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Remove warning when launching test profile #74

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maxulysse opened this issue Nov 4, 2024 · 0 comments
Open

Remove warning when launching test profile #74

maxulysse opened this issue Nov 4, 2024 · 0 comments
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enhancement New feature or request

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@maxulysse
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Description of feature

This is coming from nf-test, but we have similar output from the CLI

    > WARN: The following invalid input values have been detected:
    > 
    > * --modules_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/modules/
    > * --test_data: [sarscov2:[genome:[genome_fasta:https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta, genome_fasta_gz:https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta.gz, genome_fasta_fai:https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta.fai, genome_fasta_txt_zst:https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta.txt.zst, genome_dict:https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.dict, genome_gff3:https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.gff3, genome_gff3_gz:https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.gff3.gz, genome_gtf:https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/ge
    > 
    > 
    > WARN: Found the following unidentified headers in /nf-core/test-datasets/riboseq/samplesheet/samplesheet.csv:
    > 	- sample_description
    > 	- pair
    > 	- treatment
    > WARN: Found the following unidentified headers in /nf-core/test-datasets/riboseq/samplesheet/samplesheet.csv:
    > 	- sample_description
    > 	- pair
    > 	- treatment
    > WARN: Access to undefined parameter `salmon_index` -- Initialise it to a default value eg. `params.salmon_index = some_value`
    > WARN: Access to undefined parameter `sortmerna_index` -- Initialise it to a default value eg. `params.sortmerna_index = some_value`
    > WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
@maxulysse maxulysse added the enhancement New feature or request label Nov 4, 2024
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