feat: parse mem for samtools sort (#442)

* Fixed tmp prefix

* Parsing memory

* Removed redundant random number on prefix

* Code clean up

* Added missing import

* Fixed bug with int and str

* Tweaked mem format

* FIxed typo

bio/samtools/fastq/separate/environment.yaml

@@ -3,3 +3,4 @@ channels:
   - bioconda
 dependencies:
   - samtools =1.14
+  - snakemake-wrapper-utils =0.3

bio/samtools/fastq/separate/wrapper.py

@@ -6,35 +6,41 @@
 
 import os
 import tempfile
+from pathlib import Path
 from snakemake.shell import shell
+from snakemake_wrapper_utils.snakemake import get_mem
 
 params_sort = snakemake.params.get("sort", "")
 params_fastq = snakemake.params.get("fastq", "")
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
-prefix = os.path.splitext(snakemake.output[0])[0]
-
 # Samtools takes additional threads through its option -@
 # One thread is used bu Samtools sort
 # One thread is used by Samtools fastq
 # So snakemake.threads has to take them into account
 # before allowing additional threads through samtools sort -@
-threads = "" if snakemake.threads <= 2 else " -@ {} ".format(snakemake.threads - 2)
+threads = 0 if snakemake.threads <= 2 else snakemake.threads - 2
+
+mem = get_mem(snakemake, "MiB")
+mem = "-m {0:.0f}M".format(mem / threads) if mem and threads else ""
+
+with tempfile.TemporaryDirectory() as tmpdir:
+    tmp_prefix = Path(tmpdir) / "samtools_fastq.sort_"
 
-with tempfile.NamedTemporaryFile() as tmpfile:
     shell(
-        "(samtools sort -n "
-        " {threads} "
-        " -T {tmpfile.name} "
-        " {params_sort} "
+        "(samtools sort -n"
+        " --threads {threads}"
+        " {mem}"
+        " -T {tmp_prefix}"
+        " {params_sort}"
         " {snakemake.input[0]} | "
-        "samtools fastq "
-        " {params_fastq} "
-        " -1 {snakemake.output[0]} "
-        " -2 {snakemake.output[1]} "
-        " -0 /dev/null "
-        " -s /dev/null "
-        " -F 0x900 "
+        "samtools fastq"
+        " {params_fastq}"
+        " -1 {snakemake.output[0]}"
+        " -2 {snakemake.output[1]}"
+        " -0 /dev/null"
+        " -s /dev/null"
+        " -F 0x900"
         " - "
         ") {log}"
     )