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I'm trying to pull a docker container with singularity in a nextflow pipeline. After updating singularity to version 4.0.2 I'm having issues in pulling the container.
In the singularity cachedir, I found the container with the .img extension, but it seems singularity doesn't recognize it. Maybe it is looking for a simg extension?
If I move in the singularity directory and run singularity shell or singularity exec on the img the container works perfectly.
Steps to reproduce this behavior
docker container that I'm trying to pull in the pipeline is the following: docker://staphb/seqtk:1.3
Version of Singularity:
What version of Singularity are you using? Run:
Expected behavior
I'm trying to pull a docker container with singularity in a nextflow pipeline. After updating singularity to version 4.0.2 I'm having issues in pulling the container.
Actual behavior
Command error:
ERROR: Unknown image format/type: /home/users/scratch/work/singularity/staphb-seqtk.img
In the singularity cachedir, I found the container with the .img extension, but it seems singularity doesn't recognize it. Maybe it is looking for a simg extension?
If I move in the singularity directory and run singularity shell or singularity exec on the img the container works perfectly.
Steps to reproduce this behavior
docker container that I'm trying to pull in the pipeline is the following: docker://staphb/seqtk:1.3
What OS/distro are you running
How did you install Singularity
Singularity was installed on HPC.
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