fix tests

src/busco/busco/config.vsh.yaml

@@ -64,7 +64,7 @@ functionality:
           required: false
           direction: output
           type: file
-          example: missing_list.tsv
+          example: missing_busco_list.tsv
           description: |
             Missing list output in TSV format.
         - name: --output_dir

src/busco/busco/script.sh

@@ -66,7 +66,7 @@ if [[ -n "$par_full_table" ]]; then
     find "$tmp_dir/$prefix" -maxdepth 1 -type d -name 'run_*' -exec cp {}/full_table.tsv "$par_full_table" \;
 fi
 if [[ -n "$par_missing_busco_list" ]]; then
-    find "$tmp_dir/$prefix" -maxdepth 1 -type d -name 'run_*' -exec cp {}/missing_busco_list.txt "$par_missing_busco_list" \;
+    find "$tmp_dir/$prefix" -maxdepth 1 -type d -name 'run_*' -exec cp {}/missing_busco_list.tsv "$par_missing_busco_list" \;
 fi
 if [[ -n "$par_output_dir" ]]; then
     cp -r $tmp_dir/$prefix/run_* $par_output_dir

src/busco/busco/test.sh

@@ -1,25 +1,24 @@
 test_dir="$meta_resources_dir/test_data"
 
 echo "> Running busco"
-echo "$(busco --version 2>&1 | sed -n 's/BUSCO \([0-9.]*\)/\1/p')"
 
 "$meta_executable" \
     --input $test_dir/protein.fasta \
     --mode protein \
     --lineage_dataset stramenopiles_odb10 \
     --output_dir output 
+ls -la output/run_stramenopiles_odb10
 
 echo ">> Checking output"
-[ ! -f "output/run_stramenopiles_odb10/full_table.tsv" ] && echo "full_table.tsv does not exist" && exit 1
-[ ! -f "output/run_stramenopiles_odb10/missing_busco_list.tsv" ] && echo "missing_busco_list.tsv does not exist" && exit 1
-[ ! -f "output/run_stramenopiles_odb10/short_summary.json" ] && echo "short_summary.json does not exist" && exit 1
-[ ! -f "output/run_stramenopiles_odb10/short_summary.txt" ] && echo "short_summary.txt does not exist" && exit 1
+[ ! -f "output/full_table.tsv" ] && echo "full_table.tsv does not exist" && exit 1
+[ ! -f "output/missing_busco_list.tsv" ] && echo "missing_busco_list.tsv does not exist" && exit 1
+[ ! -f "output/short_summary.json" ] && echo "short_summary.json does not exist" && exit 1
+[ ! -f "output/short_summary.txt" ] && echo "short_summary.txt does not exist" && exit 1
 
 echo ">> Checking if output is empty"
-[ ! -s "output/run_stramenopiles_odb10/full_table.tsv" ] && echo "full_table.tsv is empty" && exit 1
-[ ! -s "output/run_stramenopiles_odb10/missing_busco_list.tsv" ] && echo "missing_busco_list.tsv is empty" && exit 1
-[ ! -s "output/run_stramenopiles_odb10/short_summary.json" ] && echo "short_summary.json is empty" && exit 1
-[ ! -s "output/run_stramenopiles_odb10/short_summary.txt" ] && echo "short_summary.txt is empty" && exit 1
-
+[ ! -s "output/full_table.tsv" ] && echo "full_table.tsv is empty" && exit 1
+[ ! -s "output/missing_busco_list.tsv" ] && echo "missing_busco_list.tsv is empty" && exit 1
+[ ! -s "output/short_summary.json" ] && echo "short_summary.json is empty" && exit 1
+[ ! -s "output/short_summary.txt" ] && echo "short_summary.txt is empty" && exit 1
 
 rm -r output/ 

src/busco/busco_list_datasets/config.vsh.yaml

@@ -0,0 +1,36 @@
+functionality:
+  name: busco
+  description: Lists the 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: Outputs
+      arguments:
+        - name: --output
+          alternatives: ["-o"]
+          direction: output
+          type: file
+          description: |
+            Output file of the available busco datasets
+          required: false
+          default: busco_dataset_list.txt
+          example: file.txt
+  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_list_datasets/script.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+busco --list-datasets > $par_output