From d0aaf80c44852f6653bcb34abee368966a75d3c6 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Tue, 10 Sep 2024 11:18:24 +0200
Subject: [PATCH] add manifest to all nextfow pipelines (#3696)

### Added

- Storing of a manifest.json file for all nextflow-based pipelines
---
 cg/resources/raredisease_bundle_filenames.yaml | 6 ++++++
 cg/resources/rnafusion_bundle_filenames.yaml   | 6 ++++++
 cg/resources/taxprofiler_bundle_filenames.yaml | 8 ++++++--
 cg/resources/tomte_bundle_filenames.yaml       | 6 ++++++
 4 files changed, 24 insertions(+), 2 deletions(-)

diff --git a/cg/resources/raredisease_bundle_filenames.yaml b/cg/resources/raredisease_bundle_filenames.yaml
index 7e96d33a1a..2c6c03ead2 100644
--- a/cg/resources/raredisease_bundle_filenames.yaml
+++ b/cg/resources/raredisease_bundle_filenames.yaml
@@ -1078,3 +1078,9 @@
   path_index: ~
   step: nextflow-config
   tag: nextflow-config
+- format: json
+  id: CASEID
+  path: PATHTOCASE/manifest.json
+  path_index: ~
+  step: manifest
+  tag: manifest
diff --git a/cg/resources/rnafusion_bundle_filenames.yaml b/cg/resources/rnafusion_bundle_filenames.yaml
index 911877b86d..ff8212de45 100644
--- a/cg/resources/rnafusion_bundle_filenames.yaml
+++ b/cg/resources/rnafusion_bundle_filenames.yaml
@@ -135,3 +135,9 @@
   path: PATHTOCASE/multiqc/multiqc_data/multiqc_picard_insertSize.json
   step: multiqc
   tag: multiqc-picard-insert-size
+- format: json
+  id: CASEID
+  path: PATHTOCASE/manifest.json
+  path_index: ~
+  step: manifest
+  tag: manifest
diff --git a/cg/resources/taxprofiler_bundle_filenames.yaml b/cg/resources/taxprofiler_bundle_filenames.yaml
index 39701b427d..ed556265ac 100644
--- a/cg/resources/taxprofiler_bundle_filenames.yaml
+++ b/cg/resources/taxprofiler_bundle_filenames.yaml
@@ -94,5 +94,9 @@
   path_index: ~
   step: multiqc-json
   tag: multiqc-kraken
-
-
+- format: json
+  id: CASEID
+  path: PATHTOCASE/manifest.json
+  path_index: ~
+  step: manifest
+  tag: manifest
diff --git a/cg/resources/tomte_bundle_filenames.yaml b/cg/resources/tomte_bundle_filenames.yaml
index f90c1e04e2..92b23dfe48 100644
--- a/cg/resources/tomte_bundle_filenames.yaml
+++ b/cg/resources/tomte_bundle_filenames.yaml
@@ -190,3 +190,9 @@
   path_index: ~
   step: multiqc
   tag: multiqc-picard-insert-size
+- format: json
+  id: CASEID
+  path: PATHTOCASE/manifest.json
+  path_index: ~
+  step: manifest
+  tag: manifest