copy bai files

Snakefile

@@ -122,6 +122,8 @@ def metrics(do_metrics=True):
 rule all:
     input:
         combined=out_path("multisample/genotyped.vcf.gz"),
+        bais=expand(out_path("{sample}/bams/{sample}.markdup.bam.bai"),
+                    sample=SAMPLES),
         stats=metrics()
 
 
@@ -226,6 +228,7 @@ rule markdup:
         tmp = ancient(out_path("tmp"))
     output:
         bam = out_path("{sample}/bams/{sample}.markdup.bam"),
+        bai = out_path("{sample}/bams/{sample}.markdup.bai"),
         metrics = out_path("{sample}/bams/{sample}.markdup.metrics")
     conda: "envs/picard.yml"
     shell: "picard MarkDuplicates CREATE_INDEX=TRUE TMP_DIR={input.tmp} "
@@ -233,6 +236,14 @@ rule markdup:
            "METRICS_FILE={output.metrics} "
            "MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=500"
 
+rule bai:
+    """Copy bai files as some genome browsers can only .bam.bai files"""
+    input:
+        bai = out_path("{sample}/bams/{sample}.markdup.bai")
+    output:
+        bai = out_path("{sample}/bams/{sample}.markdup.bam.bai")
+    shell: "cp {input.bai} {output.bai}"
+
 rule baserecal:
     """Base recalibrated BAM files"""
     input: