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Include NCBI_id, read counts and mgc arguments in motus
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3 changed files with 7 additions and 0 deletions
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@ -446,6 +446,7 @@ process {
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}
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}
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withName: MOTUS_PROFILE {
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withName: MOTUS_PROFILE {
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ext.args = { [ params.save_ncbi_id ? "-p" : "", params.save_read_counts ? "-c" : "", params.save_mgc_counts ? "-M ${task.ext.prefix}.mgc" : "" ].join(',').replaceAll(','," ") }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/motus/${meta.db_name}/" },
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path: { "${params.outdir}/motus/${meta.db_name}/" },
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@ -39,5 +39,8 @@ params {
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run_centrifuge = false
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run_centrifuge = false
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run_diamond = false
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run_diamond = false
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run_motus = true
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run_motus = true
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save_mgc_counts = true
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save_ncbi_id = true
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save_read_counts = true
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run_profile_standardisation = true
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run_profile_standardisation = true
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}
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}
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@ -140,6 +140,9 @@ params {
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// mOTUs
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// mOTUs
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run_motus = false
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run_motus = false
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save_mgc_counts = false
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save_ncbi_id = false
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save_read_counts = false
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// krona
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// krona
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run_krona = false
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run_krona = false
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