Hi all, I'm running into an interesting issue when running nf-core module rseqc/readdistribution. The error I get (sometimes, but not always) :

.command.sh: line 9: sampleA.read_distribution.txt: cannot overwrite existing file

And the command executed is:

read_distribution.py \
      -i sampleA.dedup.bam \
      -r GRCh38_gencode_v22_CTAT_lib_Mar012021.ref_annot.gtf.bed \
      > sampleA.read_distribution.txt

I assume this error is cause by the shell configuration (noclobber), but I cannot really explain why sampleA.read_distribution.txt would already be present in the working directory of that process, as the only inputs are the bam file and the bed file. sampleA.read_distribution.txt is only an output of the process. Has anyone experienced something similar before? Thanks!

Hi everyone! I'm new to nf-core pipelines and I'm looking for the best-practice workflow to assemble multiple distinct bacteriophage genomes from a metagenomic sample. From my reading, it seems like the best approach would be a two-step process: 1. First, use nf-core/mag to assemble contigs from the raw sequencing fastq files. 2. Then use the output contigs from this pipeline as input for nf-core/phageannotator to identify, bin, and annotate the individual phage genomes. Does this sound like the correct approach, or is there a more direct pipeline for this specific task? Also, would nf-core/mag work for bacteriophage genomes or should I use nf-core/viralrecon instead? Although this looks like its for single viral genomes. Thanks a lot for the help!

Easy question, in the running of a pipeline I do for example:

nextflow run <http://main.nf|main.nf> -profile apptainer  --input=testSampleSheet.csv

How can I access the actual name of the samplesheet, i.e. testSampleSheet.csv, it seems that it automatically does the processing and gives me the variables as indicated in the schema_input.json file, but is there a way that I can actually get the filename of the samplesheet?

Hi all, I'm working on a Nextflow pipeline that deploys multiple Conda environments (defined in YAML files) to ensure tool consistency and to facilitate sharing specific modules. The pipeline works perfectly in its current setup where the Conda environments are automatically deployed during execution. However, I am now trying to add Docker support so that the pipeline can run both locally (via Docker) and on a high-performance cluster (via Singularity). While the Dockerfile successfully sets up the container for tool execution, the Conda environments are not being automatically deployed as they were before containerization. Specifically, I want to maintain the automatic deployment of multiple Conda environments when the pipeline runs inside the Docker or Singularity containers. How can I modify my pipeline to automatically deploy these Conda environments within the containers, similar to the behavior I had before introducing Docker and Singularity? Below I have pasted my dockerfile code. Any suggestion will be helpful! 🙏🏼

FROM continuumio/miniconda3

# Copy environment YAML files into the image
COPY assets/kneaddata.yaml .
COPY assets/metaphlan.yaml .
COPY assets/humann.yaml .
COPY assets/analysis_r.yaml .
COPY assets/cp_r.yaml .

# Create the conda environments
RUN conda env create -f kneaddata.yaml
RUN conda env create -f metaphlan.yaml
RUN conda env create -f humann.yaml
RUN conda env create -f analysis_r.yaml
RUN conda env create -f cp_r.yaml

# List all environments to verify
RUN conda env list

# Copy R script into the image
COPY bin/analysis.R /bin/analysis.R
COPY bin/cp.R /bin/cp.R

# Set default shell to base env
CMD ["bash"]

Hi all, I’ve developed a pipeline based on the nf-core template (but not an official nf-core pipeline), and I’ve encountered issues with the

TEMPLATE

branch. At some point, changes from

dev

were merged into

TEMPLATE

, which has polluted its history. Now, when I try to update the template, it results in major problems. I want to restart the

TEMPLATE

branch from scratch by:

# Delete branch locally
git branch -D TEMPLATE
# Create a new orphan TEMPLATE branch
git checkout --orphan TEMPLATE
# Removing all files
git rm -r .
# Create a new TEMPLATE branch without affecting other branches of my pipeline
nf-core pipelines create --no-git
# Pushing this branch
git add .
git commit -m "Reset TEMPLATE branch with clean nf-core template"
git push origin TEMPLATE --force

However, I’m concerned that running

nf-core pipelines create

might overwrite or conflict with my existing pipeline files. Is this the correct approach to reset the

TEMPLATE

branch without affecting my development branches, or is there a safer/better method? Thanks for your help!

