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Download: Bugfix for AttributeError: 'ContainerError' object has no attribute 'absoluteURI' #2543

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merged 3 commits into from
Dec 9, 2023
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Download: Bugfix for AttributeError: 'ContainerError' object has no attribute 'absoluteURI' #2543

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83883b3
Bugfix for AttributeError: 'ContainerError' object has no attribute '…
MatthiasZepper Nov 27, 2023
3599a96
Small documentation improvement for --tower flag.
MatthiasZepper Nov 27, 2023
13edd4f
Merge branch 'dev' into Download_bugfix_absoluteURI
mashehu Dec 4, 2023
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,10 @@
- Use closure for multiqc ext.args ([#2509](https://github.com/nf-core/tools/pull/2509))
- Fix how the modules template references the conda environment file ([#2540](https://github.com/nf-core/tools/pull/2540))

### Download

- Bugfix for AttributeError: 'ContainerError' object has no attribute 'absoluteURI' ([#2543](https://github.com/nf-core/tools/pull/2543)).

### Linting

- Fix incorrectly failing linting if 'modules' was not found in meta.yml ([#2447](https://github.com/nf-core/tools/pull/2447))
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -433,7 +433,7 @@ If the download speeds are much slower than your internet connection is capable
Subsequently, the `*.git` folder can be moved to it's final destination and linked with a pipeline in _Tower_ using the `file:/` prefix.

:::tip
Also without access to Tower, pipelines downloaded with the `--tower` flag can be run: `nextflow run -r 2.5 file:/path/to/pipelinedownload.git`. Downloads in this format allow you to include multiple revisions of a pipeline in a single file, but require that the revision (e.g. `-r 2.5`) is always explicitly specified.
Also without access to Tower, pipelines downloaded with the `--tower` flag can be run if the _absolute_ path is specified: `nextflow run -r 2.5 file:/path/to/pipelinedownload.git`. Downloads in this format allow you to include multiple revisions of a pipeline in a single file, but require that the revision (e.g. `-r 2.5`) is always explicitly specified.
:::

## Pipeline software licences
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4 changes: 2 additions & 2 deletions nf_core/download.py
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Expand Up @@ -1081,7 +1081,7 @@ def get_singularity_images(self, current_revision=""):
continue
except ContainerError.ImageNotFound as e:
# Try other registries
if e.error_log.absoluteURI:
if e.error_log.absolute_URI:
break # there no point in trying other registries if absolute URI was specified.
else:
continue
Expand All @@ -1092,7 +1092,7 @@ def get_singularity_images(self, current_revision=""):
# Try other registries
log.error(e.message)
log.error(e.helpmessage)
if e.error_log.absoluteURI:
if e.error_log.absolute_URI:
break # there no point in trying other registries if absolute URI was specified.
else:
continue
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