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