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Hi all! Does the hic pipeline works for you at the...
# hic
e
Hi all! Does the hic pipeline works for you at the moment, the most recent release 2.1.0 ? I am just trying to set up nextflow for the first time, using all most recent versions of nextflow 25.10.3 and apptainer 1.4.5 and it is impossible to pull the containers. I’ve tried everything and made sure that my softwares and configs are correct.
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-[nf-core/hic] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK'

Caused by:
  Failed to pull singularity image
    command: apptainer pull  --name biocontainers-python-3.8.3.img.pulling.1764791847785 <docker://biocontainers/python:3.8.3> > /dev/null
    status : 255
    hint   : Try and increase apptainer.pullTimeout in the config (current is "20m")
    message:
      FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for <docker://biocontainers/python:3.8.3>: reading manifest 3.8.3 in <http://docker.io/biocontainers/python|docker.io/biocontainers/python>: requested access to the resource is denied
Is there a way to check if the urls for the images provided in the pipeline are correct? Does anyone else struggles with this too? Thank you!
s
The trick with apptainer is to use the singularity profile
As currently the apptainer profile tries to download docker images and convert them
for some reason your current command is missing the docker.registry, it should be trying to pull 
<docker://quay.io/biocontainers/python:3.8.3>
by default
it looks like this is set for docker and podman, but not for apptainer: https://github.com/nf-core/hic/blob/master/nextflow.config#L278
In the pipeline template it should be being set for apptainer too: https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/nextflow.config#L240
a
We should raise this as an issue
(speaking to Emilia in person at FOG)
Workaround: 1. Create a file called 
apptainer.config
with this:
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apptainer.registry = '<http://quay.io|quay.io>'
2. Run the pipeline: 
nextflow run nf-core/hic -c apptainer.config ...
Hmmm there hasn't been a release in 3 years. This needs some love.
💯 2
maybe try with 
-r dev
to use the development version
s
just set 
-profile singularity
, as apptainer generally comes with a symlink to say singularity = apptainer
a
I believe this didn't work for Emilia
e
Yes true, I tried all different containers and versions, it gets stuck with the same error, environments are not getting pulled at the very beginning of the pipeline
s
What is your command?
Does 
nextflow run nf-core/hic -profile test,singularity --outdir results
work for you?
nextflow run nf-core/hic -profile test,apptainer --outdir hic
fails for me, but the singularity version does work This is on a cluster with apptainer installed, but not singularity. Because 
singularity
is defined as a symlink to 
apptainer
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