Editing rules to decrease the chance of accidental overwrite or deletion of existing runs

Author: chenv3

workflow/rules/atac.smk

@@ -61,15 +61,21 @@ rule count:
         if [ -d '{params.id}' ]; then
             if ! [ -f '{output.html}' ]; then
               rm -rf '{params.id}/'
+              cellranger-atac count \\
+                  --id {params.id} \\
+                  --sample {params.sample} \\
+                  --reference {params.reference} \\
+                  --fastqs {params.fastqs} \\
+              2>{log.err} 1>{log.log}
             fi
+        else
+            cellranger-atac count \\
+                --id {params.id} \\
+                --sample {params.sample} \\
+                --reference {params.reference} \\
+                --fastqs {params.fastqs} \\
+            2>{log.err} 1>{log.log}
         fi
-
-        cellranger-atac count \\
-            --id {params.id} \\
-            --sample {params.sample} \\
-            --reference {params.reference} \\
-            --fastqs {params.fastqs} \\
-        2>{log.err} 1>{log.log}
         """
 
 rule summaryFiles:

workflow/rules/cite.smk

@@ -83,7 +83,7 @@ rule count:
         lib = join(workpath, "{sample}_libraries.csv"),
         features = features
     output:
-        join(workpath, "{sample}", "outs", "web_summary.html")
+        html = join(workpath, "{sample}", "outs", "web_summary.html")
     log:
         err = "run_{sample}_10x_cellranger_count.err",
         log ="run_{sample}_10x_cellranger_count.log"
@@ -101,17 +101,27 @@ rule count:
         # Remove output directory
         # prior to running cellranger
         if [ -d '{params.prefix}' ]; then
-            rm -rf '{params.prefix}/'
+            if ! [ -f '{output.html}' ]; then
+                rm -rf '{params.prefix}/'
+                cellranger count \\
+                    --id={params.prefix} \\
+                    --transcriptome={params.transcriptome} \\
+                    --libraries={input.lib} \\
+                    --feature-ref={input.features} \\
+                    {params.introns} \\
+                    {params.createbam} \\
+                2>{log.err} 1>{log.log}
+            fi
+        else
+            cellranger count \\
+                --id={params.prefix} \\
+                --transcriptome={params.transcriptome} \\
+                --libraries={input.lib} \\
+                --feature-ref={input.features} \\
+                {params.introns} \\
+                {params.createbam} \\
+            2>{log.err} 1>{log.log}
         fi
-
-        cellranger count \\
-            --id={params.prefix} \\
-            --transcriptome={params.transcriptome} \\
-            --libraries={input.lib} \\
-            --feature-ref={input.features} \\
-            {params.introns} \\
-            {params.createbam} \\
-        2>{log.err} 1>{log.log}
         """
 
 

workflow/rules/multi.smk

@@ -123,13 +123,19 @@ rule multi:
         # Remove output directory
         # prior to running cellranger
         if [ -d '{params.prefix}' ]; then
-            rm -rf '{params.prefix}/'
+            if ! [ -f '{output}' ]; then
+                rm -rf '{params.prefix}/'
+                cellranger multi \\
+                    --id={params.prefix} \\
+                    --csv={input} \\
+                2>{log.err} 1>{log.log}
+            fi
+        else
+            cellranger multi \\
+                --id={params.prefix} \\
+                --csv={input} \\
+            2>{log.err} 1>{log.log}
         fi
-
-        cellranger multi \\
-            --id={params.prefix} \\
-            --csv={input} \\
-        2>{log.err} 1>{log.log}
         """
 
 rule summaryFiles:

workflow/rules/multiome.smk

@@ -80,7 +80,7 @@ rule count:
     input:
         lib = join(workpath, "{sample}_libraries.csv")
     output:
-        join(workpath, "{sample}", "outs", "web_summary.html")
+        html = join(workpath, "{sample}", "outs", "web_summary.html")
     log:
         err = "run_{sample}_10x_cellranger_count.err",
         log = "run_{sample}_10x_cellranger_count.log"
@@ -95,15 +95,23 @@ rule count:
         # Remove output directory
         # prior to running cellranger
         if [ -d '{params.prefix}' ]; then
-            rm -rf '{params.prefix}/'
+            if ! [ -f '{output.html}' ]; then
+                rm -rf '{params.prefix}/'
+                cellranger-arc count \\
+                    --id={params.prefix} \\
+                    --reference={params.reference} \\
+                    --libraries={input.lib} \\
+                    {params.introns} \\
+                2>{log.err} 1>{log.log}
+            fi
+        else
+            cellranger-arc count \\
+                --id={params.prefix} \\
+                --reference={params.reference} \\
+                --libraries={input.lib} \\
+                {params.introns} \\
+            2>{log.err} 1>{log.log}
         fi
-
-        cellranger-arc count \\
-            --id={params.prefix} \\
-            --reference={params.reference} \\
-            --libraries={input.lib} \\
-            {params.introns} \\
-        2>{log.err} 1>{log.log}
         """
 
 rule summaryFiles:

workflow/rules/vdj.smk

@@ -62,15 +62,21 @@ rule count:
         if [ -d '{params.id}' ]; then
             if ! [ -f '{output.html}' ]; then
                 rm -rf '{params.id}/'
+                cellranger vdj \\
+                    --id {params.id} \\
+                    --sample {params.sample} \\
+                    --reference {params.reference} \\
+                    --fastqs {params.fastqs} \\
+                2>{log.err} 1>{log.log}
             fi
+        else
+            cellranger vdj \\
+                --id {params.id} \\
+                --sample {params.sample} \\
+                --reference {params.reference} \\
+                --fastqs {params.fastqs} \\
+            2>{log.err} 1>{log.log}
         fi
-
-        cellranger vdj \\
-            --id {params.id} \\
-            --sample {params.sample} \\
-            --reference {params.reference} \\
-            --fastqs {params.fastqs} \\
-        2>{log.err} 1>{log.log}
         """
 
 rule summaryFiles: