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Description
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