feat: Bustools sort (#513)

* [fix] (template): Missing code in wrappers' doc. Error #187

* bustools sort

* memory and tempdir used

* environment update

* fix typo

* Update bio/bustools/sort/environment.yaml

* Update bio/bustools/sort/test/Snakefile

Co-authored-by: tdayris <tdayris@gustaveroussy.fr>
Co-authored-by: tdayris <thibault.dayris@gustaveroussy.fr>
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>

bio/bustools/sort/environment.yaml

@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - bustools =0.41
+  - snakemake-wrapper-utils =0.4

bio/bustools/sort/meta.yaml

@@ -0,0 +1,17 @@
+name: bustools sort
+description: Sort raw BUS output from pseudoalignment programs
+url: https://github.com/BUStools/bustools#sort
+author:
+  - Thibault Dayris
+input:
+  - Path to bus file, or list of bus files
+output:
+  - Path to bus file
+params:
+  - extra: Optional parameters
+notes: |
+  `--temp` is automatically defined through `resources.tmpdir`
+
+  `--memory` is automatically defined through `resources.mem_mb`
+
+  Multiple bus files in input will result in a single bus file in output.

bio/bustools/sort/test/Snakefile

@@ -0,0 +1,14 @@
+rule test_bustools_sort:
+    input:
+        "file.bus",
+    output:
+        "sorted.bus",
+    threads: 1
+    resources:
+        mem_mb=765,
+    params:
+        extra="--umi",
+    log:
+        "bustools.log",
+    wrapper:
+        "master/bio/bustools/sort"

bio/bustools/sort/wrapper.py

@@ -0,0 +1,34 @@
+#!/usr/bin/env python3
+# coding: utf-8
+
+"""Snakemake wrapper for bustools sort"""
+
+__author__ = "Thibault Dayris"
+__copyright__ = "Copyright 2022, Thibault Dayris"
+__email__ = "thibault.dayris@gustaveroussy.fr"
+__license__ = "MIT"
+
+from snakemake.shell import shell
+from tempfile import TemporaryDirectory
+from snakemake_wrapper_utils.snakemake import get_mem
+
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+extra = snakemake.params.get("extra", "")
+
+bus_files = snakemake.input
+if isinstance(bus_files, list):
+    bus_files = " ".join(bus_files)
+
+mem = get_mem(snakemake, "MiB")
+
+
+with TemporaryDirectory() as tempdir:
+    shell(
+        "bustools sort "
+        "--memory {mem} "
+        "--temp {tempdir} "
+        "--threads {snakemake.threads} "
+        "--output {snakemake.output[0]} "
+        "{bus_files} "
+        "{log}"
+    )

test.py

@@ -273,6 +273,14 @@ def test_bustools_count():
         ["snakemake", "--cores", "1", "--use-conda", "-F", "buscount.mtx"]
     )
 
+@skip_if_not_modified
+def test_bustools_sort():
+    run(
+        "bio/bustools/sort",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "sorted.bus"]
+    )
+
+
 @skip_if_not_modified
 def test_open_cravat_module():
     run(