pipelines.readthedocs.io/en/latest/workflows.html">ReadTheDocs</a> page.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_18054133 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | github.com/broadinstitute/viral-pipelines/sarscov2_genbank_ingest broadinstitute <p><a href="https://github.com/broadinstitute/viral-pipelines/actions/workflows/build.yml"></a> <a href="http://viral-pipelines.readthedocs.io/en/latest/?badge=latest"></a></p> <h1>viral-pipelines</h1> <p>A set of scripts and tools for the analysis of viral NGS data.</p> <p>Workflows are written in <a href="https://github.com/openwdl/wdl">WDL</a> format. This is a portable workflow language that allows for easy execution on a wide variety of platforms:</p> <ul> <li>on individual machines (using <a href="https://github.com/chanzuckerberg/miniwdl">miniWDL</a> or <a href="https://github.com/broadinstitute/cromwell">Cromwell</a> to execute)</li> <li>on commercial cloud platforms like GCP, AWS, or Azure (using <a href="https://github.com/broadinstitute/cromwell">Cromwell</a> or <a href="https://github.com/microsoft/CromwellOnAzure">CromwellOnAzure</a>)</li> <li>on institutional HPC systems (using <a href="https://github.com/broadinstitute/cromwell">Cromwell</a>)</li> <li>on commercial platform as a service vendors (like <a href="https://dnanexus.com/">DNAnexus</a>)</li> <li>on academic cloud platforms (like <a href="https://app.terra.bio/">Terra</a>)</li> </ul> <h2>Obtaining the latest WDL workflows</h2> <p>Workflows from this repository are continuously deployed to <a href="https://dockstore.org/organizations/BroadInstitute/collections/pgs">Dockstore</a>, a GA4GH Tool Registry Service. They can then be easily imported to any bioinformatic compute platform that utilizes the TRS API and understands WDL (this includes Terra, DNAnexus, DNAstack, etc).</p> <p>Workflows are also available in the <a href="https://app.terra.bio/#workspaces/pathogen-genomic-surveillance/COVID-19">Terra featured workspace</a>.</p> <p>Workflows are continuously deployed to a <a href="https://platform.dnanexus.com/projects/F8PQ6380xf5bK0Qk0YPjB17P">DNAnexus CI project</a>.</p> <h2>Basic execution</h2> <p>The easiest way to get started is on a single, Python & Docker-capable machine (your laptop, shared workstation, or virtual machine) using <a href="https://github.com/chanzuckerberg/miniwdl">miniWDL</a> as shown above. MiniWDL can be installed either via <code>pip</code> or <code>conda</code> (via conda-forge). After confirming that it works (<code>miniwdl run_self_test</code>, you can use <a href="https://miniwdl.readthedocs.io/en/latest/getting_started.html">miniwdl run</a> to invoke WDL workflows from this repository.</p> <p>For example, to list the inputs for the assemble_refbased workflow:</p> <pre><code>miniwdl run https://raw.githubusercontent.com/broadinstitute/viral-pipelines/v2.1.8.0/pipes/WDL/workflows/assemble_refbased.wdl </code></pre> <p>This will emit:</p> <pre><code>missing required inputs for assemble_refbased: reads_unmapped_bams, reference_fasta required inputs: Array[File]+ reads_unmapped_bams File reference_fasta optional inputs: <really long list> outputs: <really long list> </code></pre> <p>To then execute this workflow on your local machine, invoke it with like this:</p> <pre><code>miniwdl run \ https://raw.githubusercontent.com/broadinstitute/viral-ngs-staging/master/pipes/WDL/workflows/assemble_refbased.wdl \ reads_unmapped_bams=PatientA_library1.bam \ reads_unmapped_bams=PatientA_library2.bam \ reference_fasta=/refs/NC_045512.2.fasta \ trim_coords_bed=/refs/NC_045512.2-artic_primers-3.bed \ sample_name=PatientA </code></pre> <p>In the above example, reads from two sequencing runs are aligned and merged together before consensus calling. The optional bed file provided turns on primer trimming at the given coordinates.</p> <h2>Available workflows</h2> <p>The workflows provided here are more fully documented at our <a href="https://viral-pipelines.readthedocs.io/en/latest/workflows.html">ReadTheDocs</a> page.</p> |
| title | github.com/broadinstitute/viral-pipelines/sarscov2_genbank_ingest |
| url | https://doi.org/10.5281/zenodo.18054133 |