10000 Unknown configuration profile: 'singularity' · Issue #1574 · nf-core/rnaseq · GitHub
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Unknown configuration profile: 'singularity' #1574
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@CampingOnSeabed

Description

@CampingOnSeabed

Description of the bug

Hi nf-core team!
I am using nf-core/rnaseq pipelines recently, but I encountered a bug. I am trying wo run pipeline on HPC, so I downloaded nf-core-rnaseq_3.13.2 using "nf-core download nf-core/rnaseq" and I click to download singularity. And in my HPC environment, I do have singularity. However the error is "Unknown configuration profile: 'singularity'"

Command used and terminal output

Here is the code
/public/slst/home/chusy2024/nextflow/nextflow-24.04.4-all run \
/public/slst/home/chusy2024/nextflow/nf-core-rnaseq_3.13.2/3_13_2/workflows/ \
--input /public/slst/home/chusy2024/RNA/LXX/0620/nextflow/samplesheet.csv \
--fasta "/public/slst/home/chusy2024/nextflow/GRCh38.primary_assembly.genome.fa" \
--transcript_fasta "/public/slst/home/chusy2024/nextflow/gencode.v48.transcripts.fa" \
--gtf "/public/slst/home/chusy2024/nextflow/gencode.v48.annotation.gtf" \
--gencode \
--trimmer fastp \
--aligner star_rsem \
--skip_qualimap \
--save_reference \
-c "/public/slst/home/chusy2024/RNA/LXX/0620/nextflow/singularity.config" \
-profile singularity

Error:
 "Unknown configuration profile: 'singularity'"

OUTS:
no change     /public/slst/home/chusy2024/miniconda/condabin/conda
no change     /public/slst/home/chusy2024/miniconda/bin/conda
no change     /public/slst/home/chusy2024/miniconda/bin/conda-env
no change     /public/slst/home/chusy2024/miniconda/bin/activate
no change     /public/slst/home/chusy2024/miniconda/bin/deactivate
no change     /public/slst/home/chusy2024/miniconda/etc/profile.d/conda.sh
no change     /public/slst/home/chusy2024/miniconda/etc/fish/conf.d/conda.fish
no change     /public/slst/home/chusy2024/miniconda/shell/condabin/Conda.psm1
no change     /public/slst/home/chusy2024/miniconda/shell/condabin/conda-hook.ps1
no change     /public/slst/home/chusy2024/miniconda/lib/python3.8/site-packages/xontrib/conda.xsh
no change     /public/slst/home/chusy2024/miniconda/etc/profile.d/conda.csh
no change     /home_data/home/slst/chusy2024/.bashrc
No action taken.

 N E X T F L O W   ~  version 24.04.4


(nextflow) [chusy2024@hpc-login nextflow]$ singularity
Usage:
  singularity [global options...] <command>

Available Commands:
  build       Build a Singularity image
  cache       Manage the local cache
  capability  Manage Linux capabilities for users and groups
  completion  generate the autocompletion script for the specified shell
  config      Manage various singularity configuration (root user only)
  delete      Deletes requested image from the library
  exec        Run a command within a container
  inspect     Show metadata for an image
  instance    Manage containers running as services
  key         Manage OpenPGP keys
  oci         Manage OCI containers
  overlay     Manage an EXT3 writable overlay image
  plugin      Manage Singularity plugins
  pull        Pull an image from a URI
  push        Upload image to the provided URI
  remote      Manage singularity remote endpoints, keyservers and OCI/Docker registry credentials
  run         Run the user-defined default command within a container
  run-help    Show the user-defined help for an image
  search      Search a Container Library for images
  shell       Run a shell within a container
  sif         Manipulate Singularity Image Format (SIF) images
  sign        Attach digital signature(s) to an image
  test        Run the user-defined tests within a container
  verify      Verify cryptographic signatures attached to an image
  version     Show the version for Singularity

Run 'singularity --help' for more detailed usage information.
(nextflow) [chusy2024@hpc-login nextflow]$

Relevant files

No response

System information

Nexflow version 24.10.4 build 5934
Hardware hpc
Container Singularity
CentOS linux
nf-core/rnaseq v3.13.2

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