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Allow specifying version of tool in nf-core modules create #1238

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jfy133 opened this issue Jul 28, 2021 · 0 comments · Fixed by #1242
Closed

Allow specifying version of tool in nf-core modules create #1238

jfy133 opened this issue Jul 28, 2021 · 0 comments · Fixed by #1242
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@jfy133
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jfy133 commented Jul 28, 2021

Is your feature request related to a problem? Please describe

There is sort a 'bug' in a bioconda package re: versioning, where older versions of the tool had versions of 0.41, 0.42, and newer versions with 0.5.1 or 0.5.2, (i.e. the older ones were missing the point release .). However nf-core tools picks up the latest version based on the highest number, and therefore doesn't pickup in some cases the latest version.

Describe the solution you'd like

In addition to specifying the conda package, to also specify the version of that package with a CLI parameter or prompt quesiton.

e.g.

Options:
  -d, --dir <directory>
  -a, --author <author>        Module author's GitHub username prefixed with
                               '@'

  -l, --label <process label>  Standard resource label for process
  -m, --meta                   Use Groovy meta map for sample information
  -n, --no-meta                Don't use meta map for sample information
  -f, --force                  Overwrite any files if they already exist
  -c, --conda-name TEXT        Name of the conda package to use
  -p --conda-package-version NUMBER Version of conda package to use   
--help                       Show this message and exit.
? Conda package version: 0.5.2

Describe alternatives you've considered

Modify after creation of the module files, however this is problematic when you have very complicated quay/galaxyproject hashed-named containers.

e.g.
https://github.com/nf-core/modules/blob/c5235a983d454787fa0c3247b02086969217163b/modules/bwa/mem/main.nf#L15-L19

Additional context

Originally derived from trying to crate a MALT module:

$  nf-core modules create -a @jfy133 -n malt -f

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.1



INFO     Press enter to use default values (shown in brackets) or type your own responses. ctrl+click underlined text to open links.                                                                   create.py:83
INFO     Using Bioconda package: 'bioconda::malt=0.41'                                                                                                                                                create.py:145
INFO     Using Docker container: 'quay.io/biocontainers/malt:0.41--1'                                                                                                                                 create.py:169
INFO     Using Singularity container: 'https://depot.galaxyproject.org/singularity/malt:0.41--1'                                                                                                      create.py:170
INFO     Provide an appropriate resource label for the process, taken from the nf-core pipeline template.                                                                                             create.py:199
         For example: process_low, process_medium, process_high, process_long 

Yet latest SHOULD be 0.5.2

https://github.com/bioconda/bioconda-recipes/pulls?q=is%3Apr+malt+is%3Aclosed

@ErikDanielsson ErikDanielsson linked a pull request Aug 18, 2021 that will close this issue
4 tasks
@ewels ewels added this to the 2.3 milestone Dec 9, 2021
@ewels ewels changed the title Allow specifying version of tool in nf-core conda create Allow specifying version of tool in nf-core modules create Dec 9, 2021
@drpatelh drpatelh modified the milestones: 2.4, 2.3 Mar 8, 2022
@ewels ewels closed this as completed Mar 14, 2022
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3 participants