# Using IRMA with nextflow

**URL:** <https://community.seqera.io/t/using-irma-with-nextflow/2347>\
**Category:** Ask for help\
**Tags:** nextflow\
**Created:** [August 28, 2025, 9:15am UTC](https://community.seqera.io/t/using-irma-with-nextflow/2347 "2025-08-28T09:15:39Z")\
**Posts on this page:** 7\
**Page:** 1

<div class="post-metadata">

**Author:** ![heksaani](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/heksaani/32/1976_2.png) [@heksaani](https://community.seqera.io/u/heksaani)\
**Post date:** [August 28, 2025, 9:15am UTC](https://community.seqera.io/t/using-irma-with-nextflow/2347/1 "2025-08-28T09:15:39Z")

</div>

I have this problem running my own written nextflow workflow.  
I am trying to use IRMA [GitHub - CDCgov/irma: IRMA (the Iterative Refinement Meta-Assembler) is a highly configurable and adaptive tool for virus genome assembly.](https://github.com/CDCgov/irma/tree/master)  
But the problem is that for some reason the result files in the folder `/sample_name/amended_consensus` are named wrong.  
With this workflow they are  
`sample_name_1, sample_name_2, sample_name_3` etc.  
and they should be  
`sample_name_A_PB2.fa` etc  
my process looks like this:

```auto
process run_irma {
    conda './envs/IRMA_env.yml'
    tag "$sample_id"

    publishDir "${params.output_dir}", mode: 'copy'

    input:
    tuple val(sample_id), path(fastqs), val(IRMA_mod), val(seq_type)

    script:
    """
    sample_dir=\$(pwd)/${sample_id}
    echo \$sample_dir
    
    if ["$seq_type" == 'minion'] ; then
        echo "using minion"
        conda run -n IRMA IRMA ${IRMA_mod} ${fastqs[0]} \$sample_dir
    elif ["$seq_type" == 'nextseq'] || ["$seq_type" == 'miseq']; then
        echo "Not using minion "
        conda run -n IRMA IRMA ${IRMA_mod} ${fastqs[0]} ${fastqs[1]} \$sample_dir
    fi
    """

}

```

Is there any reason why nextflow would make this naming problem? And more importantly is there anyway to correct / fix this ?

---

<div class="post-metadata">

**Author:** ![mribeirodantas](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/mribeirodantas/32/235_2.png) [@mribeirodantas](https://community.seqera.io/u/mribeirodantas)\
**Post date:** [August 29, 2025, 12:53pm UTC](https://community.seqera.io/t/using-irma-with-nextflow/2347/2 "2025-08-29T12:53:01Z")

</div>

Hi @heksaani,

Welcome to the community forum 🙂

Could you please share a minimum reproducible example? With this snippet alone, it isn’t easy to debug what’s going on.

The `publishDir` directive moves specified process output files to a specific location. Still, as you don’t have an `output` block in your process, no output from this process should be moved to the specified location. I believe these files are NOT being moved there. Outputs from other processes are, and you think they’re the output of this process you shared.

---

<div class="post-metadata">

**Author:** ![heksaani](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/heksaani/32/1976_2.png) [@heksaani](https://community.seqera.io/u/heksaani)\
**Post date:** [September 1, 2025, 12:30pm UTC](https://community.seqera.io/t/using-irma-with-nextflow/2347/3 "2025-09-01T12:30:50Z")

</div>

Hey @mribeirodantas ,

I’ve accidentally copied version of the code which did not include the output block since I’ve already tried different versions to resolve the problem described. Sorry for that, here’s the code with the output block, using the **workflow outputs.**

```groovy
#! /usr/bin/env nextflow

 
process run_irma {
    conda './envs/IRMA_env.yml'
    tag "$sample_id"

    input:
    tuple val(sample_id), path(fastqs), val(mode), val(seq_type)

    output:
    path("${sample_id}"), emit: out

    script:
    """
    sample_dir="${sample_id}"

    if [$seq_type == 'minion'] ; then
        conda run -n IRMA IRMA ${mode} ${fastqs[0]} \$sample_dir
    elif [$seq_type == 'nextseq'] || [$seq_type == 'miseq']; then
        conda run -n IRMA IRMA ${mode} ${fastqs[0]} ${fastqs[1]} \$sample_dir
    fi
    """

}