Hi! I used the

nf-core/scrnaseq

pipeline to run

cellranger multi

on 5' GEX data + cell hashing. 10x has updated guidance on processing cell hashing data, which I attempted to follow with the Nextflow pipeline. However, I noticed that the

hashtag_ids

column under

[samples]

was not mentioned in the documentation. As expected, this meant that the pipeline ran successfully, but did not perform hashtag-based demultiplexing. We can run this downstream, which is fine. I'm curious if the updated antibody hashing setup is supported with the Nextflow pipeline, and if so, what was the "right" way to run this? Thanks! Slack conversation

Hello! I am trying to use the Samblaster module to get discordant reads. My module config looks like this: withName: 'SAMBLASTER' { ext.args = { "-a -e -d ${meta.id}.discordant.bam -o /dev/null" } } Because I want the samblaster.out.bam to be the discordant reads. I am receiving this error upon running: [main_samview] fail to read the header from "-". I think this is because the final view command is looking for the general output. How can I address this? Thank you so much for your time!

Hi! 😁 I am trying to run a process that takes the following tuple as input:

input:

tuple val(meta), path(samplesheet), path(run_dir)

For this, I defined two parameters, that I pass from the command line as:

-- samplecsv <path to csv file> --bcldata <path to BCL tar.gz or folder>

(the val(meta) is later created) These parameters are passed from my main workflow to a subworkflow like this:

bcl_dir = params.bcldata

sample_sheet = params.samplecsv

workflow MYPIPELINE_MAIN {

take:

bcl_dir         // path: BCL input

sample_sheet    // path: SampleSheet CSV

main:

MYPIPELINE_CORE(bcl_dir, sample_sheet)

emit:

demux_fastq = MYPIPELINE_CORE.out

}

Inside the subworkflow (

MYPIPELINE_CORE

), I pass them into the process using a tuple, along with the meta ([id: 'run1']):

workflow MYPIPELINE_CORE {

take:

bcl_dir       // path to BCL tar.gz

sample_sheet  // path to samplesheet CSV

main:

Channel

.of(tuple([id: 'run1'], file(sample_sheet), file(bcl_dir)))

.set { ch_combinedTuple }

ch_combinedTuple.view { "Combined tuple-channel content: $it" }

BCL2FASTQ(ch_combinedTuple)

}

I verified via

println

statements that

sample_sheet

and

bcl_dir

are `java.lang.String`and correctly point to valid files. However, when the process has to be run i come across this error:

Combined tuple-channel content: [[id:run1], /beegfs/home/lrenteria/my_pipeline/data/Samplesheet.csv, /beegfs/home/lrenteria/my_pipeline/data/BCL_data.tar.gz]

`ERROR ~ Invalid method invocation

call

with arguments: [<data row from samplesheet>] (java.util.ArrayList) on _closure6 type` Interestingly, when I run a minimal test with only the process and the same tuple construction, everything works fine:

include { BCL2FASTQ } from './modules/nf-core/bcl2fastq'

Channel

.of( tuple([id: 'run1'], file(params.samplecsv), file(params.bcldata)) )

.set { ch_test }

workflow {

ch_test.view { "Test channel content: $it" }

BCL2FASTQ(ch_test)

}

Any idea what mught be going wrong in the subworkflow context? Thanks a lot in advance! 🤸‍♀️

I'm a single CI test away from a passing release, can someone give me a lead? Singularity is misbehaving with a Seqera container. PR here

Command error:
  INFO:    Converting SIF file to temporary sandbox...
  FATAL:   while extracting /home/runner/work/reportho/reportho/./community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-6b-6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8-data.img: root filesystem extraction failed: extract command failed: ERROR  : Failed to create container process: Operation not permitted

My pipeline is failing on recent runs at the multiqc step on an arm machine with

Illegal Instruction

error code. I believe this is due to multiqc docker image not being compatible with arm architecture?

