Automatic confluence update

.gitlab-ci.yml

@@ -0,0 +1,33 @@
+stages:
+  - generate
+  - publish
+
+generate-job:
+  stage: generate
+  tags:
+    - autoscale
+  rules:
+    - if: $CI_COMMIT_BRANCH == "devel" || $CI_COMMIT_BRANCH == "master"
+        changes:
+          - docs/**/*
+  variables:
+    REPO_METADATA_FILE: docs/includes/repo-metadata.md
+  script: >
+    echo "Created from: [$CI_PROJECT_NAMESPACE / $CI_PROJECT_TITLE]($CI_PROJECT_URL) Version: $(git describe --always)" > "$REPO_METADATA_FILE"
+  artifacts:
+    paths:
+      - "$REPO_METADATA_FILE"
+
+mark-job:
+  stage: publish
+  rules:
+    - if: $CI_COMMIT_BRANCH == "devel" || $CI_COMMIT_BRANCH == "master"
+      changes:
+        - docs/**/*
+  image: wsinpg/mark:latest
+  tags:
+    - autoscale
+  script: >
+    for f in $(find . -name includes -type d -prune -o -name 'README*.md' -prune -o -name '*.md' -print0 | xargs -0); do
+      echo 'username = ""' && echo "password = '$CONFLUENCE_PERSONAL_ACCESS_TOKEN'" | mark -c /dev/stdin -b https://ssg-confluence.internal.sanger.ac.uk -f "$f" --trace;
+    done

Changes

@@ -1,6 +1,8 @@
 LIST OF CHANGES FOR NPG-QC PACKAGE
 
  - GitHub CI - updated deprecated v2 runner action to v3
+ - docs
+  - automated creation/update of confluence pages for docs
  - Following a release on 07/09/2024, see https://metacpan.org/dist/App-perlbrew/changes
    the checksum of the script served by https://install.perlbrew.pl had changed.
    https://install.perlbrew.pl is a redirect to raw

docs/CtoA_substitution_metrics.md

@@ -1,3 +1,20 @@
+<!-- Space: NPG -->
+<!-- Parent: Illumina Sequencing -->
+<!-- Title: C->A short read sequencing substitution metrics -->
+
+<!-- Macro: :box:([^:]+):([^:]*):(.+):
+     Template: ac:box
+     Icon: true
+     Name: ${1}
+     Title: ${2}
+     Body: ${3} -->
+
+:box:info:Note:This page is automatically generated; any edits will be overwritten:
+
+###### Repository information
+
+<!-- Include: includes/repo-metadata.md -->
+
 # C->A short read sequencing substitution metrics
 
 - Author - Irina Abnizova

docs/includes/repo-metadata.md

@@ -0,0 +1 @@
+Created from: -  Version: -

docs/qc_outcomes_change_howto.md

@@ -1,3 +1,20 @@
+<!-- Space: NPG -->
+<!-- Parent: Illumina Sequencing -->
+<!-- Title: Guidance for Changing QC Outcomes -->
+
+<!-- Macro: :box:([^:]+):([^:]*):(.+):
+     Template: ac:box
+     Icon: true
+     Name: ${1}
+     Title: ${2}
+     Body: ${3} -->
+
+:box:info:Note:This page is automatically generated; any edits will be overwritten:
+
+###### Repository information
+
+<!-- Include: includes/repo-metadata.md -->
+
 # Guidance for Changing QC Outcomes
 
 - Use the correct RT ticket number.