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2025
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| Online Access: | https://doi.org/10.5281/zenodo.16811666 |
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| _version_ | 1866902340462706688 |
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| author | Valerii Pavlov |
| author_facet | Valerii Pavlov |
| contents | <h1>AltAnalyze2 SNAF Workflows</h1> <p>This repository contains two WDL workflows and supporting container code:</p> <ul> <li>Splicing analysis with AltAnalyze: <code>splicing_analysis.wdl</code></li> <li>STAR 2-pass alignment: <code>star_2.4_alignment/star_alignment.wdl</code></li> </ul> <h3>Dockstore configuration</h3> <p>The root <code>.dockstore.yml</code> registers both workflows for automatic discovery:</p> <ul> <li><code>splicing_analysis</code> with <code>primaryDescriptorPath: /splicing_analysis.wdl</code></li> <li><code>star_2pass_alignment</code> with <code>primaryDescriptorPath: /star_2.4_alignment/star_alignment.wdl</code></li> </ul> <p>You can import this repo into Dockstore to run the workflows directly.</p> <h3>Splicing analysis (AltAnalyze)</h3> <ul> <li>WDL: <code>splicing_analysis.wdl</code></li> <li>Example inputs: <code>splicing_analysis_test.json</code></li> </ul> <p>Required inputs:</p> <ul> <li><code>SplicingAnalysis.bam_files</code>: array of BAMs</li> <li><code>SplicingAnalysis.bai_files</code>: corresponding BAI indexes</li> </ul> <p>Optional:</p> <ul> <li><code>SplicingAnalysis.cpu_cores</code> (default 4)</li> <li><code>SplicingAnalysis.perform_alt_analysis</code> (Boolean, defaults based on sample count)</li> </ul> <p>Output:</p> <ul> <li><code>splicing_results</code>: <code>altanalyze_output.tar.gz</code> containing AltAnalyze results</li> </ul> <h3>STAR 2-pass alignment</h3> <ul> <li>WDL: <code>star_2.4_alignment/star_alignment.wdl</code></li> <li>Container: <code>ndeeseee/star-aligner:latest</code></li> <li>Script: <code>star_2.4_alignment/star_alignment.sh</code></li> <li>Example inputs: <code>star_2.4_alignment/star_alignment_test.json</code></li> </ul> <p>CLI (container) usage:</p> <pre><code>docker run --rm \ -v /path/to/data:/data \ ndeeseee/star-aligner:latest \ /data/input/sample.1.fastq.gz \ /data/reference/star_index \ /data/reference/genome.fa \ /data/output \ sample_001 \ 16 </code></pre> <p>WDL ensures deterministic output naming by passing <code>sample_name</code> to the script and threads via <code>cpu_cores</code>.</p> <p>Output:</p> <ul> <li><code>{sample}.bam</code> and optional <code>{sample}_Log.final.out</code></li> </ul> <h3>Development</h3> <ul> <li>Shell scripts are linted with ShellCheck via GitHub Actions.</li> <li>To run locally: <code>shellcheck **/*.sh</code></li> </ul> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_16811666 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | github.com/NDeeSeee/altanalyze2_snaf/splicing_analysis Valerii Pavlov <h1>AltAnalyze2 SNAF Workflows</h1> <p>This repository contains two WDL workflows and supporting container code:</p> <ul> <li>Splicing analysis with AltAnalyze: <code>splicing_analysis.wdl</code></li> <li>STAR 2-pass alignment: <code>star_2.4_alignment/star_alignment.wdl</code></li> </ul> <h3>Dockstore configuration</h3> <p>The root <code>.dockstore.yml</code> registers both workflows for automatic discovery:</p> <ul> <li><code>splicing_analysis</code> with <code>primaryDescriptorPath: /splicing_analysis.wdl</code></li> <li><code>star_2pass_alignment</code> with <code>primaryDescriptorPath: /star_2.4_alignment/star_alignment.wdl</code></li> </ul> <p>You can import this repo into Dockstore to run the workflows directly.</p> <h3>Splicing analysis (AltAnalyze)</h3> <ul> <li>WDL: <code>splicing_analysis.wdl</code></li> <li>Example inputs: <code>splicing_analysis_test.json</code></li> </ul> <p>Required inputs:</p> <ul> <li><code>SplicingAnalysis.bam_files</code>: array of BAMs</li> <li><code>SplicingAnalysis.bai_files</code>: corresponding BAI indexes</li> </ul> <p>Optional:</p> <ul> <li><code>SplicingAnalysis.cpu_cores</code> (default 4)</li> <li><code>SplicingAnalysis.perform_alt_analysis</code> (Boolean, defaults based on sample count)</li> </ul> <p>Output:</p> <ul> <li><code>splicing_results</code>: <code>altanalyze_output.tar.gz</code> containing AltAnalyze results</li> </ul> <h3>STAR 2-pass alignment</h3> <ul> <li>WDL: <code>star_2.4_alignment/star_alignment.wdl</code></li> <li>Container: <code>ndeeseee/star-aligner:latest</code></li> <li>Script: <code>star_2.4_alignment/star_alignment.sh</code></li> <li>Example inputs: <code>star_2.4_alignment/star_alignment_test.json</code></li> </ul> <p>CLI (container) usage:</p> <pre><code>docker run --rm \ -v /path/to/data:/data \ ndeeseee/star-aligner:latest \ /data/input/sample.1.fastq.gz \ /data/reference/star_index \ /data/reference/genome.fa \ /data/output \ sample_001 \ 16 </code></pre> <p>WDL ensures deterministic output naming by passing <code>sample_name</code> to the script and threads via <code>cpu_cores</code>.</p> <p>Output:</p> <ul> <li><code>{sample}.bam</code> and optional <code>{sample}_Log.final.out</code></li> </ul> <h3>Development</h3> <ul> <li>Shell scripts are linted with ShellCheck via GitHub Actions.</li> <li>To run locally: <code>shellcheck **/*.sh</code></li> </ul> |
| title | github.com/NDeeSeee/altanalyze2_snaf/splicing_analysis |
| url | https://doi.org/10.5281/zenodo.16811666 |