Merge pull request #139 from sanger-tol/busco_bug_full_test

Updated BTK container to ensure the right Busco ID is used

Author: muffato

.github/workflows/linting.yml

@@ -99,7 +99,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: linting-logs
           path: |

.github/workflows/sanger_test.yml

@@ -26,7 +26,7 @@ jobs:
               "use_work_dir_as_temp": true,
             }
           profiles: test,sanger,singularity,cleanup
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: Tower debug log file
           path: |

.github/workflows/sanger_test_full.yml

@@ -34,7 +34,7 @@ jobs:
               "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ env.REVISION }}",
             }
           profiles: test_full,sanger,singularity,cleanup
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: Tower debug log file
           path: |

CHANGELOG.md

@@ -22,7 +22,7 @@ Note, since the pipeline is using Nextflow DSL2, each process will be run with i
 | Dependency  | Old version       | New version     |
 | ----------- | ----------------- | --------------- |
 | blast       | 2.14.1 and 2.15.0 | only 2.15.0     |
-| blobtoolkit | 4.3.9             | 4.4.0           |
+| blobtoolkit | 4.3.9             | 4.4.4           |
 | 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   |

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     | 4.4.0    |
+| blobtoolkit       | 4.3.2     | 4.4.4    |
 | blast             | 2.12.0    | 2.14.1   |
 | blobtk            | 0.5.0     | 0.5.1    |
 | busco             | 5.3.2     | 5.5.0    |

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:4.4.0"
+    container "docker.io/genomehubs/blobtoolkit:4.4.4"
 
     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:4.4.0"
+    container "docker.io/genomehubs/blobtoolkit:4.4.4"
 
     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:4.4.0"
+    container "docker.io/genomehubs/blobtoolkit:4.4.4"
 
     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:4.4.0"
+    container "docker.io/genomehubs/blobtoolkit:4.4.4"
 
     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:4.4.0"
+    container "docker.io/genomehubs/blobtoolkit:4.4.4"
 
     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:4.4.0"
+    container "docker.io/genomehubs/blobtoolkit:4.4.4"
 
     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:4.4.0"
+    container "docker.io/genomehubs/blobtoolkit:4.4.4"
 
     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:4.4.0"
+    container "docker.io/genomehubs/blobtoolkit:4.4.4"
 
     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:4.4.0"
+    container "docker.io/genomehubs/blobtoolkit:4.4.4"
 
     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:4.4.0"
+    container "docker.io/genomehubs/blobtoolkit:4.4.4"
 
     input:
     tuple val(meta), val(fasta)