update documentation about multiQC output

nf-core · Aug 3, 2023 · 4843f58 · 4843f58
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diff --git a/docs/images/mqc_qc_of_indels.png b/docs/images/mqc_qc_of_indels.png
diff --git a/docs/images/mqc_read_processing_summary.png b/docs/images/mqc_read_processing_summary.png
diff --git a/docs/images/mqc_type_of_edition.png b/docs/images/mqc_type_of_edition.png
diff --git a/docs/output/targeted.md b/docs/output/targeted.md
@@ -250,13 +250,13 @@ This section contains the final output of the pipeline. It contains information
 
 - `cigar/`
   - `*_cutSite.json`: Contains the protospacer cut site position in the reference.
-  - `*_edition.html`: Interactive pie chart with the percentage of edition types. Reads are classified between WT (without an edit) and indels. Indels are divided between deletions, insertions and delins (deletion + insertion). Deletions and insertions can be out of frame or in frame.
+  - `*_edition.html`: Interactive pie chart with the percentage of edition types. Reads are classified between WT (without an edit) and indels. Indels are divided between deletions, insertions and delins (deletion + insertion). Deletions and insertions can be out of frame or in frame. A similar plot can be visualised in the MultiQC report.
     ![Test sample hCas9-AAVS1-a edition plot](../images/hCas9-AAVS1-a_edition.png)
   - `*_edits.csv`: Table containing the number of reads classified to each edition type. Contains the data visualized in the pie chart.
   - `*_indels.csv`: Table containing information of all reads. Edit type, edit start and length, if the edition happens above the error rate, if it's located into the common edit window, the frequency, the percentage, the pattern, surrounding nucleotides in case of insertions, the protospacer cut site, the sample id, number of aligned reads and number of reads with and without a template modification.
-  - `*_QC-indels.html`: Interactive pie chart with information about aligned reads. Reads are classified between WT and containing indels. Both types are classified between passing the filtering steps or not. Indel reads passing the filtering steps are divided in reads with a modification above the error rate and located in the common edit window, above the error rate but not in the edit region, vice versa, or any of those conditions.
+  - `*_QC-indels.html`: Interactive pie chart with information about aligned reads. Reads are classified between WT and containing indels. Both types are classified between passing the filtering steps or not. Indel reads passing the filtering steps are divided in reads with a modification above the error rate and located in the common edit window, above the error rate but not in the edit region, vice versa, or any of those conditions. A similar plot can be visualised in the MultiQC report.
     ![Test sample hCas9-AAVS1-a QC indels plot](../images/hCas9-AAVS1-a_QC-indels.png)
-  - `*_reads.html`: Interactive pie chart with percentage of the number of raw reads, reads merged with Pear, reads passing quality filters and UMI clustered reads.
+  - `*_reads.html`: Interactive pie chart with percentage of the number of raw reads, reads merged with Pear, reads passing quality filters and UMI clustered reads. A table with this information can be visualised in the MultiQC report.
     ![Test sample hCas9-AAVS1-a reads plot](../images/hCas9-AAVS1-a_reads.png)
   - `*_subs-perc.csv`: Table containing the percentage of each nucleotide found for each reference position.
 
@@ -278,6 +278,17 @@ This section contains the final output of the pipeline. It contains information
 
 Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
 
+`multiqc_report.html` contains statistics for FastQC and Cutadapt modules. It also contains a table with statistics about read processing (equivalent to `<outdir>/cigar/*_reads.html` plots), and plots summarising the found editions (equivalent to `<outdir>/cigar/*_edition.html` plots) and indel quality filters (equivalent to `<outdir>/cigar/*_QC-indels.html` plots).
+
+<details markdown="1">
+<summary>Custom sections example</summary>
+
+![Read processing table](../images/mqc_read_processing_summary.png)
+![Type of edition plot](../images/mqc_type_of_edition.png)
+![QC of indels plot](../images/mqc_qc_of_indels.png)
+
+</details>
+
 ## Pipeline information
 
 <details markdown="1">