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tower.yml
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tower.yml
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reports:
multiqc_report.html:
display: "MultiQC HTML report"
"**/fastqc/raw/*.html":
display: "A FastQC report containing quality metrics of raw reads in HTML format."
"**/fastqc/preprocessed/*.html":
display: "A FastQC report containing quality metrics of processed reads in HTML format."
"**/falco/raw/*.html":
display: "A Falco report containing quality metrics of raw reads in HTML format."
"**/falco/preprocessed/*.html":
display: "A Falco report containing quality metrics of processed reads in HTML format."
"**/fastp/*.html":
display: "Results in HTML format."
"**/fastp/*.log":
display: "A fastq log file."
"**/bracken/*_combined_reports.txt":
display: "Combined bracken results as output from Bracken's combine_bracken_outputs.py script."
"**/bracken/*/*.tsv":
display: "A TSV file containing per-sample summary of Bracken results with abundance information."
"**/bracken/*/*report_bracken_species.txt":
display: "A Kraken2 style report with Bracken abundance information."
"**/kraken2/kraken2_*_combined_reports.txt":
display: "A combined profile of all samples aligned to a given database (as generated by krakentools)."
"**/kraken2/*/*.report.txt":
display: "A Kraken2 report that summarises the fraction abundance, taxonomic ID, number of Kmers, taxonomic path of all the hits in the Kraken2 run for a given sample. Will be 6 column rather than 8 if --save_minimizers specified."
"**/krakenuniq/*/*.report.txt":
display: "A Kraken2-style report that summarises the fraction abundance, taxonomic ID, number of Kmers, taxonomic path of all the hits, with an additional column for k-mer coverage, that allows for more accurate distinguishing between false-positive/true-postitive hits."
"**/krakenuniq/*/*.classified.txt":
display: "An optional list of read IDs and the hits each read had against each database for a given sample."
"**/centrifuge/*_combined_reports.txt":
display: "A combined profile of all samples aligned to a given database (as generated by centrifuge-kreport)."
"**/centrifuge/*/*.centrifuge.report.txt":
display: "A classification report that summarises the taxonomic ID, the taxonomic rank, length of genome sequence, number of classified and uniquely classified reads."
"**/centrifuge/*/*.centrifuge.txt":
display: "A Kraken2-style report that summarises the fraction abundance, taxonomic ID, number of k-mers, taxonomic path of all the hits in the centrifuge run for a given sample."
"**/ganon/*_combined_reports.txt":
display: "A combined profile of all samples aligned to a given database (as generated by ganon table)."
"**/ganon/*/*.tre":
display: "A full ganon report file."
"**/ganon/*/*.rep":
display: "A Input 'repo' file from ganon classify."
"**/kaiju/*_combined_reports.txt":
display: "A combined profile of all samples aligned to a given database (as generated by kaiju2table)"
"**/kaiju/*/*.kaijutable.txt":
display: "Summarised Kaiju output with fraction abundance, taxonomic ID, number of reads, and taxonomic names (as generated by kaiju2table)"
"**/kmcp/*/*.profile":
display: "Tab-delimited format file with 17 columns."
"**/krona/*.html":
display: "Per-tool/per-database interactive HTML file containing hierarchical piecharts."
"**/metaphlan/*_combined_reports.txt":
display: "A combined profile of all samples aligned to a given database (as generated by metaphlan_merge_tables)."
"**/metaphlan/*/*.bowtie2out.txt":
display: "Bowtie2 alignment information (can be re-used for skipping alignment when re-running MetaPhlAn with different parameters)."
"**/metaphlan/*/*_profile.txt":
display: "A MetaPhlAn taxonomic profile including abundance estimates."
"**/motus/*_combined_reports.txt":
display: "A combined profile of all samples aligned to a given database (as generated by motus_merge)."
"**/motus/*/*.log":
display: "Standard error logging file containing summary statistics."
"**/motus/*/*.out":
display: "Results with taxonomic classification of each read."
"**/nanoq/*.stats":
display: "Summary report of reads statistics."
"**/nonpareil/*.png":
display: "PNG file of the Nonpareil curve."
"**/nonpareil/*.pdf":
display: "Plotted nonpareil curves in PDF format."
"**/porechop/*.log":
display: "Log file containing stdout information."
"**/porechop_abi/*.log":
display: "Log file containing stdout information."
"**/samtools/stats/*.stats":
display: "File containing samtools stats output."
"**/taxpasta/*tsv":
display: "Standardised taxon table containing multiple samples. The first column describes the taxonomy ID and the rest of the columns describe the read counts for each sample."