fix: bug when renaming samples (#2293)

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### Description

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Fix issue #2292 and added new tests.

### 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/bcftools/reheader/meta.yaml

@@ -4,6 +4,12 @@ url: http://www.htslib.org/doc/bcftools.html#reheader
 authors:
   - Jan Forster
   - Filipe G. Vieira
-notes: |
-  * The `uncompressed_bcf` param allows to specify that a BCF output should be uncompressed (ignored otherwise).
-  * The `extra` param allows for additional program arguments (not `--threads`, `-o/--output`, `-O/--output-type`, or `-T/--temp-prefix`).
+input:
+  - VCF/BCF file
+  - header: new header (optional if "samples" is set)
+  - samples: new sample names (optional if "header" is set)
+output:
+  - VCF/BCF file with new header
+params:
+  - uncompressed_bcf: specify that a BCF output should be uncompressed (ignored otherwise).
+  - extra:  additional program arguments (not `--threads`, `-o/--output`, `-O/--output-type`, or `-T/--temp-prefix`)

bio/bcftools/reheader/test/Snakefile

@@ -8,11 +8,22 @@ rule bcftools_reheader:
     output:
         "a.reheader.bcf",
     log:
-        "reheader.log",
+        "a.reheader.log",
     params:
         uncompressed_bcf=False,
         extra="",  # optional parameters for bcftools reheader
         view_extra="",  # optional parameters for bcftools view
     threads: 2
     wrapper:
-        "master/bio/bcftools/reheader"
+        "master//bio/bcftools/reheader"
+
+
+use rule bcftools_reheader as bcftools_reheader_map with:
+    input:
+        vcf="a.bcf",
+        header="header.txt",
+        samples="samples_map.tsv",
+    output:
+        "a.reheader_map.bcf",
+    log:
+        "a.reheader_map.log",

bio/bcftools/reheader/test/samples_map.tsv

@@ -0,0 +1 @@
+A LIB_A

bio/bcftools/reheader/wrapper.py

@@ -10,7 +10,9 @@
 from snakemake_wrapper_utils.bcftools import get_bcftools_opts
 
 
-bcftools_opts = get_bcftools_opts(snakemake, parse_ref=False, parse_memory=False)
+bcftools_opts = get_bcftools_opts(
+    snakemake, parse_ref=False, parse_samples=False, parse_memory=False
+)
 extra = snakemake.params.get("extra", "")
 view_extra = snakemake.params.get("view_extra", "")
 log = snakemake.log_fmt_shell(stdout=False, stderr=True)
@@ -19,11 +21,11 @@
 ## Extract arguments
 header = snakemake.input.get("header", "")
 if header:
-    header = f"-h {header}"
+    header = f"--header {header}"
 
 samples = snakemake.input.get("samples", "")
 if samples:
-    samples = f"-s {samples}"
+    samples = f"--samples {samples}"
 
 
 with tempfile.TemporaryDirectory() as tmpdir:

test.py

@@ -1763,6 +1763,10 @@ def test_bcftools_reheader():
         "bio/bcftools/reheader",
         ["snakemake", "--cores", "1", "a.reheader.bcf", "--use-conda", "-F"],
     )
+    run(
+        "bio/bcftools/reheader",
+        ["snakemake", "--cores", "1", "a.reheader_map.bcf", "--use-conda", "-F"],
+    )
 
 
 @skip_if_not_modified