fix: proper tempfile handling for STAR and improved documentation (#430)

* Implemented proper handling of temp files and updated version

* Added notes with link

* Added dummy folder since STAR requires tempdir to not exist

bio/star/align/environment.yaml

@@ -2,4 +2,4 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - star ==2.7.8a
+  - star ==2.7.9a

bio/star/align/meta.yaml

@@ -3,3 +3,6 @@ description: Map reads with STAR.
 authors:
   - Johannes Köster
   - Tomás Di Domenico
+notes: |
+  * The `extra` param allows for additional program arguments.
+  * For more information see, https://github.com/alexdobin/STAR

bio/star/align/test/Snakefile

@@ -2,36 +2,37 @@ rule star_pe_multi:
     input:
         # use a list for multiple fastq files for one sample
         # usually technical replicates across lanes/flowcells
-        fq1 = ["reads/{sample}_R1.1.fastq", "reads/{sample}_R1.2.fastq"],
+        fq1=["reads/{sample}_R1.1.fastq", "reads/{sample}_R1.2.fastq"],
         # paired end reads needs to be ordered so each item in the two lists match
-        fq2 = ["reads/{sample}_R2.1.fastq", "reads/{sample}_R2.2.fastq"] #optional
+        fq2=["reads/{sample}_R2.1.fastq", "reads/{sample}_R2.2.fastq"],  #optional
     output:
         # see STAR manual for additional output files
-        "star/pe/{sample}/Aligned.out.sam"
+        "star/pe/{sample}/Aligned.out.sam",
     log:
-        "logs/star/pe/{sample}.log"
+        "logs/star/pe/{sample}.log",
     params:
         # path to STAR reference genome index
         index="index",
         # optional parameters
-        extra=""
+        extra="",
     threads: 8
     wrapper:
         "master/bio/star/align"
 
+
 rule star_se:
     input:
-        fq1 = "reads/{sample}_R1.1.fastq"
+        fq1="reads/{sample}_R1.1.fastq",
     output:
         # see STAR manual for additional output files
-        "star/{sample}/Aligned.out.sam"
+        "star/{sample}/Aligned.out.sam",
     log:
-        "logs/star/{sample}.log"
+        "logs/star/{sample}.log",
     params:
         # path to STAR reference genome index
         index="index",
         # optional parameters
-        extra=""
+        extra="",
     threads: 8
     wrapper:
         "master/bio/star/align"

bio/star/align/wrapper.py

@@ -5,6 +5,7 @@
 
 
 import os
+import tempfile
 from snakemake.shell import shell
 
 extra = snakemake.params.get("extra", "")
@@ -46,14 +47,16 @@
 if outprefix == os.path.dirname(snakemake.output[0]):
     outprefix += "/"
 
-shell(
-    "STAR "
-    "{extra} "
-    "--runThreadN {snakemake.threads} "
-    "--genomeDir {snakemake.params.index} "
-    "--readFilesIn {input_str} "
-    "{readcmd} "
-    "--outFileNamePrefix {outprefix} "
-    "--outStd Log "
-    "{log}"
-)
+with tempfile.TemporaryDirectory() as tmpdir:
+    shell(
+        "STAR "
+        "{extra} "
+        "--runThreadN {snakemake.threads} "
+        "--genomeDir {snakemake.params.index} "
+        "--readFilesIn {input_str} "
+        "{readcmd} "
+        "--outFileNamePrefix {outprefix} "
+        "--outStd Log "
+        "--outTmpDir {tmpdir}/STARtmp "
+        "{log}"
+    )