MAG_DEPTHS_PLOT fails if only a single bin is produced

[d-callan]

Description of the bug

If a single mag/bin is produced upstream, then making the depths heatmap fails bc it cant calculate a distance matrix.

Command used and terminal output

cmd:

nextflow run nf-core/mag \
		 -c mag.config \
		 --input mag_samplesheet.csv \
		 --outdir mag_out \
		 -work-dir mag_work \
		 -r 3.0.1 \
		 --skip_gtdbtk \
		 --skip_spades \
		 --skip_spadeshybrid \
		 --skip_concoct \
		 --kraken2_db k2_pluspf_20240112.tar.gz \
		 --genomad_db genomad_db

ex depths file:

bin     3114327 3101140 3106384 3106237 3108596
MEGAHIT-MetaBAT2-3114327.1.fa   7.610989999999999       55.530100000000004      69.84535        12.7621 21.8551

error:

Traceback (most recent call last):
  File "/home/dcallan/.nextflow/assets/nf-core/mag/bin/plot_mag_depths.py", line 83, in <module>
    sys.exit(main())
  File "/home/dcallan/.nextflow/assets/nf-core/mag/bin/plot_mag_depths.py", line 70, in main
    sns.clustermap(
  File "/usr/local/lib/python3.9/site-packages/seaborn/_decorators.py", line 46, in inner_f
    return f(**kwargs)
  File "/usr/local/lib/python3.9/site-packages/seaborn/matrix.py", line 1402, in clustermap
    return plotter.plot(metric=metric, method=method,
  File "/usr/local/lib/python3.9/site-packages/seaborn/matrix.py", line 1220, in plot
    self.plot_dendrograms(row_cluster, col_cluster, metric, method,
  File "/usr/local/lib/python3.9/site-packages/seaborn/matrix.py", line 1065, in plot_dendrograms
    self.dendrogram_row = dendrogram(
  File "/usr/local/lib/python3.9/site-packages/seaborn/_decorators.py", line 46, in inner_f
    return f(**kwargs)
  File "/usr/local/lib/python3.9/site-packages/seaborn/matrix.py", line 784, in dendrogram
    plotter = _DendrogramPlotter(data, linkage=linkage, axis=axis,
  File "/usr/local/lib/python3.9/site-packages/seaborn/matrix.py", line 594, in __init__
    self.linkage = self.calculated_linkage
  File "/usr/local/lib/python3.9/site-packages/seaborn/matrix.py", line 661, in calculated_linkage
    return self._calculate_linkage_scipy()
  File "/usr/local/lib/python3.9/site-packages/seaborn/matrix.py", line 629, in _calculate_linkage_scipy
    linkage = hierarchy.linkage(self.array, method=self.method,
  File "/usr/local/lib/python3.9/site-packages/scipy/cluster/hierarchy.py", line 1068, in linkage
    n = int(distance.num_obs_y(y))
  File "/usr/local/lib/python3.9/site-packages/scipy/spatial/distance.py", line 2572, in num_obs_y
    raise ValueError("The number of observations cannot be determined on "
ValueError: The number of observations cannot be determined on an empty distance matrix.`, size: 2148 (max: 255)

### Relevant files

_No response_

### System information

LSF Cluster using Apptainer

[jfy133]

@d-callan thank you for this!

To further better understand the problem, could you also share the contents of .command.sh , and check what is the contents of the input depth files that don't have any values (given it's only a single sample that gets coverage).?

[d-callan]

the command:

plot_mag_depths.py --bin_depths MEGAHIT-MetaBAT2-3114327-binDepths.tsv                     --groups sample_groups.tsv                     --out "MEGAHIT-MetaBAT2-3114327-binDepths.heatmap.png"

cat <<-END_VERSIONS > versions.yml
"NFCORE_MAG:MAG:DEPTHS:MAG_DEPTHS_PLOT":
    python: $(python --version 2>&1 | sed 's/Python //g')
    pandas: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('pandas').version)")
    seaborn: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('seaborn').version)")
END_VERSIONS

the other depth files actually look better than this one. what i posted above were the contents of the file MEGAHIT-MetaBAT2-3114327-binDepths.tsv from the above command.

if, just to confirm my suspicion that the error is caused by this file having only a single row, i modify my local mag here to only attempt the clustermap if len(df.index) > 1 and run the command manually then all is well.

[jfy133]

Thank you very much @d-callan for both the issue and PR (even better <3)!