feat: added temp dir to featurecounts (#455)

* Added handling of tempdir

* Added author

* Fixed output file names and added doc

* Reformat

* Added missing argument

bio/subread/featurecounts/meta.yaml

@@ -1,15 +1,19 @@
 name: subread featureCounts
 description: >
   FeatureCounts assign mapped reads or fragments (paired-end data) to genomic features such as genes, exons and promoters.
-  For more information please see `featureCounts tutorial <http://bioinf.wehi.edu.au/featureCounts/>`_, `documentation of subread <https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf>`_ and commandline help.
 author:
   - Antonie Vietor
+  - Filipe G. Vieira
 input:
   - a list of .sam or .bam files
   - GTF, GFF or SAF annotation file
   - optional a tab separating file that determines the sorting order and contains the chromosome names in the first column
   - optional a fasta index file
 output:
-  - .featureCounts file including read counts (tab separated)
-  - .featureCounts.summary file including summary statistics (tab separated)
-  - .featureCounts.jcounts file including count number of reads supporting each exon-exon junction (tab separated)
+  - Feature counts file including read counts (tab separated)
+  - Summary file including summary statistics (tab separated)
+  - Junction counts file including count number of reads supporting each exon-exon junction (tab separated)
+notes: |
+  * The `extra` param allows for additional program arguments.
+  * For more information see, http://subread.sourceforge.net/ and https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf
+  * For a tutorial see, http://bioinf.wehi.edu.au/featureCounts/

bio/subread/featurecounts/test/Snakefile

@@ -1,22 +1,22 @@
 rule feature_counts:
     input:
-        sam="{sample}.bam", # list of sam or bam files
+        samples="{sample}.bam",  # list of sam or bam files
         annotation="annotation.gtf",
         # optional input
         # chr_names="",           # implicitly sets the -A flag
-        # fasta="genome.fasta"      # implicitly sets the -G flag
+        # fasta="genome.fasta"    # implicitly sets the -G flag
     output:
-        multiext("results/{sample}",
-                 ".featureCounts",
-                 ".featureCounts.summary",
-                 ".featureCounts.jcounts")
-    threads:
-        2
+        multiext(
+            "results/{sample}",
+            ".featureCounts",
+            ".featureCounts.summary",
+            ".featureCounts.jcounts",
+        ),
+    threads: 2
     params:
-        tmp_dir="",   # implicitly sets the --tmpDir flag
-        r_path="",    # implicitly sets the --Rpath flag
-        extra="-O --fracOverlap 0.2"
+        r_path="",  # implicitly sets the --Rpath flag
+        extra="-O --fracOverlap 0.2 -J",
     log:
-        "logs/{sample}.log"
+        "logs/{sample}.log",
     wrapper:
         "master/bio/subread/featurecounts"

bio/subread/featurecounts/wrapper.py

@@ -3,6 +3,7 @@
 __email__ = "antonie.v@gmx.de"
 __license__ = "MIT"
 
+import tempfile
 from snakemake.shell import shell
 
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
@@ -11,25 +12,23 @@
 # optional input files and directories
 fasta = snakemake.input.get("fasta", "")
 chr_names = snakemake.input.get("chr_names", "")
-tmp_dir = snakemake.params.get("tmp_dir", "")
 r_path = snakemake.params.get("r_path", "")
 
 if fasta:
     extra += " -G {}".format(fasta)
 if chr_names:
     extra += " -A {}".format(chr_names)
-if tmp_dir:
-    extra += " --tmpDir {}".format(tmp_dir)
 if r_path:
     extra += " --Rpath {}".format(r_path)
 
-shell(
-    "(featureCounts"
-    " {extra}"
-    " -T {snakemake.threads}"
-    " -J"
-    " -a {snakemake.input.annotation}"
-    " -o {snakemake.output[0]}"
-    " {snakemake.input.sam})"
-    " {log}"
-)
+with tempfile.TemporaryDirectory() as tmpdir:
+    shell(
+        "featureCounts"
+        " -T {snakemake.threads}"
+        " -a {snakemake.input.annotation}"
+        " {extra}"
+        " --tmpDir {tmpdir}"
+        " -o {snakemake.output[0]}"
+        " {snakemake.input.samples}"
+        " {log}"
+    )