search

nf-core / quantms

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
https://nf-co.re/quantms
MIT License
31 stars 0 forks source link

The run-command needs to be updated in documentation #68

Closed charmoniumQ closed 1 year ago

charmoniumQ commented 1 year ago

Description of the bug

The commands in the documentation on nf-co.re and in this repository are wrong.

On the banner on the right-hand side of https://nf-co.re/quantms, it says this pipeline can be run with:

$ nextflow run nf-core/quantms -r 1.0 -profile test --outdir ../outdir
N E X T F L O W  ~  version 22.10.4
Unknown configuration profile: 'test'

Did you mean one of these?
    oist

In the README.md in this repository, it says it can be run with:

$ nextflow run nf-core/quantms -profile test,singularity --input project.sdrf.tsv --database protein.fasta --outdir ../outdir
N E X T F L O W  ~  version 22.10.4
Project `nf-core/quantms` is currently stickied on revision: 1.0 -- you need to explicitly specify a revision with the option `-r` in order to use it

Passing the -r makes it fail like the previous one.

Perhaps going forward the config should assign one of the test_* as test, which is what other workflows with multiple tests do.

jpfeuffer commented 1 year ago

Thanks. Fixed in -r dev long ago.