Merge pull request #2 from gbouras13/dev

add release

HISTORY.md

@@ -2,7 +2,31 @@
 History
 =======
 
-0.1.0 (2023-10-08)
+0.1.0 (2023-10-09)
 ------------------
 
-* Initial release
+* 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]
+```