fix: empty emu combined output (#2899)

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I just noticed a bug for some input in the wrapper I made a few weeks
ago :( It didn't fail, but produced empty files. I have fixed it now and
and modify the test to consider more flexible filenames. I don't know
how to assert in the test whether the output file is not empty. And I'm
not sure that's something we should do in the wrapper, as it is
technically a valid output. So far, I have checked manually it now works
as expected.

### QC
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* [ ] 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),
* the `environment.yaml` pinning has been updated by running
`snakedeploy pin-conda-envs environment.yaml` on a linux machine,
* 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/emu/combine-outputs/test/Snakefile

@@ -2,7 +2,7 @@ rule combine_outputs:
     input:
         expand("{sample}_rel-abundance.tsv", sample=["sample1", "sample2"]),
     output:
-        abundances="combined_abundances.tsv",
+        abundances=ensure("combined_abundances.tsv", non_empty=True),
     log:
         "logs/emu/combined_abundances.log",
     wrapper:
@@ -11,10 +11,10 @@ rule combine_outputs:
 
 rule combine_outputs_split:
     input:
-        expand("{sample}_rel-abundance.txt", sample=["sample1", "sample2"]),
+        expand("{sample}.txt", sample=["sample1", "sample2"]),
     output:
-        abundances="counts.tsv",
-        taxonomy="taxonomy.tsv",
+        abundances = ensure("counts.tsv", non_empty=True),
+        taxonomy = ensure("taxonomy.tsv", non_empty=True),
     log:
         "logs/emu/combined_split.log",
     params:

bio/emu/combine-outputs/test/sample1.txt

@@ -0,0 +1,3 @@
+tax_id	abundance	superkingdom	phylum	class	order	family	genus	species	estimated counts
+1	1.0	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas	amygdali;	2.0
+unassigned	0.0								2.0

bio/emu/combine-outputs/test/sample1_rel-abundance.tsv

@@ -1,3 +1,3 @@
 tax_id	abundance	superkingdom	phylum	class	order	family	genus	species	estimated counts
 1	1.0	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas	amygdali;	2.0
-unassigned	0.0								2.0
+unassigned	0.0								2.0

bio/emu/combine-outputs/test/sample2.txt

@@ -0,0 +1,3 @@
+tax_id	abundance	superkingdom	phylum	class	order	family	genus	species	estimated counts
+1	1.0	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas	amygdali;	2.0
+unassigned	0.0								2.0

bio/emu/combine-outputs/test/sample2_rel-abundance.tsv

@@ -1,3 +1,3 @@
-tax_id	abundance	superkingdom	phylum	class	order	family	genus	species
-1	1.0	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas	amygdali;
-unassigned	0.0							
+tax_id	abundance	superkingdom	phylum	class	order	family	genus	species	estimated counts
+1	1.0	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas	amygdali;	2.0
+unassigned	0.0								2.0

bio/emu/combine-outputs/wrapper.py

@@ -26,10 +26,11 @@
 with tempfile.TemporaryDirectory() as tmpdir:
     for infile in snakemake.input:
         # Files has to end in tsv, and contain rel_abundances
-        temp = os.path.join(tmpdir, os.path.basename(infile))
-        if not temp.endswith("rel_abundances.tsv"):
-            temp = os.path.splitext(infile)[0] + "-rel_abundances.tsv"
-        os.symlink(infile, temp)
+        temp_basename = os.path.basename(infile)
+        if not temp_basename.endswith("_rel-abundance.tsv"):
+            temp_basename = os.path.splitext(infile)[0] + "_rel-abundance.tsv"
+        temp = os.path.join(tmpdir, temp_basename)
+        os.link(infile, temp)
     shell("emu combine-outputs {tmpdir} {rank} {extra} {log}")
     if split and counts:
         shell("mv {tmpdir}/emu-combined-taxonomy-{rank}.tsv {taxonomy}")