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Linting with nf-core tools 2.12.1 throws a warning when using multiple alias imports #2726

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TCLamnidis opened this issue Feb 2, 2024 · 1 comment
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@TCLamnidis
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Description of the bug

Using a multiple alias import like below, causes nf-core lint to throw a warning.

include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_MEM; SAMTOOLS_INDEX as SAMTOOLS_INDEX_BT2; SAMTOOLS_INDEX as SAMTOOLS_INDEX_MERGED_LANES } from '../../modules/nf-core/samtools/index/main'
Warning:
│ map   │ subworkflows/local/map.nf │ Included component 'SAMTOOLS_INDEX_MEM; SAMTOOLS_INDEX' versions are not    │
│       │                           │ added in main.nf                                                            |

In the example, the module name is read in wrong as SAMTOOLS_INDEX_MEM; SAMTOOLS_INDEX instead of SAMTOOLS_INDEX_MEM, so checks for versions and use of the module throw warnings.

Command used and terminal output

nf-core lint

System information

nf-core v2.12.1

@TCLamnidis TCLamnidis added the bug Something isn't working label Feb 2, 2024
@mashehu mashehu added this to the 2.13 milestone Feb 9, 2024
@mashehu mashehu self-assigned this Feb 16, 2024
mashehu added a commit to mashehu/tools that referenced this issue Feb 16, 2024
@mirpedrol
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Done with #2762

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