Fix kallistobus didn't run with multiple samples

[grst]

Du to a lacking collect() on the index, kallisto only ran on a single sample even when multiple ones were specified in the samplesheet.

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
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• Make sure your code lints (nf-core lint .).
• Ensure the test suite passes (nextflow run . -profile test,docker).
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• Output Documentation in docs/output.md is updated.
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[grst]

nf-core linting failure is not my fault (I think) and needs to be addressed separately in #76

[apeltzer]

Thank you Gregor!

[susheelbhanu]

Hi,

I'm running the -r dev version of scrnaseq with multiple samples and it does not yet run kallisto or bustools. Has this been pushed to the dev branch?

Here's what my processes looks like:

WARN: Access to undefined parameter `fasta` -- Initialise it to a default value eg. `params.fasta = some_value`
[-        ] process > NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:INPUT_CHECK:SAMPLESHEET_CHECK [  0%] 0 of 1
executor >  local (3)
executor >  local (3)
executor >  local (4)
executor >  local (4)
executor >  local (4)
executor >  local (5)
[41/8f3c1c] process > NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1 ✔
[3f/de24d4] process > NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:GUNZIP (10x_V3_barcode_whitelist.txt.gz)        [100%] 1 of 1 ✔
[a3/d61340] process > NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:GFFREAD_TRANSCRIPTOME (GRCh38.p13.fa)           [100%] 1 of 1 ✔
[c4/7976b9] process > NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:SALMON_INDEX (GRCh38.p13.fa.transcriptome.fa)   [  0%] 0 of 1
[b7/3e8fb7] process > NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:GFFREAD_TXP2GENE (GRCh38.p13.annotation.gtf)    [100%] 1 of 1 ✔
[-        ] process > NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:SALMON_ALEVIN                                   -
[-        ] process > NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:ALEVINQC                                        -
[-        ] process > NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:GET_SOFTWARE_VERSIONS                           -
[-        ] process > NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:MULTIQC                                         -

Thank you,
Susheel

[susheelbhanu]

Please ignore the above. Just saw that i needed to add the --aligner kallisto flag. 🤦🏽

Thank you!