fix rename script

.github/workflows/tests.yml

@@ -552,7 +552,7 @@ jobs:
         shell: micromamba-shell {0}
         if: always()
         run: |
-          cp test/bam/sample1.bam test/bam/pineapple.bam && renamebam -d test/bam/pineapple.bam pineapple1
+          cp test/bam/sample1.bam test/bam/pineapple.bam && rename_bam -d test/bam/pineapple.bam pineapple1
           harpy phase --vcf-samples -o phasevcf --vcf test/vcf/test.bcf --snakemake "--show-failed-logs" test/bam
 
   leviathan:

src/harpy/bin/rename_bam.py → src/harpy/bin/rename_bam

@@ -1,15 +1,15 @@
 #! /usr/bin/env python
 """Rename a sam/bam file and modify the @RG tag of the alignment file to reflect the change for both ID and SM."""
-import argparse
-import sys
 import os
+import sys
+import argparse
 
 parser = argparse.ArgumentParser(
     prog='rename_bam.py',
     description='Rename a sam/bam file and modify the @RG tag of the alignment file to reflect the change for both ID and SM. This process creates a new file \'newname.bam\' and you may use -d to delete the original file. Requires samtools.'
     )
 parser.add_argument("input", type=str, metavar = "input.bam", help="input bam or sam file")
-parser.add_argument("name", type=str, metavar = "new_name", help="new file/sample name")
+parser.add_argument("name", type=str, metavar = "new_name", help="new sample name")
 parser.add_argument("-d", "--delete", dest = "delete", action='store_true', help="delete the original file")
 
 if len(sys.argv) == 1:
@@ -21,8 +21,10 @@
 if not os.path.exists(args.input):
     parser.error(f"The file {args.input} does not exist :(")
 
+outdir = os.path.dirname(args.input)
+
 JOB_STATUS = os.system(
-    f"samtools addreplacerg -r \"ID:{args.name}\\tSM:{args.name}\" -o {args.name}.bam {args.input}"
+    f"samtools addreplacerg -r \"ID:{args.name}\\tSM:{args.name}\" -o {outdir}/{args.name}.bam {args.input}"
     )
 
 if JOB_STATUS != 0: