From 557f540bde27b49891afcc34b7382d394977a249 Mon Sep 17 00:00:00 2001
From: dorien-er <roosen.dorien@gmail.com>
Date: Tue, 30 Jan 2024 18:46:14 +0100
Subject: [PATCH] add outputs

---
 src/busco/busco/config.vsh.yaml | 39 +++++++++++++++++++++++++--------
 src/busco/busco/script.sh       | 28 +++++++++++++++++------
 2 files changed, 51 insertions(+), 16 deletions(-)

diff --git a/src/busco/busco/config.vsh.yaml b/src/busco/busco/config.vsh.yaml
index 142f1b13..11189536 100644
--- a/src/busco/busco/config.vsh.yaml
+++ b/src/busco/busco/config.vsh.yaml
@@ -39,20 +39,41 @@ functionality:
 
     - name: Outputs
       arguments:
-        - name: --output_dir
-          alternatives: ["-o"]
-          required: true
+        - name: --short_summary_json
+          required: false
           direction: output
           type: file
+          example: short_summary.json
           description: |
-            Path to output directory for publishing BUSCO results
-          example: output
-        - name: --output_prefix
-          type: string
+            Output file for short summary in JSON format.
+        - name: --short_summary_txt
+          required: false
+          direction: output
+          type: file
+          example: short_summary.txt
+          description: |
+            Output file for short summary in TXT format.
+        - name: --full_table
           required: false
+          direction: output
+          type: file
+          example: full_table.tsv
+          description: |
+            Full table output in TSV format.
+        - name: --missing_busco_list
+          required: false
+          direction: output
+          type: file
+          example: missing_list.tsv
+          description: |
+            Missing list output in TSV format.
+        - name: --output_dir
+          required: false
+          direction: output
+          type: file
+          example: output_dir/
           description: |
-            Name of the analysis run, output folders and files will be labeled with this name. if not specified the output will be the input file name."
-          example: busco_protein
+            The full output directory, if so desired.
 
     - name: Resource and Run Settings
       arguments:
diff --git a/src/busco/busco/script.sh b/src/busco/busco/script.sh
index b79eb285..95e16c1a 100644
--- a/src/busco/busco/script.sh
+++ b/src/busco/busco/script.sh
@@ -18,16 +18,15 @@
 [[ "$par_scaffold_composition" == "false" ]] && unset par_scaffold_composition
 [[ "$par_miniprot" == "false" ]] && unset par_miniprot
 
-if [[ -n "$par_output_prefix" ]]; then 
-    prefix="$par_output_prefix"
-else 
-    prefix="$(basename -- $par_input)"
-fi
+
+tmp_dir=$(mktemp -d -p "$meta_temp_dir" busco_XXXXXXXXX)
+prefix=$(openssl rand -hex 8)
 
 busco \
     --in "$par_input" \
     --mode "$par_mode" \
     --out "$prefix" \
+    --out_path "$tmp_dir" \
     ${meta_cpus:+--cpu "${meta_cpus}"} \
     ${par_lineage_dataset:+--lineage_dataset "$par_lineage_dataset"} \
     ${par_augustus:+--augustus} \
@@ -55,6 +54,21 @@ busco \
     ${par_download_path:+--download_path "$par_download_path"} \
     ${par_download:+--download "$par_download"} 
 
-mkdir $par_output_dir
-mv $prefix/* $par_output_dir
+
+
+if [[ -n "$par_short_summary_json" ]]; then
+    find "$tmp_dir/$prefix" -maxdepth 1 -type d -name 'run_*' -exec cp {}/short_summary.json "$par_short_summary_json" \;
+fi
+if [[ -n "$par_short_summary_txt" ]]; then
+    find "$tmp_dir/$prefix" -maxdepth 1 -type d -name 'run_*' -exec cp {}/short_summary.txt "$par_short_summary_txt" \;
+fi
+if [[ -n "$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 "$par_missing_busco_list" \;
+fi
+if [[ -n "$par_output_dir" ]]; then
+    cp -r $tmp_dir/$prefix/run_* $par_output_dir
+fi