ERROR: Problem about install

[Sawakotx]

Description of the bug

Hi,

I am trying to run nf-core/drugresponseeval (v1.1.0) on a slurm system. Specifically, the nodes cannot verify the SSL certificate for zenodo.org, so I cannot use the default -profile test as it fails with No subject alternative DNS name matching zenodo.org found.

I have manually downloaded the test datasets (TOYv1.zip and TOYv2.zip) and placed them in a local directory (./data/).

I have tried the following two approaches, but neither worked:

1. Using -profile test,singularity: This fails because the test profile seems to hardcode the remote Zenodo URLs, ignoring my local data path.

Bash

nextflow run nf-core/drugresponseeval
-r 1.1.0
-profile test,singularity
--outdir ./results
--path_data ./data
Result: Failed with Unable to stage foreign file: https://zenodo.org/...

2. Using manual parameters (attempting to mimic the test profile): I tried to bypass the test profile by manually specifying the parameters:

Bash

nextflow run nf-core/drugresponseeval
-r 1.1.0
-profile singularity
--outdir ./results
--path_data ./data
--dataset_name TOYv1
--cross_study_datasets TOYv2
--n_cv_splits 2

My Question: Could you please advise on the correct combination of parameters to run the pipeline completely offline using the local TOYv1.zip and TOYv2.zip files? Is there a specific flag to disable the automatic download attempt?

System info:

Nextflow version: 24.10.6

Pipeline version: 1.1.0

Executor: Local / Singularity

OS: Linux

Thank you for your help!

Command used and terminal output

nextflow run nf-core/drugresponseeval \
>     -r 1.1.0 \
>     -profile test,singularity \
>     --outdir ./results \
>     --path_data ./data 

N E X T F L O W   ~  version 24.10.6

Launching `https://github.com/nf-core/drugresponseeval` [compassionate_albattani] DSL2 - revision: 60890c6b5f [1.1.0]


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/drugresponseeval 1.1.0
------------------------------------------------------
Input/output options
  dataset_name              : TOYv1
  outdir                    : ./results

Data options
  path_data                 : ./data
  cross_study_datasets      : TOYv2

Additional options
  n_cv_splits               : 2

Institutional config options
  config_profile_description: Local test run

Generic options
  trace_report_suffix       : 2026-01-24_15-04-40

Core Nextflow options
  revision                  : 1.1.0
  runName                   : compassionate_albattani
  containerEngine           : singularity
  container                 : ghcr.io/daisybio/drevalpy:v1.3.5
  launchDir                 : /PROJECT/singularity
  workDir                   : /PROJECT/singularity/work
  projectDir                : /share/home/.nextflow/assets/nf-core/drugresponseeval
  userName                  : tanxu
  profile                   : singularity
  configFiles               : /share/home/.nextflow/assets/nf-core/drugresponseeval/nextflow.config

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* The nf-core framework
    https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
    https://github.com/nf-core/drugresponseeval/blob/master/CITATIONS.md

Downloading response dataset TOYv1 from Zenodo: https://zenodo.org/records/15533857/files/TOYv1.zip
executor >  local (2)
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:UNZIP_RESPONSE                         -
executor >  local (2)
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:UNZIP_RESPONSE                         -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:UNZIP_CS_RESPONSE                      -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:LOAD_RESPONSE                          -
executor >  local (2)
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:UNZIP_RESPONSE                         -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:UNZIP_CS_RESPONSE                      -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:LOAD_RESPONSE                          -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:LOAD_CS_RESPONSE                       -
executor >  local (2)
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:UNZIP_RESPONSE                         -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:UNZIP_CS_RESPONSE                      -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:LOAD_RESPONSE                          -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:LOAD_CS_RESPONSE                       -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:CV_SPLIT                               -
executor >  local (2)
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:UNZIP_RESPONSE                         -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:UNZIP_CS_RESPONSE                      -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:LOAD_RESPONSE                          -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:LOAD_CS_RESPONSE                       -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:CV_SPLIT                               -
executor >  local (2)
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:UNZIP_RESPONSE                         -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:UNZIP_CS_RESPONSE                      -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:LOAD_RESPONSE                          -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:LOAD_CS_RESPONSE                       -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:CV_SPLIT                               -
executor >  local (2)
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:UNZIP_RESPONSE                         -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:UNZIP_CS_RESPONSE                      -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:LOAD_RESPONSE                          -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:LOAD_CS_RESPONSE                       -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:CV_SPLIT                               -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:MAKE_MODELS                            -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:MAKE_BASELINES                         -
[d8/5bec02] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:HPAM_SPLIT (NaiveMeanEffectsPredictor) [100%] 2 of 2 ✔
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:TRAIN_AND_PREDICT_CV                   -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:EVALUATE_FIND_MAX                      -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:MODEL_TESTING:PREDICT_FULL                    -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:MODEL_TESTING:CONSOLIDATE_RESULTS             -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:MODEL_TESTING:EVALUATE_FINAL                  -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:MODEL_TESTING:COLLECT_RESULTS                 -
[-        ] NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:MODEL_TESTING:VISUALIZE_RESULTS               -


ERROR ~ Error executing process > 'NFCORE_DRUGRESPONSEEVAL:DRUGRESPONSEEVAL:RUN_CV:UNZIP_CS_RESPONSE (1)'

Caused by:
  Can't stage file https://zenodo.org/records/15533857/files/TOYv2.zip -- reason: No subject alternative DNS name matching zenodo.org found.



Container:
  /PROJECT/singularity/nfcore_offline/ghcr.io-daisybio-drevalpy-v1.3.5.img

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- 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

Relevant files

No response

System information

No response

[mashehu]

The link to the test data was changed in 1.2.0 to pull from the nf-core/test-datasets repo instead. can you test again?

[JudithBernett]

Hi @Sawakotx ,

sorry for the late response, I've been sick last week. @mashehu is right, there is a new version 1.2.0 that has some major changes. Did you already try out 1.2.0? You'd need to update Nextflow, though. For 1.2.0, we have decided to only support Nextflow >=25.10.0. Is that an issue?

Nevertheless, your error shouldn't happen. I tried to reproduce it on my local machine and could not. I think that your folder structure in ./data might not be correct (maybe I need to be clearer about this in the documentation).
It should look like

• data
  • TOYv1
    • cell_line_names.csv
    • …
  • TOYv2

Is that different in your setup? Did you maybe not unzip?

Hope that helps!
Best,
Judith

[JudithBernett]

Hi @Sawakotx , did you have a look at this again? Otherwise, I will close this issue.