Compare multiple runs of long read sequencing data and alignments
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false]
filelist
:file
List of all the files you want to compare, they have to be all the same filetype (either fastq, fasta, bam or Nanopore sequencing summary)
*.{fastq,fq,fna,ffn,faa,frn,fa,fasta,txt,bam}
report_html
*NanoComp-report.html
Summary of all collected statistics
lengths_violin_html
*NanoComp_lengths_violin.html
Violin plot of the sequence lengths
log_length_violin_html
*NanoComp_log_length_violin.html
Violin plot of the sequence lengths, log function applied
n50_html
*NanoComp_N50.html
Bar plot of N50 sequence length per sample
number_of_reads_html
*NanoComp_number_of_reads.html
Bar plot of number of reads per sample
overlay_histogram_html
*NanoComp_OverlayHistogram.html
Histogram of all read lengths per sample
overlay_histogram_normalized_html
*NanoComp_OverlayHistogram_Normalized.html
Normalized histogram of all read lengths per sample
overlay_log_histogram_html
*NanoComp_OverlayLogHistogram.html
Histogram of all read lengths per sample, log function applied
overlay_log_histogram_normalized_html
*NanoComp_OverlayLogHistogram_Normalized.html
Normalized histogram of all read lengths per sample, log function applied
total_throughput_html
*NanoComp_total_throughput.html
Barplot comparing throughput in bases
quals_violin_html
*NanoComp_quals_violin.html
Violin plot of base qualities, only for bam, fastq and sequencing summary input
overlay_histogram_identity_html
*NanoComp_OverlayHistogram_Identity.html
Histogram of perfect reference identity, only for bam input
overlay_histogram_phredscore_html
*NanoComp_OverlayHistogram_PhredScore.html
Histogram of phred scores, only for bam input
percent_identity_violin_html
*NanoComp_percentIdentity_violin.html
Violin plot comparing perfect reference identity, only for bam input
active_pores_over_time_html
*NanoComp_ActivePoresOverTime.html
Scatter plot of active pores over time, only for sequencing summary input
cumulative_yield_plot_gigabases_html
*NanoComp_CumulativeYieldPlot_Gigabases.html
Scatter plot of cumulative yield, only for sequencing summary input
sequencing_speed_over_time_html
*NanoComp_sequencing_speed_over_time.html
Scatter plot of sequencing speed over time, only for sequencing summary input
stats_txt
*NanoStats.txt
txt file with basic statistics
versions_nanocomp
${task.process}
:string
The name of the process
nanocomp
The name of the tool
NanoComp --version 2>&1 | sed 's/^.*NanoComp //'
:eval
The expression to obtain the version of the tool
versions
