Template update #71
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Template update #71
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maxibor
requested changes
Mar 17, 2025
conf/test_full.config
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| sam2lca_identity = 0.8 | ||
| sam2lca_acc2tax = 'adnamap' //'adnamap' for db build, 'nucl' for default | ||
| kraken2_db = 'https://github.com/nf-core/test-datasets/raw/coproid/kraken.tar.gz' | ||
| sp_sources = 'https://github.com/nf-core/test-datasets/raw/coproid/sourcepredict/test_sources.csv' | ||
| sp_labels = 'https://github.com/nf-core/test-datasets/raw/coproid/sourcepredict/test_labels.csv' | ||
| sp_sources = 'https://raw.githubusercontent.com/maxibor/sourcepredict/master/data/modern_gut_microbiomes_sources.csv' |
There was a problem hiding this comment.
These will need to be hosted on the coproID repository itself. Or in the nf-core test datasets repo.
conf/test_full.config
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| sp_sources = 'https://github.com/nf-core/test-datasets/raw/coproid/sourcepredict/test_sources.csv' | ||
| sp_labels = 'https://github.com/nf-core/test-datasets/raw/coproid/sourcepredict/test_labels.csv' | ||
| sp_sources = 'https://raw.githubusercontent.com/maxibor/sourcepredict/master/data/modern_gut_microbiomes_sources.csv' | ||
| sp_labels = 'https://raw.githubusercontent.com/maxibor/sourcepredict/master/data/modern_gut_microbiomes_labels.csv' |
nextflow.config
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| // nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs | ||
| includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/demo.config" : "/dev/null" | ||
| // Load nf-core/coproid custom profiles from different institutions. | ||
| // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs |
main.nf
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| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| */ | ||
|
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| // TODO nf-core: Remove this line if you don't need a FASTA file |
maxibor
approved these changes
Mar 19, 2025
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nextflow run . -profile test,singularity).nf-core lint .).docsis updatedCHANGELOG.mdis updatedREADME.mdis updatedLearn more about contributing: CONTRIBUTING.md