minor issue: container used in modules/local/kofamscan/download.nf does not include gnu wget so recording the version fails

[wresch]

Description of the bug

the download module for kofamscan uses the following in its script to record the version of wget:

wget --version | grep 'GNU Wget' | sed 's/GNU Wget ([0-9.]+) .*/\1/'

see
https://github.com/nf-core/metatdenovo/blob/39b9a9fc171ec99e0fad4ea0f60866395a4cc869/modules/local/kofamscan/download.nf#L28C5-L31C17

However the container https://depot.galaxyproject.org/singularity/curl:7.80.0 is based on busybox, not gnu wget so

$ singularity shell depot.galaxyproject.org-singularity-curl-7.80.0.img
(singularity)$ wget --version | grep 'GNU Wget' | sed 's/GNU Wget \([0-9.]\+\) .*/\1/'
wget: unrecognized option '--version'
BusyBox v1.32.1 (2021-04-13 11:15:36 UTC) multi-call binary.

Usage: wget [-c|--continue] [--spider] [-q|--quiet] [-O|--output-document FILE]
        [-o|--output-file FILE] [--header 'header: value'] [-Y|--proxy on/off]
        [--no-check-certificate]
        [-P DIR] [-S|--server-response] [-U|--user-agent AGENT] [-T SEC] URL...

Retrieve files via HTTP or FTP

        --spider        Only check URL existence: $? is 0 if exists
        --no-check-certificate  Don't validate the server's certificate
        -c              Continue retrieval of aborted transfer
        -q              Quiet
        -P DIR          Save to DIR (default .)
        -S              Show server response
        -T SEC          Network read timeout is SEC seconds
        -O FILE         Save to FILE ('-' for stdout)
        -o FILE         Log messages to FILE
        -U STR          Use STR for User-Agent header
        -Y on/off       Use proxy

Command used and terminal output

No response

Relevant files

No response

System information

No response

[erikrikarddaniel]

Thanks for reporting. I think we should base this on a different container.

[erikrikarddaniel]

Closing this as it should be fixed now.

[wresch]

Thanks

…

On Fri, Jan 26, 2024 at 6:03 AM Daniel Lundin ***@***.***> wrote: Closed #249 <#249> as completed. — Reply to this email directly, view it on GitHub <#249 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACCS6DMHLMFI36BKWBDXGLYQOEO7AVCNFSM6AAAAABCKXVJBCVHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJRGYYDONZSG42TAMA> . You are receiving this because you authored the thread.Message ID: ***@***.***>