Fixed broken links

HUPO-PSI · Jul 10, 2024 · ac44454 · ac44454
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diff --git a/.github/workflows/linkcheck.yml b/.github/workflows/linkcheck.yml
@@ -15,6 +15,6 @@ jobs:
     - run: pip3 install linkchecker
     - name: Link Checker
       id: link-report
-      run: linkchecker -ofailures https://hupo-psi.github.io/mzQC/
+      run: linkchecker -ofailures --ignore-url="*.md" https://hupo-psi.github.io/mzQC/
     - name: Get the result
       run: echo linkchecker/failures
diff --git a/docs/pages/use-case-stories/mzQC_for_analytical_chemists.md b/docs/pages/use-case-stories/mzQC_for_analytical_chemists.md
@@ -17,7 +17,7 @@ While many of the papers describing QC metrics for mass spectrometry have been b
 4. What fraction of MS/MS scans came from +2 precursor ions?
     _63.67%_
 
-Naturally, it’s much easier if you use software to produce these values.  In this case, I am using values reported by the QuaMeter software[1] in “IDFree” mode.
+Naturally, it’s much easier if you use software to produce these values.  In this case, I am using values reported by the QuaMeter software [1](#bumbershoot) in “IDFree” mode.
 
 
 ## Format metrics in JSON
@@ -124,5 +124,5 @@ Choosing JSON rather than XML is intended to reduce the effort required to write
 
 
 ---
-[1]: Bumbershoot from proteowizard.sourceforge.net.  X. Wang et al. Anal. Chem.. (2014) 86: 2497
+<a id="bumbershoot">[1]</a>: Bumbershoot from proteowizard.sourceforge.net.  X. Wang et al. Anal. Chem.. (2014) 86: 2497
 Original draft: https://docs.google.com/document/d/16b1n_LXYWsxLK2PQfXWj_WvtiwJOXu2EZx1Q8WzZNlc/edit#
diff --git a/docs/pages/use-cases.md b/docs/pages/use-cases.md
@@ -6,13 +6,13 @@ permalink: /use-cases/
 This page should give you a (non-exclusive) overview over the use cases covered by mzQC:
 
 ## Handover Format
-It is easy with **mzQC** to get relevant QC info, easy to put your data into context (of measurement realities). That makes it a preferred medium to handover quality information. Read more about it in [mzQC at a glance](at-a-glance/) and explore [a small mzQC example](../examples/individual-runs/).
+It is easy with **mzQC** to get relevant QC info, easy to put your data into context (of measurement realities). That makes it a preferred medium to handover quality information. Read more about it in [mzQC at a glance](at-a-glance/) and explore [a small mzQC example](../examples/intro_run/).
 
 ## Quality Reports
 With JSON at its core, mzQC follows a '_works online, works everywhere_' approach. Even for single spectra, as we show with the [universal spectrum identifier example](../examples/USI-example/).
 
 ## Archival
-The format is an optimal QC tool for the analytical chemist and instrument operators keeping track (and archive) instrument performance. Read on with an [introduction to mzQC for anlytical chemists](analytical-chemists/) or explore our [QC sample example](../examples/qc-sample-run/). You can even embed mzQC in mzML, should you choose to. [View an example here](../examples/mzML-mzQC/).
+The format is an optimal QC tool for the analytical chemist and instrument operators keeping track (and archive) instrument performance. Read on with an [introduction to mzQC for anlytical chemists](analytical-chemists/) or explore our [QC sample example](../examples/QC2-sample-example/). You can even embed mzQC in mzML, should you choose to. [View an example here](../examples/mzml-mzqc-example/).
 
 ## Common currency
 With mzQC for archival, quality reports, and as handover format, [mzQC can serve as a common currency](mzQC-common-currency/) for data repositories, journals, and collaborators.