feat: also define overhang on params.extra (#1173)

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### Description

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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/star/index/meta.yaml

@@ -1,5 +1,6 @@
 name: "STAR Index"
 description: Index fasta sequences with STAR
+url: https://github.com/alexdobin/STAR
 authors:
   - Thibault Dayris
   - Tomás Di Domenico
@@ -8,3 +9,6 @@ input:
   - A (multi)fasta formatted file
 output:
   - A directory containing the indexed sequence for downstream STAR mapping
+params:
+  - sjdbOverhang: length of the donor/acceptor sequence on each side of the junctions (optional)
+  - extra: additional program arguments.

bio/star/index/wrapper.py

@@ -10,18 +10,16 @@
 from snakemake.utils import makedirs
 
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
-
 extra = snakemake.params.get("extra", "")
-sjdb_overhang = snakemake.params.get("sjdbOverhang", "100")
 
-gtf = snakemake.input.get("gtf")
-if gtf is not None:
-    gtf = f"--sjdbGTFfile {gtf}"
+sjdb_overhang = snakemake.params.get("sjdbOverhang", "")
+if sjdb_overhang:
     sjdb_overhang = f"--sjdbOverhang {sjdb_overhang}"
-else:
-    gtf = sjdb_overhang = ""
 
-makedirs(snakemake.output)
+gtf = snakemake.input.get("gtf", "")
+if gtf:
+    gtf = f"--sjdbGTFfile {gtf}"
+
 
 with tempfile.TemporaryDirectory() as tmpdir:
     shell(

meta/bio/star_arriba/test/Snakefile

@@ -1,12 +1,13 @@
 rule star_index:
     input:
         fasta="resources/genome.fasta",
-        annotation="resources/genome.gtf",
+        gtf="resources/genome.gtf",
     output:
         directory("resources/star_genome"),
     threads: 4
     params:
-        extra=lambda wc, input: f"--sjdbGTFfile {input.annotation} --sjdbOverhang 100",
+        sjdbOverhang=100,
+        extra="--genomeSAindexNbases 2",
     log:
         "logs/star_index_genome.log",
     cache: True  # mark as eligible for between workflow caching
@@ -41,7 +42,7 @@ rule star_align:
 
 rule arriba:
     input:
-        bam="star/{sample}/Aligned.out.bam",
+        bam=rules.star_align.output.aln,
         genome="resources/genome.fasta",
         annotation="resources/genome.gtf",
         # optional: # A custom tsv containing identified artifacts, such as read-through fusions of neighbouring genes.
@@ -54,7 +55,7 @@ rule arriba:
     params:
         # required if blacklist or known_fusions is set
         genome_build="GRCh38",
-        default_blacklist=True,
+        default_blacklist=False,
         default_known_fusions=True,
         extra="",
     log: