fix: allow for arbitrary filename prefixes in the optitype wrapper (#500

)

### Description

This is a first attempt, will update with a tmp-folder based solution in
a bit.

### QC

For all wrappers added by this PR, I made sure that

* [ ] 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).

---------

Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>

bio/optitype/test/Snakefile

@@ -3,7 +3,8 @@ rule optitype:
         # list of input reads
         reads=["reads/{sample}_1.fished.fastq", "reads/{sample}_2.fished.fastq"]
     output:
-        multiext("optitype/{sample}", "_coverage_plot.pdf", "_result.tsv")
+        pdf="optitype/{sample}_coverage_plot.pdf",
+        tsv="optitype/{sample}_result.tsv",
     log:
         "logs/optitype/{sample}.log"
     params:

bio/optitype/wrapper.py

@@ -1,15 +1,15 @@
-__author__ = "Jan Forster"
+__author__ = "Jan Forster, David Lähnemann"
 __copyright__ = "Copyright 2020, Jan Forster"
 __email__ = "j.forster@dkfz.de"
 __license__ = "MIT"
 
 
 import os
+from tempfile import TemporaryDirectory
 from snakemake.shell import shell
 
 extra = snakemake.params.get("extra", "")
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
-outdir = os.path.dirname(snakemake.output[0])
 
 # get sequencing type
 seq_type = snakemake.params.get("sequencing_type", "dna")
@@ -20,13 +20,16 @@
 if any(config):
     config = "--config {}".format(config)
 
-shell(
-    "(OptiTypePipeline.py"
-    " --input {snakemake.input.reads}"
-    " --outdir {outdir}"
-    " --prefix {snakemake.wildcards.sample}"
-    " {seq_type}"
-    " {config}"
-    " {extra})"
-    " {log}"
-)
+with TemporaryDirectory() as tempdir:
+    shell(
+        "(OptiTypePipeline.py"
+        "  --input {snakemake.input.reads}"
+        "  --outdir {tempdir}"
+        "  --prefix tmp_prefix"
+        "  {seq_type}"
+        "  {config}"
+        "  {extra}; "
+        " mv {tempdir}/tmp_prefix_coverage_plot.pdf {snakemake.output.pdf:q} ;"
+        " mv {tempdir}/tmp_prefix_result.tsv {snakemake.output.tsv:q} )"
+        " {log}"
+    )