Merge pull request #534 from nf-core/tower_yml

Check if all small files are included in tower.yml

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`
 

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"

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."