I try to use Nextflow program and I would like to pull a script from nf-core repository.
It worked, I can see it is present typing nextflow list, real path points to the working directory I would like the script to be in but I cannot see it.
nextflow pull nf-core/demo
Checking nf-core/demo …
downloaded from GitHub - nf-core/demo: nf-core/demo is a simple nf-core style bioinformatics pipeline for workshops and demos. · GitHub - revision: 45904cb9d1 [master]
realpath demo.git
/home/christec/Nextflow/demo.git
How to access a script pulled from nf-core repository?
Best regards,
Camille
Related to that, the demo script for this pipeline is using containers to set up environment. There is a profile for Apptainer but I was not able to set it up to make it work.
Is there anything to know when using containers in program such as nextflow or snakemake?
Best,
Camille
Dear Camille,
After reading the documentation I follow the procedure and it seems to be working fine :
(base) (bamboo)-[rossigng@login1 ~]$ salloc --cpus-per-task=6
salloc: Pending job allocation 3850673
salloc: job 3850673 queued and waiting for resources
salloc: job 3850673 has been allocated resources
salloc: Granted job allocation 3850673
salloc: Nodes cpu001 are ready for job
(base) (bamboo)-[rossigng@cpu001 ~]$ nextflow run nf-core/demo -profile singularity --input samplesheet.csv --outdir .
bash: nextflow: command not found
(base) (bamboo)-[rossigng@cpu001 ~]$ ml Nextflow/25.10.4
(base) (bamboo)-[rossigng@cpu001 ~]$ nextflow run nf-core/demo -profile singularity --input samplesheet.csv --outdir .
N E X T F L O W ~ version 25.10.4
Launching `https://github.com/nf-core/demo` [spontaneous_curry] DSL2 - revision: 45904cb9d1 [master]
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___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
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nf-core/demo 1.1.0
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Input/output options
input : samplesheet.csv
outdir : .
Generic options
trace_report_suffix: 2026-04-14_14-20-25
Core Nextflow options
revision : master
runName : spontaneous_curry
containerEngine : singularity
launchDir : /home/users/r/rossigng
workDir : /home/users/r/rossigng/work
projectDir : /home/users/r/rossigng/.nextflow/assets/nf-core/demo
userName : rossigng
profile : singularity
configFiles : /home/users/r/rossigng/.nextflow/assets/nf-core/demo/nextflow.config
!! Only displaying parameters that differ from the pipeline defaults !!
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* The pipeline
https://doi.org/10.5281/zenodo.12192442
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/demo/blob/master/CITATIONS.md
executor > local (6)
[16/d32ac7] NFCORE_DEMO:DEMO:FASTQC (SAMPLE2_PE) | 3 of 3 ✔
[95/141ce2] NFCORE_DEMO:DEMO:SEQTK_TRIM (SAMPLE2_PE) | 3 of 3 ✔
[- ] NFCORE_DEMO:DEMO:MULTIQC -
Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9aexecutor > local (7)
[16/d32ac7] NFCORE_DEMO:DEMO:FASTQC (SAMPLE2_PE) | 3 of 3 ✔
[95/141ce2] NFCORE_DEMO:DEMO:SEQTK_TRIM (SAMPLE2_PE) | 3 of 3 ✔
[a0/19d0ad] NFCORE_DEMO:DEMO:MULTIQC | 0 of 1
Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9aexecutor > local (7)
[16/d32ac7] NFCORE_DEMO:DEMO:FASTQC (SAMPLE2_PE) | 3 of 3 ✔
[95/141ce2] NFCORE_DEMO:DEMO:SEQTK_TRIM (SAMPLE2_PE) | 3 of 3 ✔
[a0/19d0ad] NFCORE_DEMO:DEMO:MULTIQC | 0 of 1
Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9aexecutor > local (7)
[16/d32ac7] NFCORE_DEMO:DEMO:FASTQC (SAMPLE2_PE) | 3 of 3 ✔
[95/141ce2] NFCORE_DEMO:DEMO:SEQTK_TRIM (SAMPLE2_PE) | 3 of 3 ✔
[a0/19d0ad] NFCORE_DEMO:DEMO:MULTIQC | 1 of 1 ✔
Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9aexecutor > local (7)
[16/d32ac7] NFCORE_DEMO:DEMO:FASTQC (SAMPLE2_PE) | 3 of 3 ✔
[95/141ce2] NFCORE_DEMO:DEMO:SEQTK_TRIM (SAMPLE2_PE) | 3 of 3 ✔
[a0/19d0ad] NFCORE_DEMO:DEMO:MULTIQC | 1 of 1 ✔
Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data [cache /home/users/r/rossigng/work/singularity/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-34-34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d-data.img]
-[nf-core/demo] Pipeline completed successfully-
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /home/users/r/rossigng/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location
Best regards,
Thank you ! It is indeed working.
And I see how I can access the script.