add busco_download_datasets component (#19)

* add script, test, config for downalod busco datasets

* add changelog entry

* fix typos

* update changelog

* rename busco to busco run

* update changelog

* fix names and namespaces

---------

Co-authored-by: Robrecht Cannoodt <[email protected]>

CHANGELOG.md

@@ -10,7 +10,8 @@
 
 * `busco`: 
     - `busco/busco_run`: Assess genome assembly and annotation completeness with single copy orthologs (PR #6).
-    - `busco/busco_list_datasets`: Lists available busco datasets (PR #18)
+    - `busco/busco_list_datasets`: Lists available busco datasets (PR #18).
+    - `busco/busco_download_datasets`: Download busco datasets (PR #19).
 
 * `featurecounts`: Assign sequence reads to genomic features (PR #11).
 

src/busco/busco_download_datasets/config.vsh.yaml

@@ -0,0 +1,45 @@
+functionality:
+  name: busco_download_datasets
+  namespace: busco
+  description: Downloads available busco datasets
+  info:
+    keywords: [lineage datasets]
+    homepage: https://busco.ezlab.org/
+    documentation: https://busco.ezlab.org/busco_userguide.html
+    repository: https://gitlab.com/ezlab/busco
+    reference: "10.1007/978-1-4939-9173-0_14"
+    licence: MIT
+  argument_groups:
+    - name: Inputs
+      arguments:
+        - name: --download
+          type: string
+          description: |
+            Download dataset. Possible values are a specific dataset name, "all", "prokaryota", "eukaryota", or "virus".
+            The full list of available datasets can be viewed [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the busco/busco_list_datasets component.
+          required: true
+          example: stramenopiles_odb10
+    - name: Outputs
+      arguments:
+        - name: --download_path
+          direction: output
+          type: file
+          description: |
+            Local filepath for storing BUSCO dataset downloads
+          required: false
+          default: busco_downloads
+          example: busco_downloads
+  resources:
+    - type: bash_script
+      path: script.sh
+  test_resources:
+    - type: bash_script
+      path: test.sh
+platforms:
+  - type: docker
+    image: quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0
+    setup:
+      - type: docker
+        run: |
+          busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt
+  - type: nextflow

src/busco/busco_download_datasets/script.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+
+if [ ! -d "$par_download_path" ]; then
+    mkdir -p "$par_download_path"
+fi
+
+busco \
+    --download_path "$par_download_path" \
+    --download "$par_download"
+

src/busco/busco_download_datasets/test.sh

@@ -0,0 +1,15 @@
+echo "> Downloading busco stramenopiles_odb10 dataset"
+
+"$meta_executable" \
+    --download stramenopiles_odb10 \
+    --download_path downloads 
+
+echo ">> Checking output"
+[ ! -f "downloads/file_versions.tsv" ] && echo "file_versions.tsv does not exist" && exit 1
+[ ! -f "downloads/lineages/stramenopiles_odb10/dataset.cfg" ] && echo "dataset.cfg does not exist" && exit 1
+
+echo ">> Checking if output is empty"
+[ ! -s "downloads/file_versions.tsv" ] && echo "file_versions.tsv is empty" && exit 1
+[ ! -s "downloads/lineages/stramenopiles_odb10/dataset.cfg" ] && echo "dataset.cfg is empty" && exit 1
+
+rm -r downloads

src/busco/busco_list_datasets/config.vsh.yaml

@@ -1,5 +1,6 @@
 functionality:
-  name: busco
+  name: busco_list_datasets
+  namespace: busco
   description: Lists the available busco datasets
   info:
     keywords: [lineage datasets]

src/busco/busco_run/config.vsh.yaml

@@ -1,5 +1,6 @@
 functionality:
   name: busco_run
+  namespace: busco
   description: Assessment of genome assembly and annotation completeness with single copy orthologs
   info:
     keywords: [Genome assembly, quality control]
@@ -37,7 +38,9 @@ functionality:
             Specify a BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed. 
             The full list of available datasets can be viewed [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the busco/busco_list_datasets component.
             When unsure, the "--auto_lineage" flag can be set to automatically find the optimal lineage path.
-            Requested datasets will automatically be downloaded if not already present in the download folder.
+            BUSCO will automatically download the requested dataset if it is not already present in the download folder. 
+            You can optionally provide a path to a local dataset instead of a name, e.g. path/to/dataset.
+            Datasets can be downloaded using the busco/busco_download_dataset component.
           example: stramenopiles_odb10
 
     - name: Outputs