Merge pull request #236 from subwaystation/dev

prepare new release 1.1.3 - marsupial

.nf-core.yml

@@ -20,4 +20,4 @@ template:
   skip_features:
     - fastqc
     - igenomes
-  version: 1.2.0dev
+  version: 1.1.3

CHANGELOG.md

@@ -2,7 +2,17 @@
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## 1.2.0dev - marsupial
+## 1.1.3 - marsupial
+
+This release brings several template updates up to 3.2.0 and a number of tool updates.
+
+- Templete updates to 3.2.0 @heuermh @subwaystation
+- Bump odgi to 0.9.0 @heuermh @subwaystation
+- Bump MultiQC to 1.27 @heuermh @subwaystation
+- Bump local MultiQC to 1.27 @subwaystation @heuermh
+- Bump vg to 1.62 @subwaystation @heuermh
+- Bump smoothxg to 0.8.0 @heuermh @subwaystation
+- Refactor authors list of contributors @heuermh @subwaystation @Zethson @AndreaGuarracino @mirpedrol @FriederikeHanssen
 
 ## 1.1.2 - canguro
 

assets/multiqc_config.yml

@@ -1,7 +1,8 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/pangenome/tree/dev" target="_blank">nf-core/pangenome</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/pangenome/dev/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/pangenome/releases/tag/1.1.3"
+  target="_blank">nf-core/pangenome</a> analysis pipeline. For information about how
+  to interpret these results, please see the <a href="https://nf-co.re/pangenome/1.1.3/docs/output"
+  target="_blank">documentation</a>.
 report_section_order:
   "nf-core-pangenome-methods-description":
     order: -1000
@@ -17,22 +18,40 @@ disable_version_detection: true
 custom_data:
   odgi_O:
     section_name: ODGI Compressed 1D visualization
-    description: This image shows a 1D rendering of the built pangenome graph. The graph nodes are arranged from left to right, forming the pangenome sequence. Summarization of path coverage across all paths. A heatmap color-coding from https://colorbrewer2.org/#type=diverging&scheme=RdBu&n=11 is used. Dark blue means highest coverage. Dark red means lowest coverage. The path names are placed on the left. The black lines under the paths are the links, which represent the graph topology.
+    description: This image shows a 1D rendering of the built pangenome graph. The
+      graph nodes are arranged from left to right, forming the pangenome sequence.
+      Summarization of path coverage across all paths. A heatmap color-coding from
+      https://colorbrewer2.org/#type=diverging&scheme=RdBu&n=11 is used. Dark blue
+      means highest coverage. Dark red means lowest coverage. The path names are placed
+      on the left. The black lines under the paths are the links, which represent
+      the graph topology.
   odgi_viz:
     section_name: ODGI 1D visualization
-    description: This image shows a 1D rendering of the built pangenome graph. The graph nodes are arranged from left to right, forming the pangenome sequence. The colored bars represent the paths versus the pangenome sequence in a binary matrix. The path names are placed on the left. The black lines under the paths are the links, which represent the graph topology.
+    description: This image shows a 1D rendering of the built pangenome graph. The
+      graph nodes are arranged from left to right, forming the pangenome sequence.
+      The colored bars represent the paths versus the pangenome sequence in a binary
+      matrix. The path names are placed on the left. The black lines under the paths
+      are the links, which represent the graph topology.
   odgi_viz_pos:
     section_name: ODGI 1D visualization by path position
-    description: This shows a 1D rendering of the built pangenome graph where the paths are colored according to their nucleotide position. Light grey means a low path position, black is the highest path position.
+    description: This shows a 1D rendering of the built pangenome graph where the
+      paths are colored according to their nucleotide position. Light grey means a
+      low path position, black is the highest path position.
   odgi_viz_inv:
     section_name: ODGI 1D visualization by path orientation
-    description: This image shows a 1D rendering of the built pangenome graph where the paths are colored by orientation. Forward is black, reverse is red.
+    description: This image shows a 1D rendering of the built pangenome graph where
+      the paths are colored by orientation. Forward is black, reverse is red.
   odgi_viz_depth:
     section_name: ODGI 1D visualization by node depth
-    description: This shows a 1D rendering of the built pangenome graph where the paths are colored according to path depth. Using the Spectra color palette with 4 levels of path depths, white indicates no depth, while grey, red, and yellow indicate depth 1, 2, and greater than or equal to 3, respectively.
+    description: This shows a 1D rendering of the built pangenome graph where the
+      paths are colored according to path depth. Using the Spectra color palette with
+      4 levels of path depths, white indicates no depth, while grey, red, and yellow
+      indicate depth 1, 2, and greater than or equal to 3, respectively.
   odgi_viz_uncalled:
     section_name: ODGI 1D visualization by uncalled bases
-    description: This shows a 1D rendering of the built pangenome graph where the paths are colored according to the coverage of uncalled bases. The lighter the green, the higher the 'N' content of a node is.
+    description: This shows a 1D rendering of the built pangenome graph where the
+      paths are colored according to the coverage of uncalled bases. The lighter the
+      green, the higher the 'N' content of a node is.
   odgi_draw:
     section_name: ODGI 2D drawing
     description: This image shows a 2D rendering of the built pangenome graph.

nextflow.config

@@ -368,7 +368,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=24.04.2'
-    version         = '1.2.0dev'
+    version         = '1.1.3'
     doi             = 'https://doi.org/10.5281/zenodo.8202636'
 }