Fix alignstats rule to handle both BAM and CRAM inputs

- Add _alignstats_input() function: returns BAM+BAI for BAM_ALIGNERS, CRAM+CRAI otherwise
- Add _alignstats_format() function: returns bam/cram for alignstats -j flag
- Enables produce_alignstats to work with Roche BAM-only data

Author: iamh2o

workflow/rules/alignstats.smk

@@ -13,10 +13,23 @@ import os
 def fetch_alnr(wildcards):
     return wildcards.alnr
 
+
+def _alignstats_input(wildcards):
+    """Return alignment file + index, choosing BAM for BAM_ALIGNERS else CRAM."""
+    base = MDIR + f"{wildcards.sample}/align/{wildcards.alnr}/{wildcards.ddup}/{wildcards.sample}.{wildcards.alnr}.{wildcards.ddup}"
+    if wildcards.alnr in BAM_ALIGNERS:
+        return {"aln": base + ".bam", "idx": base + ".bam.bai"}
+    return {"aln": base + ".cram", "idx": base + ".cram.crai"}
+
+
+def _alignstats_format(wildcards):
+    """Return 'bam' or 'cram' for the alignstats -j flag."""
+    return "bam" if wildcards.alnr in BAM_ALIGNERS else "cram"
+
+
 rule alignstats:
     input:
-        cram=MDIR + "{sample}/align/{alnr}/{ddup}/{sample}.{alnr}.{ddup}.cram",
-        crai=MDIR + "{sample}/align/{alnr}/{ddup}/{sample}.{alnr}.{ddup}.cram.crai",
+        unpack(_alignstats_input),
     output:
         json=MDIR
         + "{sample}/align/{alnr}/{ddup}/alignqc/alignstats/{sample}.{alnr}.{ddup}.alignstats.json",
@@ -34,6 +47,7 @@ rule alignstats:
         huref=config["supporting_files"]["files"]["huref"]["fasta"]["name"],
         n=config["alignstats"]["num_reads_in_mem"],
         cluster_sample=ret_sample,
+        aln_format=_alignstats_format,
         ld_preload=" "
         if "ld_preload" not in config["malloc_alt"]
         else config["malloc_alt"]["ld_preload"],
@@ -42,7 +56,7 @@ rule alignstats:
     conda:
         config["alignstats"]["env_yaml"]
     shell:
-        "alignstats  -C -U  -i {input.cram} -T {params.huref} -o {output.json}  -j cram -v -P {threads} -p {threads} > {log};"
+        "alignstats  -C -U  -i {input.aln} -T {params.huref} -o {output.json}  -j {params.aln_format} -v -P {threads} -p {threads} > {log};"
 
 
 localrules: