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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.
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
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 with0.5.1
or0.5.2
, (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.
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:
Yet latest SHOULD be
0.5.2
https://github.com/bioconda/bioconda-recipes/pulls?q=is%3Apr+malt+is%3Aclosed
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