feat: samtools stat bed params (#418)

* Update wrapper.py feat: make it possible to input a bed file as a separate params value. * Update wrapper.py * Update wrapper.py * Update wrapper.py * Create design.bed * Update wrapper.py * Update Snakefile * Update wrapper.py * Update environment.yaml * Update wrapper.py * Update design.bed * Update design.bed
snakemake · May 13, 2022 · 28fa3a8 · 28fa3a8
1 parent 218fd39
commit 28fa3a8
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Showing 4 changed files with 13 additions and 4 deletions.
diff --git a/bio/samtools/stats/environment.yaml b/bio/samtools/stats/environment.yaml
@@ -2,5 +2,5 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - samtools =1.14
-  - snakemake-wrapper-utils =0.3
+  - samtools=1.14
+  - snakemake-wrapper-utils=0.3
diff --git a/bio/samtools/stats/test/Snakefile b/bio/samtools/stats/test/Snakefile
@@ -1,6 +1,7 @@
 rule samtools_stats:
     input:
-        "mapped/{sample}.bam",
+        bam="mapped/{sample}.bam",
+        bed="design.bed",              #Optional input, specify target regions
     output:
         "samtools_stats/{sample}.txt",
     params:

diff --git a/bio/samtools/stats/test/design.bed b/bio/samtools/stats/test/design.bed
@@ -0,0 +1 @@
+xx  5 19
diff --git a/bio/samtools/stats/wrapper.py b/bio/samtools/stats/wrapper.py
@@ -9,14 +9,21 @@
 from snakemake.shell import shell
 from snakemake_wrapper_utils.samtools import get_samtools_opts
 
+
+bed = snakemake.input.get("bed", "")
+if bed:
+    bed = "-t " + bed
+
 samtools_opts = get_samtools_opts(
     snakemake, parse_write_index=False, parse_output=False, parse_output_format=False
 )
+
+
 extra = snakemake.params.get("extra", "")
 region = snakemake.params.get("region", "")
 log = snakemake.log_fmt_shell(stdout=False, stderr=True)
 
 
 shell(
-    "samtools stats {samtools_opts} {extra} {snakemake.input} {region} > {snakemake.output} {log}"
+    "samtools stats {samtools_opts} {extra} {snakemake.input.bam} {bed} {region} > {snakemake.output} {log}"
 )