Merge pull request #161 from sanger-tol/patch

New container version

Author: muffato

.nf-core.yml

@@ -43,4 +43,4 @@ template:
   outdir: .
   skip_features:
     - igenomes
-  version: 0.7.0
+  version: 0.7.1

CHANGELOG.md

@@ -3,6 +3,18 @@
 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).
 
+## [[0.7.1](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.7.1)] – Psyduck (patch 1) – [2025-03-297
+
+- Upgraded the blobtools version which contains a bugfix
+
+### Software dependencies
+
+Note, since the pipeline is using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference. Only `Docker` or `Singularity` containers are supported, `conda` is not supported.
+
+| Dependency  | Old version | New version |
+| ----------- | ----------- | ----------- |
+| blobtoolkit | 4.4.4       | 4.4.5       |
+
 ## [[0.7.0](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.7.0)] – Psyduck – [2025-03-19]
 
 - Fetch information about the chromosomes of the assemblies. Used to power

CITATION.cff

@@ -1,5 +1,5 @@
 cff-version: 1.2.0
-title: sanger-tol/blobtoolkit v0.7.0
+title: sanger-tol/blobtoolkit v0.7.1
 authors:
   - family-names: Butt
     given-names: Zaynab
@@ -44,5 +44,5 @@ authors:
 doi: 10.5281/zenodo.13758882
 repository-code: "https://github.com/sanger-tol/blobtoolkit"
 license: MIT
-version: 0.7.0
+version: 0.7.1
 date-released: "2024-09-13"

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/sanger-tol/blobtoolkit/releases/tag/0.7.0" target="_blank">sanger-tol/blobtoolkit</a>
+  This report has been generated by the <a href="https://github.com/sanger-tol/blobtoolkit/releases/tag/0.7.1" target="_blank">sanger-tol/blobtoolkit</a>
   analysis pipeline.
 report_section_order:
   "sanger-tol-blobtoolkit-methods-description":

modules/local/blobtoolkit/chunk.nf

@@ -5,7 +5,7 @@ process BLOBTOOLKIT_CHUNK {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_CHUNK module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.4.4"
+    container "docker.io/genomehubs/blobtoolkit:4.4.5"
 
     input:
     tuple val(meta) , path(fasta)

modules/local/blobtoolkit/countbuscos.nf

@@ -5,7 +5,7 @@ process BLOBTOOLKIT_COUNTBUSCOS {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_COUNTBUSCOS module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.4.4"
+    container "docker.io/genomehubs/blobtoolkit:4.4.5"
 
     input:
     tuple val(meta), path(table, stageAs: 'dir??/*')

modules/local/blobtoolkit/createblobdir.nf

@@ -5,7 +5,7 @@ process BLOBTOOLKIT_CREATEBLOBDIR {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_BLOBDIR module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.4.4"
+    container "docker.io/genomehubs/blobtoolkit:4.4.5"
 
     input:
     tuple val(meta), path(window, stageAs: 'windowstats/*')

modules/local/blobtoolkit/extractbuscos.nf

@@ -5,7 +5,7 @@ process BLOBTOOLKIT_EXTRACTBUSCOS {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_EXTRACTBUSCOS module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.4.4"
+    container "docker.io/genomehubs/blobtoolkit:4.4.5"
 
     input:
     tuple val(meta), path(fasta)

modules/local/blobtoolkit/summary.nf

@@ -5,7 +5,7 @@ process BLOBTOOLKIT_SUMMARY {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_SUMMARY module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.4.4"
+    container "docker.io/genomehubs/blobtoolkit:4.4.5"
 
     input:
     tuple val(meta), path(blobdir)

modules/local/blobtoolkit/unchunk.nf

@@ -5,7 +5,7 @@ process BLOBTOOLKIT_UNCHUNK {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_UNCHUNK module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.4.4"
+    container "docker.io/genomehubs/blobtoolkit:4.4.5"
 
     input:
     tuple val(meta), path(blast_table)

modules/local/blobtoolkit/updateblobdir.nf

@@ -5,7 +5,7 @@ process BLOBTOOLKIT_UPDATEBLOBDIR {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_BLOBDIR module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.4.4"
+    container "docker.io/genomehubs/blobtoolkit:4.4.5"
 
     input:
     tuple val(meta), path(input, stageAs: "input_blobdir")

modules/local/blobtoolkit/updatemeta.nf

@@ -5,7 +5,7 @@ process BLOBTOOLKIT_UPDATEMETA {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_UPDATEMETA module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.4.4"
+    container "docker.io/genomehubs/blobtoolkit:4.4.5"
 
     input:
     tuple val(meta), path(input)

modules/local/blobtoolkit/windowstats.nf

@@ -4,7 +4,7 @@ process BLOBTOOLKIT_WINDOWSTATS {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_WINDOWSTATS module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.4.4"
+    container "docker.io/genomehubs/blobtoolkit:4.4.5"
 
     input:
     tuple val(meta), path(tsv)

modules/local/generate_config.nf

@@ -3,7 +3,7 @@ process GENERATE_CONFIG {
     label 'process_single'
 
     conda "conda-forge::requests=2.28.1 conda-forge::pyyaml=6.0"
-    container "docker.io/genomehubs/blobtoolkit:4.4.4"
+    container "docker.io/genomehubs/blobtoolkit:4.4.5"
 
     input:
     tuple val(meta), val(fasta)

modules/local/jsonify_taxdump.nf

@@ -3,7 +3,7 @@ process JSONIFY_TAXDUMP {
     label 'process_single'
 
     conda "conda-forge::requests=2.28.1 conda-forge::pyyaml=6.0"
-    container "docker.io/genomehubs/blobtoolkit:4.4.4"
+    container "docker.io/genomehubs/blobtoolkit:4.4.5"
 
     input:
     tuple val(meta), path(taxdump)

nextflow.config

@@ -327,7 +327,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
     nextflowVersion = '!>=24.04.2'
-    version         = '0.7.0'
+    version         = '0.7.1'
     doi             = '10.5281/zenodo.7949058'
 }
 

ro-crate-metadata.json

@@ -149,10 +149,10 @@
             },
             "url": [
                 "https://github.com/sanger-tol/blobtoolkit",
-                "https://nf-co.re/sanger-tol/blobtoolkit/0.7.0/"
+                "https://nf-co.re/sanger-tol/blobtoolkit/0.7.1/"
             ],
             "version": [
-                "0.7.0"
+                "0.7.1"
             ]
         },
         {