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Include NCBI_id, read counts and mgc arguments in motus

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sofstam 2022-11-29 11:07:29 +01:00
parent f8b769a8f0
commit 49af33f68e
3 changed files with 7 additions and 0 deletions
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1
conf/modules.config
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@ -446,6 +446,7 @@ process {
} }
withName: MOTUS_PROFILE { withName: MOTUS_PROFILE {
ext.args = { [ params.save_ncbi_id ? "-p" : "", params.save_read_counts ? "-c" : "", params.save_mgc_counts ? "-M ${task.ext.prefix}.mgc" : "" ].join(',').replaceAll(','," ") }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" } ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/motus/${meta.db_name}/" }, path: { "${params.outdir}/motus/${meta.db_name}/" },

3
conf/test_motus.config
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@ -39,5 +39,8 @@ params {
run_centrifuge = false run_centrifuge = false
run_diamond = false run_diamond = false
run_motus = true run_motus = true
save_mgc_counts = true
save_ncbi_id = true
save_read_counts = true
run_profile_standardisation = true run_profile_standardisation = true
} }

3
nextflow.config
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@ -140,6 +140,9 @@ params {
// mOTUs // mOTUs
run_motus = false run_motus = false
save_mgc_counts = false
save_ncbi_id = false
save_read_counts = false
// krona // krona
run_krona = false run_krona = false