mirdeep2_run error

[yangfeizZZ]

Description of the bug

when i nun:
nextflow run nf-core/smrnaseq -profile docker --input samplesheet.csv --genome 'GRCm38' --mirtrace_species 'mmu' --outdir ../J1EV_S1_result/
i got an error:

I don't know why~

Command used and terminal output

No response

Relevant files

No response

System information

No response

[marchoeppner]

This is caused by:

smrnaseq/modules/local/format_fasta_mirna.nf

Line 16 in 18d6c84

tuple val(meta2), path('*_idx.fa') , emit: formatted_fasta

The emission from this process, pre-formatting the mirna data, emits a [ hash, file ] Channel, while mirdeep_run expects only [ file ] here:

smrnaseq/modules/local/mirdeep2_run.nf

Line 15 in 18d6c84

path hairpin

Same for the 'mature' fasta input.

As a workaround, you can just edit the module to update the input structure for those two channels.

[yangfeizZZ]

This is caused by:

smrnaseq/modules/local/format_fasta_mirna.nf

Line 16 in 18d6c84

tuple val(meta2), path('*_idx.fa') , emit: formatted_fasta

The emission from this process, pre-formatting the mirna data, emits a [ hash, file ] Channel, while mirdeep_run expects only [ file ] here:

smrnaseq/modules/local/mirdeep2_run.nf

Line 15 in 18d6c84

path hairpin

Same for the 'mature' fasta input.

As a workaround, you can just edit the module to update the input structure for those two channels.

sorry,i am not good at nextflow. I can't understand fully what you explain. I also don't know how to solve it. Would mind me help me more carefully and use a sample word to say.
Thank you~~~

[marchoeppner]

Right, apologies, I am not a developer in this project and if the code base is unfamiliar to you, it would probably prove complicated to sort this out remotely.

Have you tried running this pipeline in an older version? I am not 100% sure when this issue was introduced, but presumably it did not exist in older stable releases

Just rerun with something like:
nextflow run nf-core/smrnaseq -r 2.1.0 ...

[yangfeizZZ]

Right, apologies, I am not a developer in this project and if the code base is unfamiliar to you, it would probably prove complicated to sort this out remotely.

Have you tried running this pipeline in an older version? I am not 100% sure when this issue was introduced, but presumably it did not exist in older stable releases

Just rerun with something like: nextflow run nf-core/smrnaseq -r 2.1.0 ...

I download this pipeline on my linux, and the version is 2.2.3

[subrahmanya-nayak]

@yangfeizZZ Did you get any solutions for this?

[apeltzer]

Should be fine on dev already, if not let us know