Updated the changelog too

sanger-tol · Nov 25, 2024 · 3976215 · 3976215
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,9 +19,13 @@ The pipeline is now considered to be a complete and suitable replacement for the
 
 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 | 4.3.9       | 4.3.13      |
+| Dependency  | Old version       | New version     |
+| ----------- | ----------------- | --------------- |
+| blast       | 2.14.1 and 2.15.0 | only 2.15.0     |
+| blobtoolkit | 4.3.9             | 4.4.0           |
+| busco       | 5.5.0             | 5.7.1           |
+| multiqc     | 1.20 and 1.21     | 1.20 and 1.25.1 |
+| samtools    | 1.18 and 1.19.2   | 1.20 and 1.21   |
 
 ## [[0.6.0](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.6.0)] – Bellsprout – [2024-09-13]
 
@@ -112,7 +116,7 @@ Note, since the pipeline is using Nextflow DSL2, each process will be run with i
 | blobtoolkit | 4.3.3         | 4.3.9             |
 | blast       | 2.14.0        | 2.15.0 and 2.14.1 |
 | multiqc     | 1.17 and 1.18 | 1.20 and 1.21     |
-| samtools    | 1.18          | 1.19.2            |
+| samtools    | 1.18          | 1.18 and 1.19.2   |
 | seqtk       | 1.3           | 1.4               |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present. </br> **NB:** Dependency has been **added** if just the new version information is present. </br> **NB:** Dependency has been **removed** if version information isn't present.

diff --git a/docs/usage.md b/docs/usage.md
@@ -272,7 +272,7 @@ List of tools for any given dataset can be fetched from the API, for example htt
 
 | Dependency        | Snakemake | Nextflow |
 | ----------------- | --------- | -------- |
-| blobtoolkit       | 4.3.2     | 4.3.13   |
+| blobtoolkit       | 4.3.2     | 4.4.0   |
 | blast             | 2.12.0    | 2.14.1   |
 | blobtk            | 0.5.0     | 0.5.1    |
 | busco             | 5.3.2     | 5.5.0    |

diff --git a/modules/local/blobtoolkit/chunk.nf b/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:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta) , path(fasta)

diff --git a/modules/local/blobtoolkit/countbuscos.nf b/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:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(table, stageAs: 'dir??/*')

diff --git a/modules/local/blobtoolkit/createblobdir.nf b/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:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(window, stageAs: 'windowstats/*')

diff --git a/modules/local/blobtoolkit/extractbuscos.nf b/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:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(fasta)

diff --git a/modules/local/blobtoolkit/summary.nf b/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:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(blobdir)

diff --git a/modules/local/blobtoolkit/unchunk.nf b/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:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(blast_table)

diff --git a/modules/local/blobtoolkit/updateblobdir.nf b/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:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(input, stageAs: "input_blobdir")

diff --git a/modules/local/blobtoolkit/updatemeta.nf b/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:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(input)

diff --git a/modules/local/blobtoolkit/windowstats.nf b/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:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(tsv)

diff --git a/modules/local/generate_config.nf b/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:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), val(fasta)