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Update usage.md, reformat test.config and modules.config
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3 changed files with 11 additions and 6 deletions
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@ -226,7 +226,7 @@ process {
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pattern: '*.txt'
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]
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ext.args = { "${meta.db_params}" }
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: CUSTOM_DUMPSOFTWAREVERSIONS {
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@ -252,6 +252,6 @@ process {
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pattern: '*.tsv'
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]
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ext.args = { "${meta.db_params}" }
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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}
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@ -24,14 +24,14 @@ params {
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// TODO nf-core: Give any required params for the test so that command line flags are not needed
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
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databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
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run_kraken2 = true
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run_malt = true
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run_metaphlan3 = true
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run_centrifuge = true
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perform_shortread_clipmerge = true
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perform_longread_clip = false
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perform_shortread_complexityfilter = true
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perform_shortread_hostremoval = true
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shortread_hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
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run_kaiju = true
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run_kraken2 = true
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run_malt = true
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run_metaphlan3 = true
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run_centrifuge = true
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}
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@ -86,6 +86,11 @@ Column specifications are as follows:
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> 💡 You can also specify the same database directory/file twice (ensuring unique `db_name`s) and specify different parameters for each database to compare the effect of different parameters during profiling.
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## Profilers
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- `kaiju`
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- The file `nodes.dmp` must be inside the database directory that is specified to `--databases` file
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## Running the pipeline
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The typical command for running the pipeline is as follows:
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