From 3627a9317bedc4f628045ed8c0e68f9b0e6d8258 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?P=C3=A1draic=20Corcoran?=
 <padraicc@users.noreply.github.com>
Date: Mon, 27 Nov 2023 16:06:09 +0100
Subject: [PATCH 1/4] feat: update samtools.smk and remove design_bed as a
 default extra

---
 workflow/rules/samtools.smk | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/workflow/rules/samtools.smk b/workflow/rules/samtools.smk
index b3d6266..c260d9d 100644
--- a/workflow/rules/samtools.smk
+++ b/workflow/rules/samtools.smk
@@ -10,11 +10,7 @@ rule samtools_stats:
     output:
         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:

From 1e9bee9f91dbe5494013d5835a8ec68d704b04a2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?P=C3=A1draic=20Corcoran?=
 <padraicc@users.noreply.github.com>
Date: Tue, 5 Dec 2023 09:35:13 +0100
Subject: [PATCH 2/4] Update workflow/rules/samtools.smk

Co-authored-by: jonca79 <54137490+jonca79@users.noreply.github.com>
---
 workflow/rules/samtools.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/rules/samtools.smk b/workflow/rules/samtools.smk
index c260d9d..999b732 100644
--- a/workflow/rules/samtools.smk
+++ b/workflow/rules/samtools.smk
@@ -8,7 +8,7 @@ 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=config.get("samtools_stats", {}).get("extra", ""),
     log:

From df5872821a5ae6f51cf261962c0fc035214fd81a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?P=C3=A1draic=20Corcoran?=
 <padraicc@users.noreply.github.com>
Date: Tue, 5 Dec 2023 09:35:39 +0100
Subject: [PATCH 3/4] feat: add schemas for samtools rules

---
 workflow/schemas/rules.schema.yaml | 41 ++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/workflow/schemas/rules.schema.yaml b/workflow/schemas/rules.schema.yaml
index 66e9ae7..a0fef0f 100644
--- 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_stats
+    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

From 1e91fee98bd99b014e8f43139599a5f8815c3ee7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?P=C3=A1draic=20Corcoran?=
 <padraicc@users.noreply.github.com>
Date: Tue, 5 Dec 2023 09:36:15 +0100
Subject: [PATCH 4/4] Update rules.schema.yaml

---
 workflow/schemas/rules.schema.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/schemas/rules.schema.yaml b/workflow/schemas/rules.schema.yaml
index a0fef0f..6e92c59 100644
--- a/workflow/schemas/rules.schema.yaml
+++ b/workflow/schemas/rules.schema.yaml
@@ -407,7 +407,7 @@ properties:
 
   samtools_idxstats:
     type: object
-    description: input and output parameters for samtools_stats
+    description: input and output parameters for samtools_idxstats
     properties:
       input:
         type: object