[d0/50472d] ABH…REQ:POOLSEQFREQ:FASTQC_BEFORE (test) | 1 of 1, cached: 1 ✔
[79/3b2dab] ABH…LSEQFREQ:POOLSEQFREQ:CUTADAPT (test) | 1 of 1, cached: 1 ✔
[8c/358ce2] ABH…FREQ:POOLSEQFREQ:FASTQC_AFTER (test) | 1 of 1, cached: 1 ✔
[9c/b8a2fb] ABH…SEQFREQ:BWAMEM2_INDEX (genome.fasta) | 1 of 1, cached: 1 ✔
[1b/c8d2b7] ABH…QFREQ:POOLSEQFREQ:BWAMEM2_MEM (test) | 1 of 1, cached: 1 ✔
[ce/202004] ABH…POOLSEQFREQ:BEDTOOLS_BAMTOBED (test) | 1 of 1, cached: 1 ✔
[35/1ecaf7] ABH…REQ:POOLSEQFREQ:PRESEQ_CCURVE (test) | 1 of 1, cached: 1 ✔
[94/fd4b65] ABH…Q:POOLSEQFREQ:PRESEQ_LCEXTRAP (test) | 1 of 1, failed: 1 ✔
[2f/3462b7] ABH…PICARD_ADDORREPLACEREADGROUPS (test) | 1 of 1, cached: 1 ✔
[52/418651] ABH…SEQFREQ:PICARD_MARKDUPLICATES (test) | 1 of 1, cached: 1 ✔
[70/0c099d] ABH…EQ:POOLSEQFREQ:SAMTOOLS_INDEX (test) | 1 of 1, cached: 1 ✔
[7e/cc6c79] ABH…EQ:POOLSEQFREQ:SAMTOOLS_STATS (test) | 1 of 1, cached: 1 ✔
[db/a21fdf] ABH…POOLSEQFREQ:SAMTOOLS_COVERAGE (test) | 1 of 1, cached: 1 ✔
[80/436447] ABH…POOLSEQFREQ:SAMTOOLS_FLAGSTAT (test) | 1 of 1, cached: 1 ✔
[3d/390a1b] ABH…POOLSEQFREQ:SAMTOOLS_IDXSTATS (test) | 1 of 1, cached: 1 ✔
[56/b23383] ABH…:POOLSEQFREQ:SAMTOOLS_MPILEUP (test) | 1 of 1, cached: 1 ✔
[b6/67ee0b] ABH…OLSEQFREQ:POOLSEQFREQ:POOLSNP (test) | 1 of 1, cached: 1 ✔
[12/324d7d] ABHILESH_POOLSEQFREQ:POOLSEQFREQ:MULTIQC | 2 of 2, failed: 2, retries: 1 ✘
[94/fd4b65] NOTE: Process `ABHILESH_POOLSEQFREQ:POOLSEQFREQ:PRESEQ_LCEXTRAP (test)` terminated with an error exit status (1) -- Error is ignored
[b4/6a41f6] NOTE: Process `ABHILESH_POOLSEQFREQ:POOLSEQFREQ:MULTIQC` terminated with an error exit status (132) -- Execution is retried (1)
ERROR ~ Error executing process > 'ABHILESH_POOLSEQFREQ:POOLSEQFREQ:MULTIQC'

Caused by:
  Process `ABHILESH_POOLSEQFREQ:POOLSEQFREQ:MULTIQC` terminated with an error exit status (132)


Command executed:

  multiqc \
      --force \
       \
      --config multiqc_config.yml \
       \
       \
       \
       \
       \
      .
  
  cat <<-END_VERSIONS > versions.yml
  "ABHILESH_POOLSEQFREQ:POOLSEQFREQ:MULTIQC":
      multiqc: $( multiqc --version | sed -e "s/multiqc, version //g" )
  END_VERSIONS

Command exit status:
  132

Command output:
  (empty)

Command error:
  .command.sh: line 17:    33 Illegal instruction     multiqc --force --config multiqc_config.yml .

Work dir:
  /Users/ad2347/Documents/Github_projects/poolseqfreq/work/12/324d7def114947e8af3efe6473147d

Container:
  quay.io/biocontainers/multiqc:1.29--pyhdfd78af_0

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details
-[abhilesh/poolseqfreq] Pipeline completed with errors-

I am running the pipeline with test data using -

nextflow run -profile docker,test,arm <http://main.nf|main.nf> -resume

and have the following in my

nextflow.config

file -

docker {
        docker.enabled          = true
        conda.enabled           = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
        docker.runOptions       = '-u $(id -u):$(id -g)'
    }
    arm {
        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'

This message was deleted.

Hi! I'm developing a new module which runs a R script that internally (through the

reticulate

R package) imports a python package and fits a model in Python. The problem I'm facing is the following: the Python installation is not automatically found inside the R script. There are

reticulate

functions to define which Python installation to use, but I'm wondering if there is a way to know in a general way the python path defined by Nextflow when running with Conda, Docker and Singularity. This is my environment definition (from which Docker and Singularity container are created):

channels:
  - conda-forge
  - bioconda
dependencies:
  - anaconda::pip=24.2
  - bioconda::r-bascule=1.0.1
  - conda-forge::compilers=1.9.0
  - conda-forge::python=3.8.20
  - conda-forge::r-ggplot2=3.5.2
  - conda-forge::r-reticulate=1.42.0
  - conda-forge::r-tidyverse=2.0.0
  - pip:
    - pybascule==1.0.1

This is the error I'm getting when running with Docker profile (you can see all the errors in GitHub actions https://github.com/nf-core/modules/actions/runs/16067091894):

Error: Installation of Python not found, Python bindings not loaded.
See the Python "Order of Discovery" here: <https://rstudio.github.io/reticulate/articles/versions.html#order-of-discovery>.
Execution halted

I hope this is clear. If any of you have suggestions regarding this please let me know!

