fix: auto memory calculation (#1210)

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### Description
Added better memory calculation

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### QC
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* [x] I confirm that:

For all wrappers added by this PR, 

* there is a test case which covers any introduced changes,
* `input:` and `output:` file paths in the resulting rule can be changed
arbitrarily,
* either the wrapper can only use a single core, or the example rule
contains a `threads: x` statement with `x` being a reasonable default,
* rule names in the test case are in
[snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell
what the rule is about or match the tools purpose or name (e.g.,
`map_reads` for a step that maps reads),
* all `environment.yaml` specifications follow [the respective best
practices](https://stackoverflow.com/a/64594513/2352071),
* wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`),
* all fields of the example rules in the `Snakefile`s and their entries
are explained via comments (`input:`/`output:`/`params:` etc.),
* `stderr` and/or `stdout` are logged correctly (`log:`), depending on
the wrapped tool,
* temporary files are either written to a unique hidden folder in the
working directory, or (better) stored where the Python function
`tempfile.gettempdir()` points to (see
[here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
this also means that using any Python `tempfile` default behavior
works),
* the `meta.yaml` contains a link to the documentation of the respective
tool or command,
* `Snakefile`s pass the linting (`snakemake --lint`),
* `Snakefile`s are formatted with
[snakefmt](https://github.com/snakemake/snakefmt),
* Python wrapper scripts are formatted with
[black](https://black.readthedocs.io).
* Conda environments use a minimal amount of channels, in recommended
ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as
conda-forge should have highest priority and defaults channels are
usually not needed because most packages are in conda-forge nowadays).

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}"
     )