fix: auto memory calculation

bio/fastqc/environment.yaml

@@ -4,3 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - fastqc =0.12.1
+  - snakemake-wrapper-utils =0.5.3

bio/fastqc/meta.yaml

@@ -1,6 +1,7 @@
 name: fastqc
 description: |
   Generate fastq qc statistics using fastqc.
+url: https://github.com/s-andrews/FastQC
 authors:
   - Julian de Ruiter
 input:

bio/fastqc/test/Snakefile

@@ -4,9 +4,12 @@ rule fastqc:
     output:
         html="qc/fastqc/{sample}.html",
         zip="qc/fastqc/{sample}_fastqc.zip" # the suffix _fastqc.zip is necessary for multiqc to find the file. If not using multiqc, you are free to choose an arbitrary filename
-    params: "--quiet"
+    params:
+        extra = "--quiet"
     log:
         "logs/fastqc/{sample}.log"
     threads: 1
+    resources:
+        mem_mb = 1024
     wrapper:
         "master/bio/fastqc"

bio/fastqc/wrapper.py

@@ -9,10 +9,13 @@
 from os import path
 import re
 from tempfile import TemporaryDirectory
-
 from snakemake.shell import shell
+from snakemake_wrapper_utils.snakemake import get_mem
 
+extra = snakemake.params.get("extra", "")
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+# Define memory per thread (https://github.com/s-andrews/FastQC/blob/master/fastqc#L201-L222)
+mem_mb = int(get_mem(snakemake, "MiB") / snakemake.threads)
 
 
 def basename_without_ext(file_path):
@@ -35,8 +38,12 @@ def basename_without_ext(file_path):
 # use the same fastqc dir, we create a temp dir.
 with TemporaryDirectory() as tempdir:
     shell(
-        "fastqc {snakemake.params} -t {snakemake.threads} "
-        "--outdir {tempdir:q} {snakemake.input[0]:q}"
+        "fastqc"
+        " --threads {snakemake.threads}"
+        " --memory {mem_mb}"
+        " {extra}"
+        " --outdir {tempdir:q}"
+        " {snakemake.input[0]:q}"
         " {log}"
     )