Is there comprehensive list of steps required that that exists to implement viralrecon for any amplicon regardless of the pathogen? I am currently trying to implement for WNV Virus but I feel as though I am playing whack-a-mole with the errors it feels heavily tailored to SARS-CoV-2. Is there another potential pipeline I should use? I am trying to get consensus sequences and VCF files with intrahost variance from a PrimalSeq library prep of West Nile Virus field samples.

Hello, 👋 did anyone use RefTrace for linting already? I tried to install it via pip but got:

ERROR: Could not find a version that satisfies the requirement reftrace (from versions: none)
ERROR: No matching distribution found for reftrace

Hi guys, I tried to merge the template 3.3.1 on my own fort of the pipeline, but get some git issue when pushing the changes

To <https://github.com/nservant/nf-core-hic>
 ! [remote rejected] merging-template-updates -> merging-template-updates (refusing to allow a Personal Access Token to create or update workflow `.github/workflows/awsfulltest.yml` without `workflow` scope)

Anything to do to fix that ?

thanks

This message was deleted.

Hello everyone, is there someone who successfully runs nf-core pipelines for somatic variant calling (esp rnadnavar, but others would work) on danish computerome HPC? I would ask for some help

SamplesheetToList problems Hi, was just testing out samplesheetTolist in an empty pipeline (runs no process, emits empty channel for the default pipeline format i.e multiqc_report) I took the example CSV, example schema_input.json from here: https://nextflow-io.github.io/nf-schema/latest/samplesheets/samplesheetToList/#basic-example I then run

ch_input = Channel.fromList(samplesheetToList(params.input,file("assets/schema_input.json")))
ch_input.view()

so the output then looks like this:

[mysample1, input1_R1.fq.gz, input1_R2.fq.gz, forward]
[mysample2, input2_R1.fq.gz, input2_R2.fq.gz, forward]
ERROR ~ Invalid method invocation `call` with arguments: [mysample1, input1_R1.fq.gz, input1_R2.fq.gz, forward] (java.util.ArrayList) on _closure6 type

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details
-[nf-core/bactiseq] Pipeline completed with errors-

I am not sure what is giving this error? the channel gets made, it gets view() and it matches with the example output. Does it have to do with the workflow code from main.nf?

workflow {

    main:
    //
    // SUBWORKFLOW: Run initialisation tasks
    //
    PIPELINE_INITIALISATION (
        params.version,
        params.validate_params,
        params.monochrome_logs,
        args,
        params.outdir,
        params.input
    )

    //
    // WORKFLOW: Run main workflow
    //
    NFCORE_BACTISEQ (
        PIPELINE_INITIALISATION.out.samplesheet
    )
    //
    // SUBWORKFLOW: Run completion tasks
    //
    PIPELINE_COMPLETION (
        params.email,
        params.email_on_fail,
        params.plaintext_email,
        params.outdir,
        params.monochrome_logs,
        params.hook_url,
        NFCORE_BACTISEQ.out.multiqc_report
    )

Hello, I hope you are doing well. I am analyzing bulk RNAseq of bacterial genome. In Fastqc I found many Kmers sequences.(high content) should I eleminate them? How can I proceed with! THank you for your support

Hello, I am trying to run nfcore/mag. I cleared the work directory from a previous run and am trying to start from scratch again with a different set of samples. It is run on SLURM using the departmental config. The job will run for about 15 seconds and then fail every time. Here is a portion of the .out:

