perf: autobump bio/hisat2/align (#1079)

Automatic update of bio/hisat2/align.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>

bio/hisat2/align/environment.yaml

@@ -3,5 +3,5 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - hisat2 =2.1
-  - samtools =1.15
+  - hisat2 =2.2.1
+  - samtools =1.16.1

bio/hisat2/align/meta.yaml

@@ -1,4 +1,6 @@
 name: hisat2 align
+description: Graph-based alignment of next generation sequencing reads to a population of genomes.
+url: http://daehwankimlab.github.io/hisat2
 authors:
   - Wibowo Arindrarto
 description: |

bio/hisat2/align/test/Snakefile

@@ -1,13 +1,13 @@
 rule hisat2_align:
     input:
-      reads=["reads/{sample}_R1.fastq", "reads/{sample}_R2.fastq"]
+        reads=["reads/{sample}_R1.fastq", "reads/{sample}_R2.fastq"],
+        idx="index/",
     output:
-      "mapped/{sample}.bam"
+        "mapped/{sample}.bam",
     log:
-        "logs/hisat2_align_{sample}.log"
+        "logs/hisat2_align_{sample}.log",
     params:
-      extra="",
-      idx="index/",
+        extra="",
     threads: 2
     wrapper:
-      "master/bio/hisat2/align"
+        "master/bio/hisat2/align"

bio/hisat2/align/wrapper.py

@@ -4,6 +4,8 @@
 __license__ = "BSD"
 
 
+import os
+from pathlib import Path
 from snakemake.shell import shell
 
 # Placeholder for optional parameters
@@ -24,11 +26,14 @@
         "Reads parameter must contain at least 1 and at most 2" " input files."
     )
 
+ht2_files = Path(snakemake.input.idx).glob("*.ht2")
+idx_prefix = os.path.commonprefix(list(ht2_files)).rstrip(".")
+
 # Executed shell command
 shell(
     "(hisat2 {extra} "
     "--threads {snakemake.threads} "
-    " -x {snakemake.params.idx} {input_flags} "
+    " -x {idx_prefix} {input_flags} "
     " | samtools view -Sbh -o {snakemake.output[0]} -) "
     " {log}"
 )