```

and the main.nf

```groovy

nextflow.preview.output = true
params.now = new Date().format("yyyy-MM-dd_HH-mm")
params.input_dir = null
params.output_dir = "irma_results_${params.now}"
params.input_type = null // 'nextseq', 'miseq', or 'minion'

/*
Import modules
*/
include { run_irma } from './modules/runIrma.nf'

workflow {
    main:

    if (!params.input_dir) {
        error "Please provide a folder path using --input_dir"
    }

    if (params.input_type == 'nextseq') {
        println "Processing NextSeq data"
        def mode = 'FLU'
        println "Mode is set to $mode "
        sample_files = Channel
        .fromFilePairs("${params.input_dir}/*_{R1,R2}*.fastq.gz")
        .ifEmpty { error "No sample fastqs found in: ${params.input_dir}" }

        irma_inputs = sample_files
            .map { sample_id, fastqs -> 
                sample_id = sample_id.tokenize('_')[0]
                tuple(sample_id, fastqs, mode, params.input_type)
            }

    } else {
        error "Unsupported input type: ${params.input_type}. Supported types are: nextseq"
    }
    run_irma(irma_inputs)
    publish:
    irma_results = run_irma.out
}

output {
  irma_results {
    path { _path -> "${params.output_dir}" }
  }
}

```

These produce following folders for two test samples

/results/irma\_results\_2025-09-01\_13-54/test\_sample1/

/results/irma\_results\_2025-09-01\_13-54/test\_sample2/

in these folders are IRMA’s results.

However, the FASTA files in the amended\_consensus/ subfolder are misnamed.

Running IRMA directly on the command line / or with conda produces segment-specific names:

/results/irma\_results\_2025-09-01\_13-54/test\_sample1/amended\_consensus/test\_sample1\_HA.fa

/results/irma\_results\_2025-09-01\_13-54/test\_sample1/amended\_consensus/test\_sample1\_NA.fa

Running IRMA via Nextflow produces generic numbered names:

amended\_consensus/test\_sample1\_1.fa

amended\_consensus/test\_sample1\_2.fa

The segment names (\_HA, \_NA) are lost in the Nextflow run. This naming is important for downstream analyses, because these suffixes indicate the viral segment in each FASTA file.

---

<div class="post-metadata">

**Author:** ![bentsherman](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/bentsherman/32/52_2.png) [@bentsherman](https://community.seqera.io/u/bentsherman)\
**Post date:** [September 16, 2025, 1:38pm UTC](https://community.seqera.io/t/using-irma-with-nextflow/2347/4 "2025-09-16T13:38:20Z")

</div>

I think this is happening because you staged the input files as a single collection rather than as separate paths.

When you declare the input files as `path(fastqs)`, sometimes they are automatically staged with numbered suffixes like `1`, `2`, etc. You could try declaring separate inputs:

```auto
    input:
    tuple val(sample_id), path(fastq_1), path(fastq_2), val(mode), val(seq_type)

```

The second path appears to be optional, so you’ll need to pass an empty list `[]` instead of `null` when the second path is missing, due to the current limitations with path inputs.

I’m not 100% sure about this, but I think it’s worth trying

---

<div class="post-metadata">

**Author:** ![Muneeb](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/muneeb/32/1181_2.png) [@Muneeb](https://community.seqera.io/u/Muneeb)\
**Post date:** [September 28, 2025, 5:06am UTC](https://community.seqera.io/t/using-irma-with-nextflow/2347/5 "2025-09-28T05:06:12Z")

</div>

@heksaani

I’m not sure if this is the root cause, but I noticed an unusual setup!  
IRMA is being run inside a Conda environment within the Nextflow process using `conda run -n IRMA`, while the process itself is also configured to activate a Conda environment via the `conda './envs/IRMA_env.yml'` directive.

This creates a nested Conda environment situation, which may interfere with IRMA’s normal behavior and might be leading to the generic numbered filenames instead of the expected segment-specific names. 😀

---

<div class="post-metadata">

**Author:** ![heksaani](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/heksaani/32/1976_2.png) [@heksaani](https://community.seqera.io/u/heksaani)\
**Post date:** [October 8, 2025, 1:10pm UTC](https://community.seqera.io/t/using-irma-with-nextflow/2347/6 "2025-10-08T13:10:09Z")

</div>

I tried this one but it seems that it had no effect on the results

---

<div class="post-metadata">

**Author:** ![heksaani](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/heksaani/32/1976_2.png) [@heksaani](https://community.seqera.io/u/heksaani)\
**Post date:** [October 8, 2025, 1:11pm UTC](https://community.seqera.io/t/using-irma-with-nextflow/2347/7 "2025-10-08T13:11:09Z")

</div>

Oh good catch, thank you. I also took out the conda call but it did not affect the file naming error