Merge branch 'main' into workflows/VGP-assembly-v2/kmer-profiling-hif…

…i-trio-VGP2
workflow4metabolomics · Nov 9, 2023 · 76a8103 · 76a8103
2 parents 8ef1c7e + 5c10f46
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diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md
@@ -11,11 +11,6 @@
 - `toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1`
 - `toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1`
 
-All notable changes to this project will be documented in this file.
-
-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).
-
 ## [0.1.3] - 2023-11-08
 
 - Added tags `hifiasm_Assembly_Haplotype_1` and `hifiasm_Assembly_Haplotype_2` to fasta outputs of hifiasm, so they can be easily identified for feeding to purge_dups workflow

diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/CHANGELOG.md
@@ -1,10 +1,5 @@
 # Changelog
 
-All notable changes to this project will be documented in this file.
-
-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).
-
 ## [0.1] - 2023-09-27
 
 Creation of workflow for Trio assembly. 

diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/CHANGELOG.md
@@ -1,10 +1,5 @@
 # Changelog
 
-All notable changes to this project will be documented in this file.
-
-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).
-
 ## [0.1] - 2023-09-26
 
 Addition of the workflow to the iwc repository.
diff --git a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md
@@ -1,10 +1,5 @@
 # Changelog
 
-All notable changes to this project will be documented in this file.
-
-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).
-
 ## [0.3] - 2023-11-08
 
 ### Added

diff --git a/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/CHANGELOG.md b/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/CHANGELOG.md
@@ -1,10 +1,5 @@
 # Changelog
 
-All notable changes to this project will be documented in this file.
-
-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).
-
 ## [0.1] - 2023-11-01
 
 Addition of the workflow to the iwc repository.
diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md
@@ -1,10 +1,5 @@
 # Changelog
 
-All notable changes to this project will be documented in this file.
-
-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).
-
 ## [0.1.1] - 2023-10-26
 
 Added tags for better visibility of outputs in the history, and exposure of the BUSCO lineage parameter

diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md
@@ -1,8 +1,8 @@
 # Changelog
-All notable changes to this project will be documented in this file.
 
-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).
+## [0.1.3] 2023-11-09
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2`
 
 ## [0.1.2] - 2023-11-07
 ### Changed

diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga
@@ -14,7 +14,7 @@
     ],
     "format-version": "0.1",
     "license": "CC-BY-4.0",
-    "release": "0.1.2",
+    "release": "0.1.3",
     "name": "kmer-profiling-hifi-VGP1",
     "steps": {
         "0": {
@@ -247,7 +247,7 @@
         },
         "6": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
             "errors": null,
             "id": 6,
             "input_connections": {
@@ -352,15 +352,15 @@
                     "output_name": "transformed_log_plot"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
             "tool_shed_repository": {
-                "changeset_revision": "3169a38c2656",
+                "changeset_revision": "01210c4e9144",
                 "name": "genomescope",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"advanced_options\": {\"topology\": null, \"initial_repetitiveness\": null, \"initial_heterozygosities\": \"\", \"transform_exp\": null, \"testing\": true, \"true_params\": \"\", \"trace_flag\": false, \"num_rounds\": null}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"kmer_length\": {\"__class__\": \"ConnectedValue\"}, \"lambda\": null, \"max_kmercov\": null, \"output_options\": {\"output_files\": [\"model_output\", \"summary_output\"], \"no_unique_sequence\": false}, \"ploidy\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2.0+galaxy1",
+            "tool_version": "2.0+galaxy2",
             "type": "tool",
             "uuid": "955de351-ef19-42dc-89d7-ca213994515a",
             "when": null,

diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/CHANGELOG.md b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/CHANGELOG.md
@@ -4,10 +4,6 @@
 
 ### Automatic update
 - `toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2`
-All notable changes to this project will be documented in this file.
-
-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).
 
 ## [0.1] - 2023-10-30
 

diff --git a/workflows/genome-assembly/polish-with-long-reads/CHANGELOG.md b/workflows/genome-assembly/polish-with-long-reads/CHANGELOG.md
@@ -1,9 +1,4 @@
 # Changelog
 
-All notable changes to this project will be documented in this file.
-
-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).
-
 ## [0.1] 2023-07-15
 First release.