adding samtools faidx command

LiaOb21 · Jan 3, 2024 · e6712ec · e6712ec
1 parent 2487890
commit e6712ec
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/workflow/rules/two_read_bam_combiner.smk b/workflow/rules/two_read_bam_combiner.smk
@@ -17,5 +17,6 @@ rule two_read_bam_combiner:
     shell:
         """
         mkdir -p results/arima_mapping_pipeline/TMP_DIR
+        samtools faidx {input.REF}
         perl scripts/two_read_bam_combiner.pl {input.bam1_filt} {input.bam2_filt} samtools {config[arima][MAPQ_FILTER]} | samtools view -bS -t {input.REF}.fai - | samtools sort -@ {config[arima][CPU]} -o {output.tmp_bam} - >> {log} 2>&1
         """