From 2adb321cefe6cde8abad93dc551b38aa94bac63e Mon Sep 17 00:00:00 2001
From: aclum <aclum@users.noreply.github.com>
Date: Fri, 22 Nov 2024 11:11:14 -0800
Subject: [PATCH] Update workflows.yaml

Updates for changes made to accommodate both a short and a long read workflow.
---
 .../config/workflows/workflows.yaml           | 20 +++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/nmdc_automation/config/workflows/workflows.yaml b/nmdc_automation/config/workflows/workflows.yaml
index 065abf63..23b1350e 100644
--- a/nmdc_automation/config/workflows/workflows.yaml
+++ b/nmdc_automation/config/workflows/workflows.yaml
@@ -103,9 +103,9 @@ Workflows:
     - Reads QC Interleave
     Input_prefix: jgi_metaASM
     Inputs:
-      input_file: do:Filtered Sequencing Reads
-      rename_contig_prefix: "{workflow_execution_id}"
+      input_files: do:Filtered Sequencing Reads
       proj: "{workflow_execution_id}"
+      shortRead: false
     Workflow Execution:
       name: "Metagenome Assembly for {id}"
       type: nmdc:MetagenomeAssembly
@@ -135,30 +135,34 @@ Workflows:
       scaf_powsum: "{outputs.stats.scaf_powsum}"
       scaffolds: "{outputs.stats.scaffolds}"
     Outputs:
-      - output: contig
+      - output: sr_contig
         name: Final assembly contigs fasta
         data_object_type: Assembly Contigs
         description: "Assembly contigs for {id}"
-      - output: scaffold
+      - output: sr_scaffold
         name: Final assembly scaffolds fasta
         data_object_type: Assembly Scaffolds
         description: "Assembly scaffolds for {id}"
-      - output: covstats
+      - output: sr_covstats
         name: Assembled contigs coverage information
         data_object_type: Assembly Coverage Stats
         description: "Coverage Stats for {id}"
-      - output: agp
+      - output: sr_agp
         name: An AGP format file that describes the assembly
         data_object_type: Assembly AGP
         description: "AGP for {id}"
-      - output: bam
+      - output: sr_bam
         name: Sorted bam file of reads mapping back to the final assembly
         data_object_type: Assembly Coverage BAM
         description: "Sorted Bam for {id}"
-      - output: asminfo
+      - output: sr_asminfo
         name: File containing assembly info
         data_object_type: Assembly Info File
         description: "Assembly info for {id}"
+      - output: sr_bbcms_fq
+        name: bbcms error corrected reads
+        data_object_type: Error Corrected Reads
+        description: "Error corrected reads for {id}"
 
   - Name: Metagenome Annotation
     Type: nmdc:MetagenomeAnnotation