Samtools: super awesome update

.github/workflows/changelog.py

@@ -24,7 +24,7 @@
 import sys
 from pathlib import Path
 
-REPO_URL = "https://github.com/ewels/MultiQC"
+REPO_URL = "https://github.com/vladsavelyev/MultiQC"
 MODULES_DIR = "multiqc/modules"
 
 # Assumes the environment is set by the GitHub action.

.github/workflows/changelog.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
     if: >
-      github.repository_owner == 'ewels' &&
+      github.repository_owner == 'vladsavelyev' &&
       github.event.issue.pull_request &&
       startsWith(github.event.comment.body, '@multiqc-bot changelog')
 
@@ -27,9 +27,9 @@ jobs:
       # Action runs on the issue comment, so we don't get the PR by default.
       # Use the GitHub CLI to check out the PR:
       - name: Checkout Pull Request
-        run: gh pr checkout ${{ github.event.issue.number }}
         env:
-          GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+          GH_TOKEN: ${{ secrets.MQC_BOT_GITHUB_TOKEN }}
+        run: gh pr checkout ${{ github.event.issue.number }}
 
       - uses: actions/setup-python@v3
 
@@ -38,6 +38,7 @@ jobs:
           PR_TITLE: ${{ github.event.issue.title }}
           PR_NUMBER: ${{ github.event.issue.number }}
           COMMENT: ${{ github.event.comment.body }}
+          GH_TOKEN: ${{ secrets.MQC_BOT_GITHUB_TOKEN }}
         run: python ${GITHUB_WORKSPACE}/.github/workflows/changelog.py
 
       - name: Check if CHANGELOG.md actually changed

CHANGELOG.md

@@ -11,6 +11,12 @@
 
 ### Module updates
 
+- **NanoStat**: Support new format ([#1997](https://github.com/ewels/MultiQC/pull/1997)).
+- **RSeQC**: Fix `max() arg is an empty sequence` error ([#1985](https://github.com/ewels/MultiQC/issues/1985))
+- **RSeQC**: Fix division by zero on all-zero input ([#2040](https://github.com/ewels/MultiQC/pull/2040))
+- **Samtools**: Flagstat: add random change ([#23](https://github.com/ewels/MultiQC/pull/23))
+- **Samtools**: Stats: fix "Percent Mapped" plot when samtools was run with read filtering ([#1972](https://github.com/ewels/MultiQC/pull/1972))
+
 ## [MultiQC v1.16](https://github.com/ewels/MultiQC/releases/tag/v1.16) - 2023-09-22
 
 ### Highlight: Software versions

multiqc/modules/samtools/flagstat.py

@@ -1,6 +1,8 @@
 # coding: utf-8
 """ MultiQC submodule to parse output from Samtools flagstat """
 
+# CHANGED
+
 import logging
 import re
 from collections import OrderedDict