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nf-core download fails with version 3.8 of the pipeline #834

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JoseEspinosa opened this issue May 26, 2022 · 1 comment
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nf-core download fails with version 3.8 of the pipeline #834

JoseEspinosa opened this issue May 26, 2022 · 1 comment
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@JoseEspinosa
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JoseEspinosa commented May 26, 2022

Description of the bug

When using nf-core tools to download the pipeline and its containers the following error is raised:

INFO     Saving 'nf-core/rnaseq'                                                                                                                             download.py:160
          Pipeline revision: '3.8'
          Pull containers: 'singularity'
          Output directory: 'nf-core-rnaseq-3.8'
INFO     Downloading workflow files from GitHub                                                                                                              download.py:163
INFO     Downloading centralised configs from GitHub                                                                                                         download.py:167
ERROR    Cannot parse container string, skipping: ${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?              download.py:485

As discussed on slack with @drpatelh, the problem is the non-standard definition of containers to enable the star_align module deal with different STAR indexes (different versions), see here

Command used and terminal output

nf-core download rnaseq -r 3.8 -c singularity -x none

Relevant files

No response

System information

nf-core: 2.4.1
nf-core/rnaseq 3.8

@JoseEspinosa JoseEspinosa added the bug Something isn't working label May 26, 2022
drpatelh added a commit to drpatelh/nf-core-rnaseq that referenced this issue May 27, 2022
@drpatelh
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Will be fixed in #835

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