Support matrix.mtx.gz cellbender remove-background input

[alecw]

cellbender remove-background can use as input the file triplet matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz. This change enables this input format via:

• passing the 3 files in the h5ad input parameter;
• and setting task.ext.input = '.', which tells remove-background to look for the 3 files in the working directory.

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[alecw]

I am not able to run tests with nf-core modules test cellbender/removebackground --profile docker. I get an error that appears to be unrelated to this module.

I have submitted a PR in nf-core/test-datasets for 10X-style matrix market files. Rather than waiting for that PR to be merged, I was able to get nf-test test modules/nf-core/cellbender/removebackground/tests/main.nf.test --profile docker to pass by setting modules_testdata_base_path = 'https://raw.githubusercontent.com/alecw/nf-core_test-datasets/alecw_10x_mtx/data/'

I don't have easy access to a GPU so I haven't tested that flavor, but I believe I have demonstrated that 1) my change doesn't break the existing functionality; and 2) setting ext.input='.' works to read 10X-MatrixMarket.

[famosab]

Please join the nf-core organization on GitHub to enable the CI-tests to run on your PR. You can request to join the organization via #github-invitations in the nf-core slack. You can join the nf-core slack via https://nf-co.re/join.

[alecw]

Hi @famosab , thanks, I just joined the organization.