Run Minimap2 to align long read data against genome file. Default Minimap set for PacBio data.
---
- param output_dir:
Working directory path.
@@ -98,9 +97,6 @@- type num_threads:
- -
int, default 1
- return:
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"Genblast Module Documentation": [[3, "module-ensembl.tools.anno.protein_annotation.genblast"]], "Minimap2 Module Documentation": [[7, "module-ensembl.tools.anno.transcriptomic_annotation.minimap"]]}, "indexentries": {"ensembl.tools.anno.transcriptomic_annotation.minimap": [[7, "module-ensembl.tools.anno.transcriptomic_annotation.minimap"]], "module": [[7, "module-ensembl.tools.anno.transcriptomic_annotation.minimap"]], "run_minimap2() (in module ensembl.tools.anno.transcriptomic_annotation.minimap)": [[7, "ensembl.tools.anno.transcriptomic_annotation.minimap.run_minimap2"]]}}) \ No newline at end of file diff --git a/src/python/ensembl/tools/anno/transcriptomic_annotation/minimap.py b/src/python/ensembl/tools/anno/transcriptomic_annotation/minimap.py index 9e51d10..6b874a5 100644 --- a/src/python/ensembl/tools/anno/transcriptomic_annotation/minimap.py +++ b/src/python/ensembl/tools/anno/transcriptomic_annotation/minimap.py @@ -48,20 +48,21 @@ def run_minimap2( """ Run Minimap2 to align long read data against genome file. Default Minimap set for PacBio data. - :param output_dir: Working directory path. - :type output_dir: Path - :param long_read_fastq_dir: Long read directory path. - :type long_read_fastq_dir: Path - :param genome_file: Genome file path. - :type genome_file: Path - :param minimap2_bin: Software path. - :type minimap2_bin: Path, default minimap2 - :param paftools_bin: Software path. - :type paftools_bin: Path, default paftools.js - :param max_intron_length: The maximum intron size for alignments. Defaults to 100000. - :type max_intron_length: int, default 100000 - :param num_threads: Number of available threads. - :type num_threads: int, default 1 + + :param output_dir: Working directory path. + :type output_dir: Path + :param long_read_fastq_dir: Long read directory path. + :type long_read_fastq_dir: Path + :param genome_file: Genome file path. + :type genome_file: Path + :param minimap2_bin: Software path. + :type minimap2_bin: Path, default minimap2 + :param paftools_bin: Software path. + :type paftools_bin: Path, default paftools.js + :param max_intron_length: The maximum intron size for alignments. Defaults to 100000. + :type max_intron_length: int, default 100000 + :param num_threads: Number of available threads. + :type num_threads: int, default 1 :return: None :rtype: None
None