deploy: 2970ed4

index.html

@@ -265,5 +265,5 @@ <h2 id="license">📝 License</h2>
 
 <!--
 MkDocs version : 1.6.0
-Build Date UTC : 2024-05-13 17:33:31.987922+00:00
+Build Date UTC : 2024-05-23 15:59:46.573858+00:00
 -->

workflows/dnaseq-core/index.html

@@ -197,6 +197,7 @@ <h4 id="required">Required</h4>
 </ul>
 <h4 id="optional">Optional</h4>
 <ul>
+<li><code>sample_override</code> (String?): Value to override the SM field of <em>every</em> read group.</li>
 <li><code>rg_merge.basic_merge.new_header</code> (File?)</li>
 <li><code>rg_merge.final_merge.new_header</code> (File?)</li>
 <li><code>rg_merge.inner_merge.new_header</code> (File?)</li>

workflows/dnaseq-standard-fastq/index.html

@@ -200,6 +200,7 @@ <h4 id="required">Required</h4>
 </ul>
 <h4 id="optional">Optional</h4>
 <ul>
+<li><code>dnaseq_core_experimental.sample_override</code> (String?)</li>
 <li><code>dnaseq_core_experimental.rg_merge.basic_merge.new_header</code> (File?)</li>
 <li><code>dnaseq_core_experimental.rg_merge.final_merge.new_header</code> (File?)</li>
 <li><code>dnaseq_core_experimental.rg_merge.inner_merge.new_header</code> (File?)</li>
@@ -210,7 +211,7 @@ <h4 id="defaults">Defaults</h4>
 <li><code>reads_per_file</code> (Int, default=10000000): Controls the number of reads per FASTQ file for internal split to run BWA in parallel.</li>
 <li><code>subsample_n_reads</code> (Int, default=-1): Only process a random sampling of <code>n</code> reads. Any <code>n</code>&lt;=<code>0</code> for processing entire input.</li>
 <li><code>use_all_cores</code> (Boolean, default=false): Use all cores? Recommended for cloud environments.</li>
-<li><code>validate_input</code> (Boolean, default=true): Ensure input BAM is well-formed before beginning harmonization?</li>
+<li><code>validate_input</code> (Boolean, default=true): Ensure input FASTQs ares well-formed before beginning harmonization?</li>
 <li><code>fqlint.disable_validator_codes</code> (Array[String], default=[])</li>
 <li><code>fqlint.modify_disk_size_gb</code> (Int, default=0)</li>
 <li><code>fqlint.modify_memory_gb</code> (Int, default=0)</li>

workflows/dnaseq-standard/index.html

@@ -202,6 +202,7 @@ <h4 id="required">Required</h4>
 </ul>
 <h4 id="optional">Optional</h4>
 <ul>
+<li><code>sample_override</code> (String?): Value to override the SM field of <em>every</em> read group.</li>
 <li><code>validate_input_bam.reference_fasta</code> (File?)</li>
 <li><code>dnaseq_core_experimental.rg_merge.basic_merge.new_header</code> (File?)</li>
 <li><code>dnaseq_core_experimental.rg_merge.final_merge.new_header</code> (File?)</li>
@@ -215,7 +216,6 @@ <h4 id="defaults">Defaults</h4>
 <li><code>subsample_n_reads</code> (Int, default=-1): Only process a random sampling of <code>n</code> reads. Any <code>n</code>&lt;=<code>0</code> for processing entire input.</li>
 <li><code>use_all_cores</code> (Boolean, default=false): Use all cores? Recommended for cloud environments.</li>
 <li><code>validate_input</code> (Boolean, default=true): Ensure input BAM is well-formed before beginning harmonization?</li>
-<li><code>dnaseq_core_experimental.use_all_cores</code> (Boolean, default=false): Use all cores? Recommended for cloud environments.</li>
 <li><code>get_ReadGroups.modify_disk_size_gb</code> (Int, default=0)</li>
 <li><code>subsample.modify_disk_size_gb</code> (Int, default=0)</li>
 <li><code>subsample.ncpu</code> (Int, default=2)</li>