Update examples for v1.25 (#105)

* Group general stats samples

* Update to use generalstats_* and module_order

* Update configs

* Update examples

* Update configs

* Update option name

* Update reports

public/examples/bs-seq/multiqc_config.yaml

@@ -0,0 +1,14 @@
+module_order:
+  - "bismark"
+  - "cutadapt"
+  - "fastqc":
+      name: "FastQC: trimmed"
+      anchor: "fqc_trimmed"
+      path_filters:
+        - "*_trimmed*"
+  - "fastqc":
+      name: "FastQC: raw"
+      anchor: "fqc_raw"
+      path_filters_exclude:
+        - "*_trimmed*"
+      generalstats: false

public/examples/hi-c/multiqc_config.yaml

@@ -1,4 +1,14 @@
-extra_fn_clean_exts:
-    - .C8DRAANXX
-    - .C8LFMANXX
-    - .C8H0KANXX
+extra_fn_clean_trim:
+  - ".r_1_2"
+  - ".s_1"
+  - ".s_2"
+  - ".s_3"
+  - ".C8DRAANXX"
+  - ".C8LFMANXX"
+  - ".C8H0KANXX"
+
+# Search patterns for grouping paired samples in general stats (e.g. FastQ R1/R2)
+# Affects the modules that support it (e.g. fastqc, fastp)
+table_sample_merge:
+  "R1": ".r_1"
+  "R2": ".r_2"

public/examples/ngi-rna/multiqc_config.yaml

@@ -1,8 +1,5 @@
 template: 'ngi'
 disable_ngi: false
-extra_fn_clean_exts:
-    - '_1.'
-    - '_2.'
 report_section_order:
     ngi-rnaseq-module:
         order: -1000
@@ -12,3 +9,16 @@ report_comment: >
     This report has been generated by the <a href="https://github.com/SciLifeLab/NGI-RNAseq" target="_blank">NGI-RNAseq</a>
     analysis pipeline. Some additional functionality is added to the report using the
     <a href="https://github.com/ewels/MultiQC_NGI" target="_blank">MultiQC_NGI plugin</a>.
+
+extra_fn_clean_exts:
+    - '_trimming_report.txt'
+
+# Search patterns for grouping paired samples in general stats (e.g. FastQ R1/R2)
+# Affects the modules that support it (e.g. fastqc, fastp)
+table_sample_merge:
+  "R1":
+    - type: regex
+      pattern: "_1$"
+  "R2":
+    - type: regex
+      pattern: "_2$"

public/examples/rna-seq/multiqc_config.yaml

@@ -1,3 +1,19 @@
-extra_fn_clean_exts:
-    - _1
-    - _2
+# Search patterns for grouping paired samples in general stats (e.g. FastQ R1/R2)
+# Affects the modules that support it (e.g. fastqc, fastp)
+table_sample_merge:
+  "R1": "_1"
+  "R2": "_2"
+
+module_order:
+  - "cutadapt"
+  - "fastqc":
+      name: "FastQC: trimmed"
+      anchor: "fqc_trimmed"
+      path_filters:
+        - "*_val*"
+  - "fastqc":
+      name: "FastQC: raw"
+      anchor: "fqc_raw"
+      path_filters_exclude:
+        - "*_val*"
+      generalstats: false

public/examples/wgs/multiqc_config.yaml

@@ -1,14 +1,20 @@
 fn_ignore_files:
     - '*.indel.annotated.vcf.gz.snpEff.summary.csv'
+
 extra_fn_clean_exts:
-    - .clean
-    - _S1
-    - _S2
-    - _S3
-    - _S4
-    - _S5
-    - _S6
-    - .AHJHNYCCXX
+    - ".clean"
+    - ".AHJHNYCCXX"
+    - pattern: _S\d_L00\d
+      type: regex
+
+extra_fn_clean_trim:
+    - "_001"
+
+# Search patterns for grouping paired samples in general stats (e.g. FastQ R1/R2)
+# Affects the modules that support it (e.g. fastqc, fastp)
+table_sample_merge:
+  "R1": "_R1"
+  "R2": "_R2"
 
 table_columns_visible:
     FastQC: