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Added PhiX and Lambda references to summary #89

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Aug 13, 2020
Merged

Added PhiX and Lambda references to summary #89

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2 changes: 2 additions & 0 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -300,13 +300,15 @@ summary['Adapter reverse'] = params.adapter_reverse
summary['Mean quality'] = params.mean_quality
summary['Trimming quality'] = params.trimming_quality
summary['Keep phix reads'] = params.keep_phix ? 'Yes' : 'No'
if (!params.keep_phix) summary['PhiX reference'] = params.phix_reference
if (params.host_genome) summary['Host Genome'] = params.host_genome
else if(params.host_fasta) summary['Host Fasta Reference'] = params.host_fasta
if (params.host_genome || params.host_fasta) summary['Host removal setting'] = params.host_removal_verysensitive ? 'very-sensitive' : 'sensitive'

if (params.manifest) {
summary['Skip adapter trimming'] = params.skip_adapter_trimming ? 'Yes' : 'No'
summary['Keep lambda reads'] = params.keep_lambda ? 'Yes' : 'No'
if (!params.keep_lambda) summary['Lambda reference'] = params.lambda_reference
summary['Long reads min length'] = params.longreads_min_length
summary['Long reads keep percent'] = params.longreads_keep_percent
summary['Long reads length weight'] = params.longreads_length_weight
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