feat: Added specific param for strandness (#474)

* Added specific param for strandness * Added explanation to params.strand option
snakemake · Apr 25, 2022 · 12b7978 · 12b7978
1 parent 4672e5b
commit 12b7978
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Showing 3 changed files with 21 additions and 11 deletions.
diff --git a/bio/subread/featurecounts/meta.yaml b/bio/subread/featurecounts/meta.yaml
@@ -1,6 +1,7 @@
 name: subread featureCounts
 description: >
   FeatureCounts assign mapped reads or fragments (paired-end data) to genomic features such as genes, exons and promoters.
+url: http://subread.sourceforge.net/
 author:
   - Antonie Vietor
   - Filipe G. Vieira
@@ -14,6 +15,5 @@ output:
   - Summary file including summary statistics (tab separated)
   - Junction counts file including count number of reads supporting each exon-exon junction (tab separated)
 notes: |
+  * The `strand` param allows to specify the strandness of the library (0: unstranded, 1: stranded, and 2: reversely stranded)
   * 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/
diff --git a/bio/subread/featurecounts/test/Snakefile b/bio/subread/featurecounts/test/Snakefile
@@ -1,10 +1,11 @@
 rule feature_counts:
     input:
-        samples="{sample}.bam",  # list of sam or bam files
+        # list of sam or bam files
+        samples="{sample}.bam",
         annotation="annotation.gtf",
         # optional input
-        # chr_names="",           # implicitly sets the -A flag
-        # fasta="genome.fasta"    # implicitly sets the -G flag
+        #chr_names="",           # implicitly sets the -A flag
+        #fasta="genome.fasta"    # implicitly sets the -G flag
     output:
         multiext(
             "results/{sample}",
@@ -14,6 +15,7 @@ rule feature_counts:
         ),
     threads: 2
     params:
+        strand=0,  # optional; strandness of the library (0: unstranded [default], 1: stranded, and 2: reversely stranded)
         r_path="",  # implicitly sets the --Rpath flag
         extra="-O --fracOverlap 0.2 -J",
     log:

diff --git a/bio/subread/featurecounts/wrapper.py b/bio/subread/featurecounts/wrapper.py
@@ -10,22 +10,30 @@
 extra = snakemake.params.get("extra", "")
 
 # optional input files and directories
-fasta = snakemake.input.get("fasta", "")
-chr_names = snakemake.input.get("chr_names", "")
-r_path = snakemake.params.get("r_path", "")
+strand = snakemake.params.get("strand", 0)
 
+fasta = snakemake.input.get("fasta", "")
 if fasta:
-    extra += " -G {}".format(fasta)
+    fasta = f"-G {fasta}"
+
+chr_names = snakemake.input.get("chr_names", "")
 if chr_names:
-    extra += " -A {}".format(chr_names)
+    chr_names = f"-A {chr_names}"
+
+r_path = snakemake.params.get("r_path", "")
 if r_path:
-    extra += " --Rpath {}".format(r_path)
+    r_path = f"--Rpath {r_path}"
+
 
 with tempfile.TemporaryDirectory() as tmpdir:
     shell(
         "featureCounts"
         " -T {snakemake.threads}"
+        " -s {strand}"
         " -a {snakemake.input.annotation}"
+        " {fasta}"
+        " {chr_names}"
+        " {r_path}"
         " {extra}"
         " --tmpDir {tmpdir}"
         " -o {snakemake.output[0]}"