File path built with wildcards do not recognize "sample1.fastq.gz" as a single file if

Got some kind suggestions from <a href="https://unix.stackexchange.com/questions/59655

It works for my case, thanks! <a

Fixed with <a href="https://github.com/zhxiaokang/RASflow/commit/e7d6a8f1da4a1aa7af388

Wildcards for fastq files about rasflow HOT 4 CLOSED

JFK24 commented on September 14, 2024

Wildcards for fastq files

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Comments (4)

zhxiaokang commented on September 14, 2024

Well spotted! It's a good point that I didn't think of. Thank you!

But your solution misses this type of file naming: {wildcards.sample}.something_else.f*q.gz. And this is the reason I put a * after {wildcards.sample}. But now I see the issue caused by the *.

I don't have a better solution so far. I've posted the question on StackExchange

Let's see whether we can get a better solution.

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zhxiaokang commented on September 14, 2024

Got some kind suggestions from StackExchange. I found shopt -s extglob very simple and useful. Could you try it out to see if it works for you?

rule getReads:
    output:
        read = temp(intermediate_path + "/reads/{sample}.fastq.gz")
    params:
        key = key,
        input_path = input_path
    shell:
        """
        shopt -s extglob
        scp -i {params.key} {params.input_path}/{wildcards.sample}?(.*).f*q.gz {output.read}
        """

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JFK24 commented on September 14, 2024

It works for my case, thanks!

…

On Mon, 6 Jul 2020 at 12:00, xkzhang ***@***.***> wrote: Got some kind suggestions from StackExchange <https://unix.stackexchange.com/questions/596551/how-to-use-shell-glob-as-what-does-in-regular-expression>. I found shopt -s extglob very simple and useful. Could you try it out to see if it works for you? rule getReads: output: read = temp(intermediate_path + "/reads/{sample}.fastq.gz") params: key = key, input_path = input_path shell: """ shopt -s extglob scp -i {params.key} {params.input_path}/{wildcards.sample}?(.*).f*q.gz {output.read} """ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#13 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHPU4NXRRFMMNPLWNMKQBWLR2GODLANCNFSM4ONOHKRQ> .

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zhxiaokang commented on September 14, 2024

Fixed with commit

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