executor >  slurm (9)
[25/e87748] NFC…FASTQC_RAW (N073_run0_raw) | 0 of 4 ✘
[8d/869603] NFC…OCESSING:FASTP (N073_run0) | 0 of 4 ✘
[dc/ec7b0e] NFC…SM259684v1_genomic.fna.gz) | 0 of 1
[-        ] NFC…BOWTIE2_PHIX_REMOVAL_ALIGN -
[-        ] NFC…EPROCESSING:FASTQC_TRIMMED -
[-        ] NFC…AD_PREPROCESSING:CAT_FASTQ -
[-        ] NFC…PREPROCESSING:NANOPLOT_RAW -
[-        ] NFC…PREPROCESSING:PORECHOP_ABI -
[-        ] NFC…EAD_PREPROCESSING:NANOLYSE -
[-        ] NFC…EAD_PREPROCESSING:FILTLONG -
[-        ] NFC…OCESSING:NANOPLOT_FILTERED -
[-        ] NFC…:MAG:CENTRIFUGE_CENTRIFUGE -
[-        ] NFC…MAG:MAG:CENTRIFUGE_KREPORT -
[-        ] NFCORE_MAG:MAG:KRAKEN2         -
[-        ] NFCORE_MAG:MAG:POOL_LONG_READS -
[-        ] NFCORE_MAG:MAG:METASPADES      -
[-        ] NFC…E_MAG:MAG:METASPADESHYBRID -
[-        ] NFCORE_MAG:MAG:MEGAHIT         -
[-        ] NFC…_MAG:MAG:GUNZIP_ASSEMBLIES -
[-        ] NFCORE_MAG:MAG:QUAST           -
Plus 31 more processes waiting for tasks…
Pulling Singularity image <https://depot.galaxyproject.org/singularity/fastp:0.23.4--h5f740d0_0> [cache /home/neckersl/scratch/private/nfcore_mag/work/singularity/depot.galaxyproject.org-singularity-fastp-0.23.4--h5f740d0_0.img]
Pulling Singularity image <https://depot.galaxyproject.org/singularity/bowtie2:2.4.2--py38h1c8e9b9_1> [cache /home/neckersl/scratch/private/nfcore_mag/work/singularity/depot.galaxyproject.org-singularity-bowtie2-2.4.2--py38h1c8e9b9_1.img]
Pulling Singularity image <https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0> [cache /home/neckersl/scratch/private/nfcore_mag/work/singularity/depot.galaxyproject.org-singularity-fastqc-0.12.1--hdfd78af_0.img]
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /home/neckersl/scratch/private/nfcore_mag/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location
[nf-core/mag] ERROR: no bins passed the bin size filter specified between --bin_min_size 0 and --bin_max_size null. Please adjust parameters.
ERROR ~ Error executing process > 'NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD (GCA_002596845.1_ASM259684v1_genomic.fna.gz)'

Caused by:
  Process `NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD (GCA_002596845.1_ASM259684v1_genomic.fna.gz)` terminated with an error exit status (1)


Command executed:

  mkdir bowtie
  bowtie2-build --threads 1 GCA_002596845.1_ASM259684v1_genomic.fna.gz GCA_002596845

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD":
      bowtie2: $(echo $(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*$//')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  WARNING: Skipping mount /var/lib/apptainer/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  bash: .command.run: No such file or directory

Work dir:
  /home/neckersl/scratch/private/nfcore_mag/work/dc/ec7b0eb2e8becb57f9f20e81f5f4eb

Container:
  /home/neckersl/scratch/private/nfcore_mag/work/singularity/depot.galaxyproject.org-singularity-bowtie2-2.4.2--py38h1c8e9b9_1.img

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details
-[nf-core/mag] Pipeline completed with errors-

The script I used was the same as one I have used previously that worked fine, just the raw reads are different:

#!/bin/bash
#SBATCH --job-name=nfcore_mag
#SBATCH --output=../logs/%x_%j.out
#SBATCH --error=../logs/%x_%j.err
#SBATCH --cpus-per-task=8
#SBATCH --mem=32G
#SBATCH --partition=long


# Activate Conda
source /mnt/apps/users/neckersl/conda/etc/profile.d/conda.sh
conda activate nfcore

# Run the pipeline
nextflow run nf-core/mag -r 4.0.0 \
  -profile cropdiversityhpc \
  --input "$HOME/scratch/private/nfcore_mag/data/N072-75_fb_samplesheet.csv" \
  --outdir "$HOME/scratch/private/nfcore_mag/output/spades_fb" \
  --gtdb_db /mnt/shared/datasets/databases/gtdb/GTDB_280324 \
  -work-dir "$HOME/scratch/private/nfcore_mag/work"

Any help would be greatly appreciated. Thanks.

Hello everyone, I'm trying to exclude some chromosomes before aligning / processing bulk RNA-seq, is there any function that one could add customized script in nf-core rnaseq or do i just have to remove some chromosomes in the gtf-level? Thanks in advance 🙂

Hello, I am stuck troubleshooting a subworkflow nf-test for “Diamond”. When I run the nf-test

nf-test test subworkflows/local/diamond/tests/main.nf.tests

, I get an output of

No tests to execute

. This subworkflow is to execute four modules:

