Docs

CHANGELOG.md

@@ -10,7 +10,7 @@
 
 - **fastp**: correctly parse sample name from --in1/--in2 command. Prefer file name if not `fastp.json`; fallback to file name when error ([#2139](https://github.com/ewels/MultiQC/pull/2139))
 - **Picard**: Generalize to directly support Sentieon and Parabricks outputs ([#2110](https://github.com/ewels/MultiQC/pull/2110))
-- **Sentieon**: Removed the module in favour of directly supporting the outputs in the **Picard** module. Note that `-m sentieon` will no longer work. The exported plos and data files will be prefixed as `picard` rather than `sentieon` ([#2110](https://github.com/ewels/MultiQC/pull/2110))
+- **Sentieon**: Removed the module in favour of directly supporting the outputs in the **Picard** module. Note that `-m sentieon` will no longer work. The exported plot and data files will be prefixed as `picard` rather than `sentieon` ([#2110](https://github.com/ewels/MultiQC/pull/2110))
 
 ## [MultiQC v1.17](https://github.com/ewels/MultiQC/releases/tag/v1.17) - 2023-10-17
 

docs/modules/picard.md

@@ -205,24 +205,21 @@ significantly.
 
 ### Sample names
 
-Historically, MultiQC supported Picard tools QC outputs merged together into one file
-from different samples and tools. In order to handle this correctly, MultiQC needed
-to take the sample name elsewhere rather than the file name, so it tried to parse
-the command line recorded in the output header. E.g., `GcBias` tool output contains
-a header line like this:
+MultiQC supports outputs from multiple runs of a Picard tool merged together into one
+file. In order to handle multiple sample data in on file correctly, MultiQC needed
+to take the sample name elsewhere rather than the file name. For this reason, MultiQC
+attempts to parse the command line recorded in the output header. For example, an
+output from the `GcBias` tool contains a header line like this:
 
 ```
 # net.sf.picard.analysis.CollectGcBiasMetrics REFERENCE_SEQUENCE=/reference/genome.fa
 INPUT=/alignments/P0001_101/P0001_101.bam OUTPUT=P0001_101.collectGcBias.txt ...
 ```
 
-So MultiQC would extract the BAM file name that goes after `INPUT=` and take
-`P0001_101` as a sample name.
-
-For legacy reasons, this approach is still the default (with a fallback to the file
-name if the command cannot be found or parsed), however, it is possible to switch
-to using the file names as sample names by default. To do so, use the following
-config option:
+MultiQC would extract the BAM file name that goes after `INPUT=` and take `P0001_101`
+as a sample name. If MultiQC fails to parse the command line for any reason, it will
+fall back to using the file name. It is also possible to force using the file names
+as sample names by enabling the following config option:
 
 ```yaml
 picard_config: