fix: update rasusa usage for latest version

.github/workflows/ci.yaml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     name: check conventional commit compliance
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
           # pick the pr HEAD instead of the merge commitonly if it's a PR, otherwise use the default
@@ -27,7 +27,7 @@ jobs:
         python-version: [ 3.8 ]
         os: [ ubuntu-latest, macos-latest ]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v2
         with:
           python-version: ${{ matrix.python-version }}
@@ -52,7 +52,7 @@ jobs:
         shell: bash -l {0}
         run: just test-ci
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v4
         with:
           file: ./coverage.xml
           flags: unittests

README.md

@@ -13,14 +13,28 @@
 
 # Table of Contents
 
-- [Synopsis](#synopsis)
-- [Citation](#citation)
-- [Installation](#installation)
-- [Configuring the decontamination database index](#configuring-the-decontamination-database-index)
-- [Performance](#performance)
-- [Usage](#usage)
-
-# Synopsis
+- [TBpore](#tbpore)
+- [Table of Contents](#table-of-contents)
+  - [Synopsis](#synopsis)
+  - [Citation](#citation)
+  - [Installation](#installation)
+    - [conda](#conda)
+    - [pip](#pip)
+      - [Dependencies](#dependencies)
+    - [Container](#container)
+      - [`singularity`](#singularity)
+      - [`docker`](#docker)
+  - [Configuring the decontamination database index](#configuring-the-decontamination-database-index)
+  - [Performance](#performance)
+    - [`tbpore process`](#tbpore-process)
+    - [`tbpore cluster`](#tbpore-cluster)
+  - [Usage](#usage)
+    - [General usage](#general-usage)
+    - [process](#process)
+    - [cluster](#cluster)
+    - [download](#download)
+
+## Synopsis
 
 `tbpore` is a tool with two main goals.
 First is to process Nanopore Mycobacterium tuberculosis sequencing data to describe
@@ -75,7 +89,7 @@ installed through PyPI.
 
 #### Dependencies
 
-* [`rasusa`](https://github.com/mbhall88/rasusa)
+* [`rasusa`](https://github.com/mbhall88/rasusa) version 2.x
 * [`psdm`](https://github.com/mbhall88/psdm) version 0.1.x
 * [`samtools`](https://github.com/samtools/samtools) version 1.13
 * [`bcftools`](https://github.com/samtools/bcftools) version 1.13

environment.yaml

@@ -9,7 +9,7 @@ dependencies:
   - ripgrep
   - poetry=1.3
   - mykrobe=0.12
-  - rasusa
+  - "rasusa>=2.0,<3.0"
   - nanoq=0.9
   - samtools=1.13
   - bcftools=1.13

tbpore/tbpore.py

@@ -356,9 +356,9 @@ def process(
         subsampled_reads = f"{tmp}/{name}.subsampled.fastq.gz"
         rasusa = ExternalTool(
             tool="rasusa",
-            input=f"-i {sorted_fastq}",
+            input=f"{sorted_fastq}",
             output=f"-o {subsampled_reads}",
-            params=f'-c {coverage} {config["rasusa"]["params"]}',
+            params=f'reads -c {coverage} {config["rasusa"]["params"]}',
             logdir=logdir,
         )
     else:

tests/test_tbpore_process.py

@@ -1,4 +1,5 @@
 """Integration tests"""
+
 import gzip
 import subprocess
 import sys
@@ -94,7 +95,7 @@ def test_whole_execution___minimum_params___check_all_external_tools_are_called_
             rasusa_cl = self.get_command_line_from_mock(run_core_mock, 6)
             assert (
                 rasusa_cl
-                == f"rasusa -c 150 -g 4411532 -s 88 -o {td}/{TMP_NAME}/in.subsampled.fastq.gz -i {td}/{TMP_NAME}/in.sorted.fastq.gz"
+                == f"rasusa reads -c 150 -g 4411532 -s 88 -o {td}/{TMP_NAME}/in.subsampled.fastq.gz {td}/{TMP_NAME}/in.sorted.fastq.gz"
             )
 
             nanoq_cl = self.get_command_line_from_mock(run_core_mock, 7)
@@ -480,8 +481,8 @@ def test_whole_execution___several_params_affecting_tools_command_lines___check_
             rasusa_cl = self.get_command_line_from_mock(run_core_mock, 6)
             assert (
                 rasusa_cl
-                == f"rasusa -c 150 -g 4411532 -s 88 -o {td}/custom_tmp/custom_name.subsampled.fastq.gz "
-                f"-i {td}/custom_tmp/custom_name.sorted.fastq.gz"
+                == f"rasusa reads -c 150 -g 4411532 -s 88 -o {td}/custom_tmp/custom_name.subsampled.fastq.gz "
+                f"{td}/custom_tmp/custom_name.sorted.fastq.gz"
             )
 
             nanoq_cl = self.get_command_line_from_mock(run_core_mock, 7)