hox fixes

tdayris · Nov 27, 2023 · 1183aa0 · 1183aa0
1 parent 7c58997
commit 1183aa0
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Showing 3 changed files with 6 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,7 +2,9 @@
 
 ## Features:
 
+* Protect bam output
 * Speed-up with wildcards constraints
+* Speed-up Picard with BAI inclusion in input files
 
 ## Fix:
 

diff --git a/workflow/rules/bowtie2_sambamba_meta.smk b/workflow/rules/bowtie2_sambamba_meta.smk
@@ -78,7 +78,7 @@ use rule sambamba_markdup from bowtie2_sambamba with:
     input:
         "tmp/sambamba/view/{species}.{build}.{release}.{datatype}/{sample}.bam",
     output:
-        "results/Mapping/{species}.{build}.{release}.{datatype}/{sample}.bam",
+        protected("results/Mapping/{species}.{build}.{release}.{datatype}/{sample}.bam"),
     log:
         "logs/sambamba/markdup/{species}.{build}.{release}.{datatype}/{sample}.log",
     benchmark:
@@ -93,7 +93,7 @@ use rule sambamba_index from bowtie2_sambamba with:
     input:
         "results/Mapping/{species}.{build}.{release}.{datatype}/{sample}.bam",
     output:
-        "results/Mapping/{species}.{build}.{release}.{datatype}/{sample}.bam.bai",
+        protected("results/Mapping/{species}.{build}.{release}.{datatype}/{sample}.bam.bai"),
     log:
         "logs/sambamba/index/{species}.{build}.{release}.{datatype}/{sample}.log",
     benchmark:

diff --git a/workflow/rules/picard_metrics.smk b/workflow/rules/picard_metrics.smk
@@ -1,6 +1,7 @@
-rule picard_create_multiple_metrics_raw:
+rule picard_create_multiple_metrics:
     input:
         bam="results/Mapping/{species}.{build}.{release}.{datatype}/{sample}.bam",
+        bai="results/Mapping/{species}.{build}.{release}.{datatype}/{sample}.bam.bai",
         ref="reference/{species}.{build}.{release}.{datatype}.fasta",
     output:
         temp(