update multiqc config files to arrange preprocessing sections

nf-core · Sep 13, 2024 · b308a95 · b308a95
1 parent 488b5ab
commit b308a95
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diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -2,6 +2,27 @@ report_comment: >
   This report has been generated by the <a href="https://github.com/nf-core/bacass/tree/dev" target="_blank">nf-core/bacass</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/bacass/dev/docs/output" target="_blank">documentation</a>.
+
+
+max_table_rows: 10000
+
+module_order:
+  - fastqc:
+      name: "PREPROCESS: FastQC (raw reads)"
+      info: "This section of the report shows FastQC results for the raw reads before adapter trimming."
+      path_filters:
+        - "./fastqc/*.zip"
+  - fastqc:
+      name: "PREPROCESS: FastQC (trimmed reads)"
+      info: "This section of the report shows FastQC results for the processed and trimmed reads."
+      path_filters:
+        - "./fastqc_trim/*.zip"
+  - fastp:
+      name: "PREPROCESS: fastp (adapter trimming)"
+      info: "This section of the report shows fastp results for reads after adapter and quality trimming."
+      path_filters:
+        - "./fastp/*.json"
+
 report_section_order:
   "nf-core-bacass-methods-description":
     order: -1000

diff --git a/assets/multiqc_config_hybrid.yml b/assets/multiqc_config_hybrid.yml
@@ -28,6 +28,11 @@ module_order:
       info: "This section of the report shows FastQC results for the raw reads before adapter trimming."
       path_filters:
         - "./fastqc/*.zip"
+  - fastqc:
+      name: "PREPROCESS: FastQC (trimmed reads)"
+      info: "This section of the report shows FastQC results for the processed and trimmed reads."
+      path_filters:
+        - "./fastqc_trim/*.zip"
   - fastp:
       name: "PREPROCESS: fastp (adapter trimming)"
       info: "This section of the report shows fastp results for reads after adapter and quality trimming."

diff --git a/assets/multiqc_config_short.yml b/assets/multiqc_config_short.yml
@@ -25,6 +25,11 @@ module_order:
       info: "This section of the report shows FastQC results for the raw reads before adapter trimming."
       path_filters:
         - "./fastqc/*.zip"
+  - fastqc:
+      name: "PREPROCESS: FastQC (trimmed reads)"
+      info: "This section of the report shows FastQC results for the processed and trimmed reads."
+      path_filters:
+        - "./fastqc_trim/*.zip"
   - fastp:
       name: "PREPROCESS: fastp (adapter trimming)"
       info: "This section of the report shows fastp results for reads after adapter and quality trimming."