does this work

snakePipes/shared/rules/whatshap.snakefile

@@ -1,4 +1,4 @@
-rule whatshap_haplotag:
+checkpoint whatshap_haplotag:
         input:
             ref = genome_fasta,
             pvcf = pvcf,
@@ -15,7 +15,7 @@ rule whatshap_haplotag:
             whatshap haplotag --ignore-read-groups -o {output.hbam} --reference {input.ref} --output-threads={threads} --output-haplotag-list={output.hlist} {input.pvcf} {input.bam}
             """
 
-rule whatshap_split:
+checkpoint whatshap_split:
         input:
             hbam = "allelic_bams/{sample}.allele_flagged.sorted.bam",
             hlist = "allelic_bams/{sample}_haplotype_list.tsv"
@@ -30,13 +30,21 @@ rule whatshap_split:
             whatshap split  --output-h1 {output.h1bam} --output-h2 {output.h2bam} --output-untagged {output.unbam} {input.hbam} {input.hlist}
             """
 
-wildcard_constraints:
-    suffix = ['allele_flagged', 'genome1', 'genome2', 'unassigned']
+#wildcard_constraints:
+#    suffix = ['allele_flagged', 'genome1', 'genome2', 'unassigned']
 
 
+def collect_split_bams(wildcards):
+      checkpoint_output_a = checkpoints.whatshap_haplotag.get(**wildcards).output["hbam"]
+      checkpoint_output_b = checkpoints.whatshap_split.get(**wildcards).output
+      checkpoint_output = checkpoint_output_a + checkpoint_output_b
+      return ("allelic_bams/{sample}.{suffix}.sorted.bam",
+                  suffix=glob_wildcards("allelic_bams/{sample}.{suffix}.sorted.bam")).suffix)
+
 rule BAMindex_allelic:
     input:
-        "allelic_bams/{sample}.{suffix}.sorted.bam"
+#        "allelic_bams/{sample}.{suffix}.sorted.bam"
+        collect_split_bams
     output:
         "allelic_bams/{sample}.{suffix}.sorted.bam.bai"
     conda: CONDA_SHARED_ENV