MIRDEEP2_MIRDEEP2 task no same

[ladygagaclass]

Description of the bug

when chioce bowtie_index is folder ，folder hava *.ebwt

MIRDEEP2_MIRDEEP2 task size = 1

but choice bowtie_index is tar
MIRDEEP2_MIRDEEP2 task size == sample size

Command used and terminal output

Relevant files

No response

System information

No response

[kopichris]

Hi @ladygagaclass, I am not the repository maintainer, but happy to help troubleshoot. If you could provide additional details, such as the command used and terminal output, this would be really helpful in identifying the source of the issue.

[ladygagaclass]

Hi @ladygagaclass, I am not the repository maintainer, but happy to help troubleshoot. If you could provide additional details, such as the command used and terminal output, this would be really helpful in identifying the source of the issue.

my input have 3 sample ,when bowtie_index chioce is a bowtie_index.tar file or no chioce bowtie_index ,the process have 3 task. but bowtie_index chioce a directory ,The data in the folder is same with the bowtie_index.tar data，the process hava 1 task

[kopichris]

Hi @ladygagaclass, would it be possible to share the specific command you used and the corresponding terminal output; or a copy of the nextflow.log file? Providing this information is really helpful in troubleshooting these types of issues.

[nschcolnicov]

@ladygagaclass @kopichris I'll take a look at this error too, could be that the bowtie_index channel is being consumed by what you describe. I'll run some tests and get back to you

[nschcolnicov]

I was able to reproduce the error, will submit a fix soon

[nschcolnicov]

Hi @ladygagaclass please try running the same command you tried before but using the patched branch, and let me know if the problem was fixed. It worked in my tests.

You can do this by adding "-r issue_496 -latest" to the command you used, -r to provide the branch, and -latest to make sure that the latest version gets pulled before running.

Note: If you were running the pipeline locally, i.e: "nextflow run main.nf ...", you will need to modify the command to run the pipeline remotely.

An example of a remote execution would be:
nextflow run nf-core/smrnaseq -r issue_496 -latest ...(the rest of the command should be the same)

[ladygagaclass]

Hi @ladygagaclass please try running the same command you tried before but using the patched branch, and let me know if the problem was fixed. It worked in my tests.

You can do this by adding "-r issue_496 -latest" to the command you used, -r to provide the branch, and -latest to make sure that the latest version gets pulled before running.

Note: If you were running the pipeline locally, i.e: "nextflow run main.nf ...", you will need to modify the command to run the pipeline remotely.

An example of a remote execution would be: nextflow run nf-core/smrnaseq -r issue_496 -latest ...(the rest of the command should be the same)

OK, Thank you ,I try running solved this problem。Can you help me solve the same problem this project version 2.3.1
NFCORE_SMRNASEQ:MIRDEEP2:MIRDEEP2_RUN process ?

[nschcolnicov]

Hi @ladygagaclass, I'm happy to hear that! Unfortunately, I can't fix an older version that has already been released, I can only fix it and release a new version.
If you really need to use the version 2.3.1 you can try applying these changes to your local copy of the pipeline. Here is the PR so you can see how I fixed this issue: https://github.com/nf-core/smrnaseq/pull/498/files#diff-4268eecd776ab2fd87defb0194d42ef7b1c0b6213e23b08f23056c6d85e3ccb0

[ladygagaclass]

Hi @ladygagaclass, I'm happy to hear that! Unfortunately, I can't fix an older version that has already been released, I can only fix it and release a new version. If you really need to use the version 2.3.1 you can try applying these changes to your local copy of the pipeline. Here is the PR so you can see how I fixed this issue: https://github.com/nf-core/smrnaseq/pull/498/files#diff-4268eecd776ab2fd87defb0194d42ef7b1c0b6213e23b08f23056c6d85e3ccb0

OK，Thank you

[nschcolnicov]

Closing this ticket, the fixes are now available in the dev branch