NCBIREFSEQDOWNLOAD

,

DIAMONDPREPARETAXA

,

DIAMOND_MAKEDB

, and

DIAMOND_BLASTP

. The first two modules are local modules and nf-testing succeeds while the later two are nf-core installed modules. Here is a link to the github PR: https://github.com/nf-core/proteinannotator/pull/50 Here is the subworkflow main.nf

include { NCBIREFSEQDOWNLOAD } from '../../../modules/local/ncbirefseqdownload/main'
include { DIAMONDPREPARETAXA } from '../../../modules/local/diamondpreparetaxa/main'
include { DIAMOND_MAKEDB } from '../../../modules/nf-core/diamond/makedb/main'
include { DIAMOND_BLASTP  } from '../../../modules/nf-core/diamond/blastp/main'

/*
* Pipeline parameters
*/
// params.refseq_release = 'complete'
// params.taxondmp_zip = '<<ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz>>'
// params.taxonmap = '<<ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz>>'
// params.diamond_outfmt = 6
// params.diamond_blast_columns = qseqid

workflow DIAMOND {
    take:
    ch_fasta // channel: [ val(meta), [ fasta ] ]

    main:

    ch_versions = Channel.empty()

    // TODO nf-core: substitute modules here for the modules of your subworkflow
    NCBIREFSEQDOWNLOAD(
        params.refseq_release
    )
    ch_diamond_reference_fasta = NCBIREFSEQDOWNLOAD.out.refseq_fasta
    ch_versions = ch_versions.mix(NCBIREFSEQDOWNLOAD.out.versions.first())

    DIAMONDPREPARETAXA (
        params.taxondmp_zip
    )
    ch_taxonnodes = DIAMONDPREPARETAXA.out.taxonnodes
    ch_taxonnames = DIAMONDPREPARETAXA.out.taxonnames
    ch_versions = ch_versions.mix(DIAMONDPREPARETAXA.out.versions.first())

    DIAMOND_MAKEDB (
        ch_diamond_reference_fasta,
        params.taxonmap, // make default <<ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz>>
        ch_taxonnodes,
        ch_taxonnames
    )
    ch_diamond_db = DIAMOND_MAKEDB.out.db
    ch_versions = ch_versions.mix(DIAMOND_MAKEDB.out.versions.first())

    //ch_diamond_db = Channel.of( [ [id:"diamond_db"], file(params.diamond_db, checkIfExists: true) ] )

    DIAMOND_BLASTP (
        ch_fasta,
        ch_diamond_db,
        params.diamond_outfmt,
        params.diamond_blast_columns,
    )
    emit:
    ch_versions = ch_versions.mix(DIAMOND_BLASTP.out.versions.first())
    ch_diamond_tsv = DIAMOND_BLASTP.out.tsv

Here is the main.nf.test:

nextflow_workflow {

    name "Test Subworkflow DIAMOND"
    script "../main.nf"
    workflow "DIAMOND"

    tag "subworkflows"
    tag "subworkflows_"
    tag "subworkflows/diamond"
    // TODO nf-core: Add tags for all modules used within this subworkflow. Example:
    tag "ncbirefseqdownload"
    tag "diamondpreparetaxa"
    tag "diamond/makedb"
    tag "diamond/blastp"

    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
    setup {
        run("NCBIREFSEQDOWNLOAD") {
            script "../../../../modules/local/ncbirefseqdownload/main.nf"
            process {
                """
                input[0] = 'other'
                """
            }
        }
        run("DIAMONDPREPARETAXA") {
            script "../../../../modules/local/diamondpreparetaxa/main.nf"
            process {
                """
                input[0] = '<<ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz>>'
                """
            }
        }
        run("DIAMOND_MAKEDB") {
            script "../../../../modules/nf-core/diamond/makedb/main.nf"
            process {
                """
                input[0] = [ [id:'test2'], [ NCBIREFSEQDOWNLOAD.out.refseq_fasta ] ]
                input[1] = '<<ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz>>'
                input[2] = DIAMONDPREPARETAXA.out.taxonnodes
                input[3] = DIAMONDPREPARETAXA.out.taxonnames
                """
            }
        }
        run("DIAMOND_BLASTP") {
            script "../../../../modules/nf-core/diamond/makedb/main.nf"
            process {
                """
                input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) ]
                input[1] = DIAMOND_MAKEDB.out.db
                input[2] = 6
                input[3] = 'qseqid qlen'
                """
            }
        }
    }
    test("Test Diamond subworkflow succeeds") {

        when {
            params {
                params.refseq_release = 'complete'
                params.taxondmp_zip = '<<ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz>>'
                params.taxonmap = '<<ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz>>'
                params.diamond_outfmt = 6
                params.diamond_blast_columns = 'qseqid'
            }
            workflow {
                """
                input[0] = file("test1.fasta", checkIfExists: true)
                """
            }
        }

        then {
            assertAll(
                { assert workflow.success},
                { assert snapshot(workflow.out).match()}
                //TODO nf-core: Add all required assertions to verify the test output.
            )
        }
    }
}

Thank you to any and all help.

