feat: update samtools.smk and remove design_bed as a default extra (#112

) * feat: update samtools.smk and remove design_bed as a default extra * Update workflow/rules/samtools.smk Co-authored-by: jonca79 <[email protected]> * feat: add schemas for samtools rules * Update rules.schema.yaml --------- Co-authored-by: jonca79 <[email protected]>
hydra-genetics · Dec 5, 2023 · da66130 · da66130
1 parent 7618a3f
commit da66130
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Showing 2 changed files with 44 additions and 7 deletions.
diff --git a/workflow/rules/samtools.smk b/workflow/rules/samtools.smk
@@ -8,13 +8,9 @@ rule samtools_stats:
     input:
         bam="alignment/samtools_merge_bam/{sample}_{type}.bam",
     output:
-        temp("qc/samtools_stats/{sample}_{type}.samtools-stats.txt"),
+        stats=temp("qc/samtools_stats/{sample}_{type}.samtools-stats.txt"),
     params:
-        extra="%s -t %s"
-        % (
-            config.get("samtools_stats", {}).get("extra", ""),
-            config.get("reference", {}).get("design_bed", ""),
-        ),
+        extra=config.get("samtools_stats", {}).get("extra", ""),
     log:
         "qc/samtools_stats/{sample}_{type}.samtools-stats.txt.log",
     benchmark:
@@ -34,7 +30,7 @@ rule samtools_stats:
     message:
         "{rule}: calculate qc using samtools for {input.bam}"
     wrapper:
-        "0.79.0/bio/samtools/stats"
+        "v3.0.0/bio/samtools/stats"
 
 
 rule samtools_idxstats:

diff --git a/workflow/schemas/rules.schema.yaml b/workflow/schemas/rules.schema.yaml
@@ -405,6 +405,47 @@ properties:
             type: string
             description: WGS statistics used by MultiQC
 
+  samtools_idxstats:
+    type: object
+    description: input and output parameters for samtools_idxstats
+    properties:
+      input:
+        type: object
+        description: list of inputs
+        properties:
+          bam:
+            type: string
+            description: Aligned bam file
+          bai:
+            type: string
+            description: Bam index file
+      output:
+        type: object
+        description: list of outputs
+        properties:
+          stats:
+            type: string
+            description: Alignment summary statistics from samtools idxstats
+
+  samtools_stats:
+    type: object
+    description: input and output parameters for samtools_stats
+    properties:
+      input:
+        type: object
+        description: list of inputs
+        properties:
+          bam:
+            type: string
+            description: Aligned bam file
+      output:
+        type: object
+        description: list of outputs
+        properties:
+          stats:
+            type: string
+            description: Alignment summary statistics from samtools stats
+
   verifybamid2:
     type: object
     description: input and output parameters for verifybamid2