From 7ca376ca6e454e8b01200cf814a293aae62f7bd0 Mon Sep 17 00:00:00 2001
From: Michal-Babins <mbabins5@uoregon.edu>
Date: Thu, 6 Jul 2023 08:17:42 -0600
Subject: [PATCH] removed unused variables

---
 ReadbasedAnalysis.wdl | 35 -----------------------------------
 1 file changed, 35 deletions(-)

diff --git a/ReadbasedAnalysis.wdl b/ReadbasedAnalysis.wdl
index c08df65..3c615ae 100644
--- a/ReadbasedAnalysis.wdl
+++ b/ReadbasedAnalysis.wdl
@@ -10,12 +10,7 @@ workflow ReadbasedAnalysis {
     Int cpu = 8
     String input_file
     String proj
-    String resource
-    String informed_by
-    String?  git_url="https://github.com/microbiomedata/mg_annotation/releases/tag/0.1"
-    String?  url_root="https://data.microbiomedata.org/data/"
     String prefix
-    String? outdir
     Boolean? paired = false
     String bbtools_container="microbiomedata/bbtools:38.96"
     String? docker = "microbiomedata/nmdc_taxa_profilers:1.0.4"
@@ -79,12 +74,8 @@ workflow ReadbasedAnalysis {
             input:
             proj=proj,
             start=stage.start,
-            git_url=git_url,
-            url_root=url_root,
             input_file=stage.read_in,
             container="microbiomedata/workflowmeta:1.1.1",
-            informed_by=informed_by,
-            resource=resource,
             gottcha2_report_tsv=profilerGottcha2.report_tsv,
             gottcha2_full_tsv=profilerGottcha2.full_tsv,
             gottcha2_krona_html=profilerGottcha2.krona_html,
@@ -106,7 +97,6 @@ workflow ReadbasedAnalysis {
         File final_kraken2_classification_tsv = finish_reads.kr_classification_tsv
         File final_kraken2_report_tsv = finish_reads.kr_report_tsv
         File final_kraken2_krona_html = finish_reads.kr_krona_html
-        File reads_objects = finish_reads.objects
         File? info_file = make_info_file.profiler_info
         String? info = make_info_file.profiler_info_text
     }
@@ -202,34 +192,9 @@ task finish_reads {
         fi
         ln ${kraken2_krona_html} ${prefix}_kraken2_krona.html
 
-        /scripts/generate_object_json.py \
-            --type "nmdc:ReadBasedAnalysisActivity" \
-            --set read_based_taxonomy_analysis_activity_set \
-            --part ${proj} \
-            -p "name=ReadBased Analysis Activity for ${proj}" \
-                was_informed_by=${informed_by} \
-                started_at_time=${start} \
-                ended_at_time=$end \
-                execution_resource="${resource}" \
-                git_url=${git_url} \
-                version="v1.0.2-beta" \
-            --url ${url_root}${proj}/ReadbasedAnalysis/ \
-            --inputs ${input_file} \
-            --outputs \
-            ${prefix}_gottcha2_report.tsv "GOTTCHA2 classification report file" "GOTTCHA2 Classification Report" "GOTTCHA2 Classification for ${proj}"\
-            ${prefix}_gottcha2_full_tsv "GOTTCHA2 report file" "GOTTCHA2 Report Full" "GOTTCHA2 Full Report for ${proj}" \
-            ${prefix}_gottcha2_krona.html "GOTTCHA2 krona plot HTML file" "GOTTCHA2 Krona Plot" "GOTTCHA2 Krona for ${proj}"\
-            ${prefix}_centrifuge_classification.tsv "Centrifuge output read classification file" "Centrifuge Taxonomic Classification" "Centrifuge Classification for ${proj}"\
-            ${prefix}_centrifuge_report.tsv "Centrifuge Classification Report" "Centrifuge output report file" "Centrifuge Report for ${proj}"\
-            ${prefix}_centrifuge_krona.html "Centrifug krona plot HTML file" "Centrifuge Krona Plot" "Centrifuge Krona for ${proj}"\
-            ${prefix}_kraken2_classification.tsv "Kraken2 output read classification file" "Kraken2 Taxonomic Classification" "Kraken2 Classification for ${proj}" \
-            ${prefix}_kraken2_report.tsv "Kraken2 output report file" "Kraken2 Classification Report" "Kraken2 Report for ${proj}" \
-            ${prefix}_kraken2_krona.html "Kraken2 Krona plot HTML file" "Kraken2 Krona Plot" "Kraken2 Krona for ${proj}"
     >>>
 
     output {
-
-       File objects="objects.json"
        File g2_report_tsv="${prefix}_gottcha2_report.tsv"
        File g2_full_tsv="${prefix}_gottcha2_full_tsv"
        File g2_krona_html="${prefix}_gottcha2_krona.html"