Remove unused argument

README.md

@@ -266,4 +266,5 @@ conda env create -y -f environment.yml
 conda activate hostile
 pip install --editable '.[dev]'
 pytest
+pre-commit install
 ```

src/hostile/aligner.py

@@ -102,7 +102,6 @@ def gen_clean_cmd(
         aligner_args: str,
         threads: int,
         force: bool,
-        offline: bool,
     ) -> str:
         fastq, out_dir = Path(fastq), Path(out_dir)
         out_dir.mkdir(exist_ok=True, parents=True)
@@ -163,7 +162,6 @@ def gen_paired_clean_cmd(
         aligner_args: str,
         threads: int,
         force: bool,
-        offline: bool,
     ) -> str:
         fastq1, fastq2, out_dir = Path(fastq1), Path(fastq2), Path(out_dir)
         out_dir.mkdir(exist_ok=True, parents=True)

src/hostile/lib.py

@@ -173,7 +173,6 @@ def clean_fastqs(
             aligner_args=aligner_args,
             threads=threads,
             force=force,
-            offline=offline,
         )
         for fastq in fastqs
     ]
@@ -225,8 +224,8 @@ def clean_paired_fastqs(
     index_path = aligner.value.check_index(index, offline=offline)
     backend_cmds = [
         aligner.value.gen_paired_clean_cmd(
-            fastq1=pair[0],
-            fastq2=pair[1],
+            fastq1=fastq_pair[0],
+            fastq2=fastq_pair[1],
             out_dir=out_dir,
             index_path=index_path,
             invert=invert,
@@ -235,9 +234,8 @@ def clean_paired_fastqs(
             aligner_args=aligner_args,
             threads=threads,
             force=force,
-            offline=offline,
         )
-        for pair in fastqs
+        for fastq_pair in fastqs
     ]
     logging.debug(f"{backend_cmds=}")
     logging.info("Cleaning…")