From c3a8c500d240c5b523e3d811d8252e3bb0625920 Mon Sep 17 00:00:00 2001 From: gbouras13 Date: Mon, 9 Oct 2023 12:48:06 +1030 Subject: [PATCH] add release --- HISTORY.md | 28 ++++++++++++++++++++++++++-- 1 file changed, 26 insertions(+), 2 deletions(-) diff --git a/HISTORY.md b/HISTORY.md index 5f61e37..13ac903 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -2,7 +2,31 @@ History ======= -0.1.0 (2023-10-08) +0.1.0 (2023-10-09) ------------------ -* Initial release \ No newline at end of file +* Initial release + +``` +Usage: pypolca run [OPTIONS] + + Python implementation of the POLCA polisher from MaSuRCA + +Options: + -h, --help Show this message and exit. + -V, --version Show the version and exit. + -a, --assembly PATH Path to assembly contigs or scaffolds. [required] + -1, --reads1 PATH Path to polishing reads R1 FASTQ. Can be FASTQ or + FASTQ gzipped. Required. [required] + -2, --reads2 PATH Path to polishing reads R2 FASTQ. Can be FASTQ or + FASTQ gzipped. Optional. Only use -1 if you have + single end reads. + -t, --threads INTEGER Number of threads. [default: 1] + -o, --output PATH Output directory path [default: output_polca] + -f, --force Force overwrites the output directory + -n, --no_polish do not polish, just create vcf file, evaluate the + assembly and exit + -m, --memory_limit TEXT Memory per thread to use in samtools sort, set to + 2G or more for large genomes [default: 2G] + -p, --prefix TEXT prefix for output files [default: polca] +``` \ No newline at end of file