diff --git a/CHANGELOG.md b/CHANGELOG.md index e1250b27..f5f29517 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,7 +13,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#508](https://github.com/nf-core/taxprofiler/pull/508) Add `nanoq` as a filtering tool for nanopore reads (added by @LilyAnderssonLee) - [#511](https://github.com/nf-core/taxprofiler/pull/511) Add `porechop_abi` as an alternative adapter removal tool for long reads nanopore data (added by @LilyAnderssonLee) - [#512](https://github.com/nf-core/taxprofiler/pull/512) Update all tools to the latest version and include nf-test (updated by @LilyAnderssonLee & @jfy133) -- [#512](https://github.com/nf-core/taxprofiler/pull/532) Configure MultiQC to collapse stats of paired-read files into one line (by @jfy133) ### `Fixed` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 73256fa4..5b58b5db 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -24,9 +24,9 @@ report_section_order: nonpareil: order: 600 bbduk: - order: 500 - prinseqplusplus: order: 550 + prinseqplusplus: + order: 500 porechop: order: 450 porechop_abi: @@ -357,17 +357,6 @@ table_columns_name: reads_mapped: "Nr. Mapped Reads" reads_mapped_percent: "% Mapped Reads" -## Allow collapsing of file names with _R1/_R2 or _1/_2 at the end -table_sample_merge: - "Read 1": - - "_R1" - - type: regex - pattern: "[_.-][rR]?1$" - "Read 2": - - "_R2" - - type: regex - pattern: "[_.-][rR]?2$" - extra_fn_clean_exts: - "kraken2.report.txt" - ".txt" diff --git a/tower.yml b/tower.yml index 1101572e..d3296955 100644 --- a/tower.yml +++ b/tower.yml @@ -3,22 +3,16 @@ reports: display: "MultiQC HTML report" "**/fastqc/raw/*.html": display: "A FastQC report containing quality metrics of raw reads in HTML format." - "**/fastqc/raw/*.txt": - display: "A FastQC report containing quality metrics of raw reads in TXT format." "**/fastqc/preprocessed/*.html": display: "A FastQC report containing quality metrics of processed reads in HTML format." - "**/fastqc/preprocessed/*.txt": - display: "A FastQC report containing quality metrics of processed reads in TXT format." "**/falco/raw/*.html": display: "A Falco report containing quality metrics of raw reads in HTML format." - "**/falco/raw/*.txt": - display: "A Falco report containing quality metrics of raw reads in TXT format." "**/falco/preprocessed/*.html": display: "A Falco report containing quality metrics of processed reads in HTML format." - "**/falco/preprocessed/*.txt": - display: "A Falco report containing quality metrics of processed reads in TXT format." "**/fastp/*.html": - display: "A Log file in HTML format." + 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": @@ -27,11 +21,11 @@ reports: 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/*/*.kraken2.report.txt": + "**/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/*.krakenuniq.report.txt": + "**/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/*.krakenuniq.classified.txt": + "**/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)." @@ -41,19 +35,41 @@ reports: 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": + "**/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": + "**/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."