Comments (2)
grst
commented on June 24, 2024
afaik nf-core doesn't host any singularity images for custom containers and relies entirely on singularity's docker-to-singularity conversion (This is different for the containers provided by Biocontainers, where galaxyhub hosts img files).
In principle, the container we have should be alright, as it runs successfully on CI. Maybe it was just a temporary issue with the download. Have you tried cleaning your docker/singularity caches and trying again?
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rhodesch
commented on June 24, 2024
Ah, yep that seemed to fix it. After clearing the caches, the seurat image (quay.io/nf-core/seurat:4.3.0) did docker-to-singularity conversion correctly. Entire workflow completed successfully. Thanks for the feedback. Closing issue.
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Related Issues (20)
- Switch to use central nf-core modules
- Autorenaming of files in new cellranger module leads to erroneous renaming of sample ID containing R1 in it, like in SRR ids HOT 2
- Multi-omics support (meta-issue) HOT 1
- exceeded running time limit (8h) HOT 3
- Crash when specifying existing --star_index using star aligner HOT 6
- Bump up kb to 0.28.0 HOT 3
- Use nf-validation plugin HOT 1
- Update or remove universc HOT 8
- Tests for cellranger-arc HOT 1
- MuData conversion
- Utilize central modules for simpleaf workflow HOT 1
- The cellrangerarc cannot start successfully HOT 2
- When aligner is cellrangerarc the step MTX_TO_SEURAT failed HOT 3
- Avoid error on unknown headers in input.csv HOT 4
- Issues with samplesheet.csv as well as additional columns in the samplesheet HOT 3
- Samplesheet Check Bug HOT 1
- Flexible input read format with STARsolo with --soloBarcodeReadLength HOT 1
- Make scrnaseq pipeline v2.5.1 compatible with nextflow v22.04.0 HOT 1
- Clean up mtx conversion code
- Update to the latest simpleaf HOT 3
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