feat: automatically set temp dir tempfile (#446)

* Implemented tempdir through tempfile

* Added missing import

* Change rule name

* Trigger retest

bio/biobambam2/bamsormadup/meta.yaml

@@ -1,6 +1,6 @@
 name: BioBamBam2 BamSorMaDup
 description: |
-  Mark PCR and optical duplicates, followed with sorting, with BioBamBam2 tools
+  Mark PCR and optical duplicates, followed with sorting, with BioBamBam2 tools.
 authors:
   - Filipe G. Vieira
 input:
@@ -11,5 +11,5 @@ output:
   - BAM index file (optional)
   - metrics file (optional)
 notes: |
-  * The `extra` param allows for additional program arguments (not `inputformat` or `outputformat`).
+  * The `extra` param allows for additional program arguments (not `inputformat`, `outputformat` or `tmpfile`).
   * For more information see, https://gitlab.com/german.tischler/biobambam2

bio/biobambam2/bamsormadup/test/Snakefile

@@ -1,15 +1,15 @@
-rule mark_duplicates:
+rule mark_duplicates_bamsormadup:
     input:
-        "mapped/{sample}.bam"
+        "mapped/{sample}.bam",
     output:
         bam="dedup/{sample}.bam",
         index="dedup/{sample}.bai",
         metrics="dedup/{sample}.metrics.txt",
     log:
-        "logs/{sample}.log"
+        "logs/{sample}.log",
     params:
-        extra="SO=coordinate"
+        extra="SO=coordinate",
     resources:
-        mem_mb=1024
+        mem_mb=1024,
     wrapper:
         "master/bio/biobambam2/bamsormadup"

bio/biobambam2/bamsormadup/wrapper.py

@@ -4,6 +4,9 @@
 
 
 import os
+import random
+import tempfile
+from pathlib import Path
 from snakemake.shell import shell
 
 
@@ -28,6 +31,18 @@
     metrics = f"M={metrics}"
 
 
-shell(
-    "bamsormadup threads={snakemake.threads} inputformat={in_format} outputformat={out_format} {index} {metrics} {extra} < {snakemake.input[0]} > {snakemake.output[0]} {log}"
-)
+with tempfile.TemporaryDirectory() as tmpdir:
+    # This folder must not exist; it is created by BamSorMaDup
+    tmpdir_bamsormadup = Path(tmpdir) / "bamsormadup_{:06d}".format(
+        random.randrange(10 ** 6)
+    )
+
+    shell(
+        "bamsormadup threads={snakemake.threads}"
+        " inputformat={in_format}"
+        " tmpfile={tmpdir_bamsormadup}"
+        " outputformat={out_format}"
+        " {index} {metrics} {extra}"
+        " < {snakemake.input[0]} > {snakemake.output[0]}"
+        " {log}"
+    )