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Hello, I'm currently trying to add a subworkflow i...
# help
j
Hello, I'm currently trying to add a subworkflow in a pipeline however I've been unable to find in the documentation what was the proper way to update test snapshots at a pipeline level. Because 
nf-core pipelines test --update
isn't available I tried 
nf-test test tests/ --update-snapshot
however I get input errors when running locally.
✅ 1
m
For now you need to run it by calling nf-test directly like you did in the second example. does 
nf-test test --tag pipeline --update-snapshot
work?
j
It didn't work I got the same input issues and the resulting snapshots were obviously wrong.
m
do you have a link so i can have a look at the files?
j
Here : https://github.com/nf-core/rnaseq/pull/1755 However the results that I get when running the tests on my machine are completely different than the ones through the GitHub CI/CD runner.
m
and the pipeline runs with 
nextflow run . -profile docker,test
?
j
I just tried and it don't work anymore
also an input, output issue telling that the parameters are missing
m
what is the exact error you get?
j
Copy code
nextflow run . --profile docker,test

 N E X T F L O W   ~  version 25.10.4

Launching `./main.nf` [curious_escher] DSL2 - revision: 2981791ab0


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/rnaseq 3.24.0dev
------------------------------------------------------

UMI options
  umi_discard_read                         : 0

Alignment options
  min_mapped_reads                         : 5

Generic options
  trace_report_suffix                      : 2026-04-08_12-26-46

Core Nextflow options
  runName                                  : curious_escher
  container..*STAR_ALIGN_IGENOMES          : <http://community.wave.seqera.io/library/star_samtools_gawk:79ca42311e583cdc|community.wave.seqera.io/library/star_samtools_gawk:79ca42311e583cdc>
  container.STAR_GENOMEGENERATE_IGENOMES   : <http://community.wave.seqera.io/library/star_samtools_gawk:79ca42311e583cdc|community.wave.seqera.io/library/star_samtools_gawk:79ca42311e583cdc>
  container..*PARABRICKS_STARGENOMEGENERATE: <http://community.wave.seqera.io/library/htslib_samtools_star_gawk:4de2f983041d42e6|community.wave.seqera.io/library/htslib_samtools_star_gawk:4de2f983041d42e6>
  launchDir                                : /workspaces/rnaseq
  workDir                                  : /workspaces/rnaseq/work
  projectDir                               : /workspaces/rnaseq
  userName                                 : root
  profile                                  : standard
  configFiles                              : /workspaces/rnaseq/nextflow.config

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------

* The pipeline
    <https://doi.org/10.5281/zenodo.1400710>

* The nf-core framework
    <https://doi.org/10.1038/s41587-020-0439-x>

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

ERROR ~ Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* Missing required parameter(s): input, outdir

 -- Check script 'subworkflows/nf-core/utils_nfschema_plugin/main.nf' at line: 68 or see '.nextflow.log' file for more details
I checked utils_nfschema_plugin and I have include errors because it points toward the plugin folders which isn't present
m
the plugins are handled by nextflow so no need to have a specific folder there
j
@mashehu Hi ! Just wanted to say that I found what was missing for updating the snapshots I needed to specify the test profile so 
nf-test test --tag pipeline --profile=test,singularity --update-snapshot
because otherwise the default profile is a null value
And thank you for trying to help me !
m
I would recommend doing --profile=+singularity
j
I did try but I got input errors and in the content's section of the updated sections I only had "pipeline_info" written instead of the tools versions and filenames.
m
interesting
do you have some code available that I could look at?
j
You can pull my PR branch if you want : https://github.com/nf-core/rnaseq/pull/1755
👀 1
m
and which tests are you trying to work with?
because I don't see pipeline tests here, only modules and subworkflows
j
the test in the tests/ folder ?
m
ok, so you're not adding tests, just wanting to run existing tests, am I right?
j
yes exactly
so I can update the snapshots and pass the CI/CD check for my PR
m
ok
I see, the setup in #CE8SSJV3N is slightly non-standard
you are on the right path
👍 1
from what I can see, from the way the tests are run, I would recommend using 
--profile=+test,singularity
I'd recommend going in #C06TPECB95H to go forward with this discussion
j
Ok thanks !
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