fix: Add index checks for BAM and reference inputs (#4693)

Author: fxwiegand

bio/alignoth/meta.yaml

@@ -6,9 +6,11 @@ description: |
 url: https://github.com/alignoth/alignoth
 input:
   - bam: Path to indexed BAM file
+  - bam_idx: Path to BAM index file
   - reference: Path to indexed reference FASTA file
+  - reference_idx: Path to index of reference FASTA file
   - vcf: Path to indexed VCF file (Optional)
-  - idx: Path to index of VCF file (required when VCF is used)
+  - vcf_idx: Path to index of VCF file (required when VCF is used)
   - bed: Path to BED file (Optional)
 output: "HTML, JSON or directory path"
 authors:

bio/alignoth/test/Snakefile

@@ -1,9 +1,11 @@
 rule alignoth_json:
     input:
         bam="NA12878.bam",
+        bam_idx="NA12878.bam.bai",
         reference="ref.fa",
+        reference_idx="ref.fa.fai",
         vcf="1257A.vcf.gz",
-        idx="1257A.vcf.gz.csi"
+        vcf_idx="1257A.vcf.gz.csi"
     output:
         "out/json_plot.vl.json"
     params:
@@ -16,9 +18,11 @@ rule alignoth_json:
 rule alignoth_html:
     input:
         bam="NA12878.bam",
+        bam_idx="NA12878.bam.bai",
         reference="ref.fa",
+        reference_idx="ref.fa.fai",
         vcf="1257A.vcf.gz",
-        idx="1257A.vcf.gz.csi"
+        vcf_idx="1257A.vcf.gz.csi"
     output:
         "out/plot.html"
     params:
@@ -31,9 +35,11 @@ rule alignoth_html:
 rule alignoth_output_dir:
     input:
         bam="NA12878.bam",
+        bam_idx="NA12878.bam.bai",
         reference="ref.fa",
+        reference_idx="ref.fa.fai",
         vcf="1257A.vcf.gz",
-        idx="1257A.vcf.gz.csi"
+        vcf_idx="1257A.vcf.gz.csi"
     output:
         directory("output-dir/")
     params:

bio/alignoth/wrapper.py

@@ -13,19 +13,25 @@
 
 # BAM input
 if snakemake.input.get("bam", ""):
-    cmd.append(f"-b {snakemake.input.bam}")
+    if snakemake.input.get("bam_idx", ""):
+        cmd.append(f"-b {snakemake.input.bam}")
+    else:
+        raise ValueError("BAM input given without bai index")
 else:
     raise ValueError("BAM input required")
 
 # Reference
 if snakemake.input.get("reference", ""):
-    cmd.append(f"-r {snakemake.input.reference}")
+    if snakemake.input.get("reference_idx", ""):
+        cmd.append(f"-r {snakemake.input.reference}")
+    else:
+        raise ValueError("Reference input given without fai index")
 else:
     raise ValueError("Reference input required")
 
 # Optional VCF with required csi/tbi index
 if snakemake.input.get("vcf", ""):
-    if snakemake.input.get("idx", ""):
+    if snakemake.input.get("vcf_idx", ""):
         cmd.append(f"-v {snakemake.input.vcf}")
     else:
         raise ValueError("VCF input given without csi/tbi index")