Hi! I was using rnadnavar pipeline, and had error in process NFCORE_RNADNAVARRNADNAVARBAM_PROCESSINGBAM GATK PREPROCESSINGBAM_SPLITNCIGARREADSCRAM MERGE INDEX SAMTOOLSMERGE_CRAM related to pulling sing image, then ended up pulling it manually and hardcoding path to it in main.nf. Now get this error that makes no sense, does anyone hace any idea what to do? ERROR ~ Error executing process > 'NFCORE_RNADNAVARRNADNAVARBAM_PROCESSINGBAM GATK PREPROCESSINGBAM_SPLITNCIGARREADSCRAM MERGE INDEX SAMTOOLSMERGE_CRAM (1)' Caused by: Not a valid path value type: java.util.LinkedHashMap ([id:[GCA_000001405.15_GRCh38_full_analysis_set]]) Container: /home/projects/..../singularity-cache/biocontainers-samtools\:v1.9-4-deb_cv1 Tip: view the complete command output by changing to the process work dir and entering the command

cat .command.out

-- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details

Hello again! I am trying to use the Multi-QC module that comes with the NF-core template. I want to display custom content as described here: https://docs.seqera.io/multiqc/custom_content I have used this strategy: https://github.com/MultiQC/test-data/blob/main/data/custom_content/embedded_config/bargraph_multiple_samples_no_sort_mqc.csv I think I am having a problem similar to the one discussed here that was marked as resolved: https://github.com/MultiQC/MultiQC/issues/2666 There is no error generated, but the content is not shown. Do you have any advice for me?

Hello, I'm trying to use 'wave' in the latest template build (3.3.2) and it doesn't seem to be defaulting to containers after checking for a dockerfile. I've set the appropriate line in my nextflow.config (going by this documentation: https://www.nextflow.io/docs/latest/wave.html) to

wave.strategy           = ['dockerfile','container']

And the only thing in the pipeline is multiqc. If I run the pipeline using:

nextflow run main.nf -profile wave,test --outdir test

Then I get an error that the multiqc executable was not found.

(nextflow) mbeavitt@ORIGIN-LT-27:~/Code/Nextflow/test$ ./run.sh

 N E X T F L O W   ~  version 25.04.6

Launching `main.nf` [sad_gilbert] DSL2 - revision: 3b35870dc7

Input/output options
  input                     : <https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv>
  outdir                    : test

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Generic options
  trace_report_suffix       : 2025-07-09_20-31-46

Core Nextflow options
  runName                   : sad_gilbert
  launchDir                 : /home/mbeavitt/Code/Nextflow/test
  workDir                   : /home/mbeavitt/Code/Nextflow/test/work
  projectDir                : /home/mbeavitt/Code/Nextflow/test
  userName                  : mbeavitt
  profile                   : wave,test
  configFiles               : /home/mbeavitt/Code/Nextflow/test/nextflow.config

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
executor >  local (1)
[6b/5aa8b1] ORIGINSCIENCES_REPAQ2FASTQ:REPAQ2FASTQ:MULTIQC [  0%] 0 of 1
ERROR ~ Error executing process > 'ORIGINSCIENCES_REPAQ2FASTQ:REPAQ2FASTQ:MULTIQC'

executor >  local (1)
[6b/5aa8b1] ORIGINSCIENCES_REPAQ2FASTQ:REPAQ2FASTQ:MULTIQC [  0%] 0 of 1 ✘
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'ORIGINSCIENCES_REPAQ2FASTQ:REPAQ2FASTQ:MULTIQC'

Caused by:
  Process `ORIGINSCIENCES_REPAQ2FASTQ:REPAQ2FASTQ:MULTIQC` terminated with an error exit status (127)

executor >  local (1)
[6b/5aa8b1] ORIGINSCIENCES_REPAQ2FASTQ:REPAQ2FASTQ:MULTIQC [  0%] 0 of 1 ✘
Execution cancelled -- Finishing pending tasks before exit
-[originsciences/repaq2fastq] Pipeline completed with errors-
ERROR ~ Error executing process > 'ORIGINSCIENCES_REPAQ2FASTQ:REPAQ2FASTQ:MULTIQC'

