bugfix docstring minimap

Ensembl · Sep 28, 2023 · 7ae4f41 · 7ae4f41
1 parent e6d2263
commit 7ae4f41
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Showing 6 changed files with 31 additions and 33 deletions.
diff --git a/docs/build/.doctrees/environment.pickle b/docs/build/.doctrees/environment.pickle
diff --git a/docs/build/.doctrees/minimap.doctree b/docs/build/.doctrees/minimap.doctree
diff --git a/docs/build/_modules/ensembl/tools/anno/transcriptomic_annotation/minimap.html b/docs/build/_modules/ensembl/tools/anno/transcriptomic_annotation/minimap.html
@@ -88,20 +88,21 @@ <h1>Source code for ensembl.tools.anno.transcriptomic_annotation.minimap</h1><di
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Run Minimap2 to align long read data against genome file.</span>
 <span class="sd">    Default Minimap set for PacBio data.</span>
-<span class="sd">            :param output_dir: Working directory path.</span>
-<span class="sd">            :type output_dir: Path</span>
-<span class="sd">            :param long_read_fastq_dir: Long read directory path.</span>
-<span class="sd">            :type long_read_fastq_dir: Path</span>
-<span class="sd">            :param genome_file: Genome file path.</span>
-<span class="sd">            :type genome_file: Path</span>
-<span class="sd">            :param minimap2_bin: Software path.</span>
-<span class="sd">            :type minimap2_bin: Path, default minimap2</span>
-<span class="sd">            :param paftools_bin: Software path.</span>
-<span class="sd">            :type paftools_bin: Path, default paftools.js</span>
-<span class="sd">            :param max_intron_length: The maximum intron size for alignments. Defaults to 100000.</span>
-<span class="sd">            :type max_intron_length: int, default 100000</span>
-<span class="sd">            :param num_threads: Number of available threads.</span>
-<span class="sd">            :type num_threads: int, default 1</span>
+<span class="sd">    </span>
+<span class="sd">        :param output_dir: Working directory path.</span>
+<span class="sd">        :type output_dir: Path</span>
+<span class="sd">        :param long_read_fastq_dir: Long read directory path.</span>
+<span class="sd">        :type long_read_fastq_dir: Path</span>
+<span class="sd">        :param genome_file: Genome file path.</span>
+<span class="sd">        :type genome_file: Path</span>
+<span class="sd">        :param minimap2_bin: Software path.</span>
+<span class="sd">        :type minimap2_bin: Path, default minimap2</span>
+<span class="sd">        :param paftools_bin: Software path.</span>
+<span class="sd">        :type paftools_bin: Path, default paftools.js</span>
+<span class="sd">        :param max_intron_length: The maximum intron size for alignments. Defaults to 100000.</span>
+<span class="sd">        :type max_intron_length: int, default 100000</span>
+<span class="sd">        :param num_threads: Number of available threads.</span>
+<span class="sd">        :type num_threads: int, default 1</span>
 <span class="sd">               </span>
 <span class="sd">        :return: None</span>
 <span class="sd">        :rtype: None</span>

diff --git a/docs/build/minimap.html b/docs/build/minimap.html
@@ -54,7 +54,6 @@
 <dd><p>Run Minimap2 to align long read data against genome file.
 Default Minimap set for PacBio data.</p>
 <blockquote>
-<div><blockquote>
 <div><dl class="field-list simple">
 <dt class="field-odd">param output_dir<span class="colon">:</span></dt>
 <dd class="field-odd"><p>Working directory path.</p>
@@ -98,9 +97,6 @@
 <dt class="field-even">type num_threads<span class="colon">:</span></dt>
 <dd class="field-even"><p>int, default 1</p>
 </dd>
-</dl>
-</div></blockquote>
-<dl class="field-list simple">
 <dt class="field-odd">return<span class="colon">:</span></dt>
 <dd class="field-odd"><p>None</p>
 </dd>