Docstrings and update readme

README.md

@@ -52,8 +52,8 @@ pytest
 ## Command line usage
 
 ```bash
-hostile clean --help
-usage: hostile clean [-h] --fastq1 FASTQ1 [--fastq2 FASTQ2] [--aligner {bowtie2,minimap2,auto}] [--index INDEX] [--out-dir OUT_DIR] [--threads THREADS] [--debug]
+$ hostile clean --help
+usage: hostile clean [-h] --fastq1 FASTQ1 [--fastq2 FASTQ2] [--aligner {bowtie2,minimap2,auto}] [--index INDEX] [--rename] [--out-dir OUT_DIR] [--threads THREADS] [--force] [--debug]
 
 Remove host reads from paired fastq(.gz) files
 
@@ -69,12 +69,15 @@ options:
                         (default: None)
   --rename              replace read names with incrementing integers
                         (default: False)
-  --out-dir OUT_DIR     output directory for decontaminated fastq.gz files
-                        (default: /Users/bede/Research/Git/hostile)
+  --out-dir OUT_DIR     path to output directory
+                        (default: ./)
   --threads THREADS     number of CPU threads to use
                         (default: 10)
+  --force               overwrite existing output files
+                        (default: False)
   --debug               show debug messages
                         (default: False)
+
 ```
 
 ### Short reads

src/hostile/__init__.py

@@ -1,2 +1,2 @@
-"""Host read removal"""
-__version__ = "0.0.2"
+"""Accurate host read removal"""
+__version__ = "0.0.3"

src/hostile/cli.py

@@ -35,8 +35,9 @@ def clean(
     :arg aligner: alignment algorithm
     :arg index: path to custom genome or index. For Bowtie2, provide an index path without the .bt2 extension
     :arg rename: replace read names with incrementing integers
-    :arg out_dir: output directory for decontaminated fastq.gz files
+    :arg out_dir: path to output directory
     :arg threads: number of CPU threads to use
+    :arg force: overwrite existing output files
     :arg debug: show debug messages
     """
 
@@ -89,7 +90,7 @@ def clean(
 #     :arg fastqs: path to fastq(.gz) or bam file(s). Paired fastq paths should be comma-separated, e.g. reads_1.fastq.gz,reads_2.fastq.gz
 #     :arg aligner: alignment algorithm
 #     :arg index: path to custom genome or index. For Bowtie2, provide an index path without the .bt2 extension
-#     :arg out_dir: output directory for decontaminated fastq.gz files
+#     :arg out_dir: path to output directory
 #     :arg threads: number of threads to use
 #     :arg debug: show debug messages
 #     """
@@ -118,7 +119,7 @@ def mask(
 
     :arg reference: path to reference genome in fasta[.gz] format
     :arg target: path to target genome(s) in fasta[.gz] format
-    :arg out_dir: path of output directory
+    :arg out_dir: path to output directory
     :arg threads: number of threads to use
     """
     lib.mask(reference=reference, target=target, out_dir=out_dir, threads=threads)