Fastp: search pattern: look at content instead of file name

.github/workflows/multiqc.yml

@@ -127,7 +127,7 @@ jobs:
         if: matrix.python-version == env.latest_python
         run: |
           cd test_data
-          multiqc -m star test_data/data/modules/star --no-report -n no-report
+          multiqc -m star data/modules/star --no-report -n no-report
           if [[ -f no-report.html ]]; then
             echo "Running with the --no-report flag should not produce an HTML" >&2
             exit 1

.gitignore

@@ -1,8 +1,10 @@
-
-# MultiQC files
+# MultiQC results
 multiqc_config.yaml
 multiqc_report.html
 multiqc_data
+examples/
+result/
+tmp/
 
 # Generated by the CI tests
 full_report.html
@@ -22,8 +24,6 @@ eggs/
 *.egg
 build/
 dist/
-tmp/
-examples/
 
 # OS generated files
 .DS_Store
@@ -40,9 +40,11 @@ runTest.sh
 # Prevent direnv from cluttering the repo
 .envrc
 .direnv/*
-/result
-venv
 
+# Typical name for virtualenv
+venv/
+
+# Related repos
 test_data/
 website/
 usage/

CHANGELOG.md

@@ -14,9 +14,9 @@
 - When trying indexing lists/dicts while accessing config parameters, catch TypeError as well ([#2211](https://github.com/ewels/MultiQC/pull/2211))
 - Fix running `--no-report` ([#2212](https://github.com/ewels/MultiQC/pull/2212))
 - Add `.cram` to sample name cleaning defaults ([#2209](https://github.com/ewels/MultiQC/pull/2209))
+- Fastp: search pattern: look at content instead of file name ([#2213](https://github.com/ewels/MultiQC/pull/2213))
 - Custom content plot: do not assume first row are samples ([#2208](https://github.com/ewels/MultiQC/pull/2208))
 
-
 ### New Modules
 
 ### Module updates

docs/modules/fastp.md

@@ -6,7 +6,7 @@ description: >
 ---
 
 The Fastp module parses results generated by
-[Fastp](https://github.com/OpenGene/fastp). Fastp can simply go through all fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of paramaters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.
+[Fastp](https://github.com/OpenGene/fastp). Fastp can simply go through all fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.
 
 By default, the module generates the sample names based on the input FastQ file names in
 the command line used by fastp. If you prefer, you can tell the module to use

multiqc/utils/search_patterns.yaml

@@ -321,7 +321,9 @@ dragen_fastqc:
 eigenstratdatabasetools:
   fn: "*_eigenstrat_coverage.json"
 fastp:
-  fn: "*fastp.json"
+  fn: "*.json"
+  contents: '"before_filtering": {'
+  num_lines: 3
 fastq_screen:
   fn: "*_screen.txt"
 fastqc/data: