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Update workflows.yaml
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Updates for changes made to accommodate both a short and a long read workflow.
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aclum authored Nov 22, 2024
1 parent 54a3228 commit 2adb321
Showing 1 changed file with 12 additions and 8 deletions.
20 changes: 12 additions & 8 deletions nmdc_automation/config/workflows/workflows.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
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