Caused by:
  Process `ORIGINSCIENCES_REPAQ2FASTQ:REPAQ2FASTQ:MULTIQC` terminated with an error exit status (127)

executor >  local (1)
[6b/5aa8b1] ORIGINSCIENCES_REPAQ2FASTQ:REPAQ2FASTQ:MULTIQC [  0%] 0 of 1 ✘
Execution cancelled -- Finishing pending tasks before exit
-[originsciences/repaq2fastq] Pipeline completed with errors-
ERROR ~ Error executing process > 'ORIGINSCIENCES_REPAQ2FASTQ:REPAQ2FASTQ:MULTIQC'

Caused by:
  Process `ORIGINSCIENCES_REPAQ2FASTQ:REPAQ2FASTQ:MULTIQC` terminated with an error exit status (127)


Command executed:

  multiqc \
      --force \
       \
      --config multiqc_config.yml \
       \
       \
       \
       \
       \
      .

  cat <<-END_VERSIONS > versions.yml
  "ORIGINSCIENCES_REPAQ2FASTQ:REPAQ2FASTQ:MULTIQC":
      multiqc: $( multiqc --version | sed -e "s/multiqc, version //g" )
  END_VERSIONS

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 3: multiqc: command not found

Work dir:
  /home/mbeavitt/Code/Nextflow/test/work/6b/5aa8b1d054a0a65276379388988010

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details

Any ideas? What am I doing wrong? It seems from the .nextflow.log file that the wave container is being requested and returned successfully:

Jul-09 20:31:55.966 [Actor Thread 22] DEBUG io.seqera.wave.plugin.WaveClient - Wave config: WaveConfig(enabled:true, endpoint:<https://wave.seqera.io>, containerConfigUrl:[], tokensCacheMaxDuration:30m, condaOpts:CondaOpts(mambaImage=mambaorg/micromamba:1.5.10-noble; basePackages=conda-forge::procps-ng, commands=null), strategy:[dockerfile, container], bundleProjectResources:null, buildRepository:null, cacheRepository:null, retryOpts:RetryOpts(delay:450ms, maxDelay:1m 30s, maxAttempts:10, jitter:0.25), httpClientOpts:HttpOpts(), freezeMode:false, preserveFileTimestamp:null, buildMaxDuration:40m, mirrorMode:null, scanMode:null, scanAllowedLevels:null)
Jul-09 20:31:56.011 [Actor Thread 22] DEBUG io.seqera.wave.plugin.WaveClient - Request limiter blocked PT0.001S
Jul-09 20:31:56.012 [Actor Thread 22] DEBUG io.seqera.wave.plugin.WaveClient - Wave request: <https://wave.seqera.io/v1alpha2/container>; attempt=1 - request: SubmitContainerTokenRequest(towerAccessToken:<redacted>, towerRefreshToken:null, towerWorkspaceId:null, towerEndpoint:<https://api.cloud.seqera.io>, containerImage:quay.io/biocontainers/multiqc:1.29--pyhdfd78af_0, containerFile:null, containerConfig:ContainerConfig(), condaFile:null, containerPlatform:linux/amd64, buildRepository:null, cacheRepository:null, timestamp:2025-07-09T20:31:56.010626154+01:00, fingerprint:68285522bb7722ef8aea452fcae38e1d, freeze:false, format:null, dryRun:false, workflowId:null, containerIncludes:null, packages:null, nameStrategy:null, mirror:false, scanMode:null, scanLevels:null)
Jul-09 20:31:56.653 [Actor Thread 22] DEBUG io.seqera.wave.plugin.WaveClient - Wave response: statusCode=200; body={"requestId":"8f9ffe7cc83e","containerToken":"8f9ffe7cc83e","targetImage":"wave.seqera.io/wt/8f9ffe7cc83e/biocontainers/multiqc:1.29--pyhdfd78af_0","expiration":"2025-07-11T07:31:56.732752494Z","containerImage":"quay.io/biocontainers/multiqc:1.29--pyhdfd78af_0","freeze":false,"mirror":false,"succeeded":true}

Please find my code at this repo with a run.sh script if you'd like to try and reproduce this: https://github.com/mbeavitt/example_wave_pipeline

Hello I Hope you are doing well, I am analyzing bulk RNAseq of bacterial genome.and I Have biological replicates,2 for each condition. shall I analyze them seperatly before downstrem analysis? or merging fastq files before alignement? which method and strategy is more appropriate! thank you

hello guys is there any efficient way to combine gvcf using multi threading i have 128 cpu core HPC i have tired GenomeInfoDB but that too took lot of time and in between shutting down the engine

Hello, I've tried updating the

blastn

module by adding

taxid

as input in this pr. I would like to add taxid testdata to properly test the update, in which folder should I place this testdata?