chore: rename workflow outputs for Terra table column naming

carze · carze · commit 0a7f99b449e6 · 2026-04-06T13:03:58.000-04:00
- parse_kraken2_reads: read_taxonomy -&gt; kraken2_reads_classified
- summarize_kb_extract_reads: summary_tsv_zst -&gt; kallisto_read_classifications
- classify_virnucpro_contigs: contig_classifications -&gt; virnucpro_contigs_classifications
- classify_reads_by_contig: read_classifications -&gt; virnucpro_reads_classifications
- join_read_classifications: classifications_parquet -&gt; classifications_summary
diff --git a/pipes/WDL/workflows/classify_reads_by_contig.wdl b/pipes/WDL/workflows/classify_reads_by_contig.wdl
@@ -29,6 +29,6 @@ workflow classify_reads_by_contig {
     }
 
     output {
-        File read_classifications = classify_reads.read_classifications
+        File virnucpro_reads_classifications = classify_reads.read_classifications
     }
 }
diff --git a/pipes/WDL/workflows/classify_virnucpro_contigs.wdl b/pipes/WDL/workflows/classify_virnucpro_contigs.wdl
@@ -31,6 +31,6 @@ workflow classify_virnucpro_contigs {
     }
 
     output {
-        File contig_classifications = classify_contigs.contig_classifications
+        File virnucpro_contigs_classifications = classify_contigs.contig_classifications
     }
 }
diff --git a/pipes/WDL/workflows/join_read_classifications.wdl b/pipes/WDL/workflows/join_read_classifications.wdl
@@ -28,6 +28,6 @@ workflow join_read_classifications {
     }
 
     output {
-        File classifications_parquet = join_reads.classifications_parquet
+        File classifications_summary = join_reads.classifications_parquet
     }
 }
diff --git a/pipes/WDL/workflows/parse_kraken2_reads.wdl b/pipes/WDL/workflows/parse_kraken2_reads.wdl
@@ -26,6 +26,6 @@ workflow parse_kraken2_reads {
     }
 
     output {
-        File read_taxonomy = parse_reads.read_taxonomy
+        File kraken2_reads_classified = parse_reads.read_taxonomy
     }
 }
diff --git a/pipes/WDL/workflows/summarize_kb_extract_reads.wdl b/pipes/WDL/workflows/summarize_kb_extract_reads.wdl
@@ -24,6 +24,6 @@ workflow summarize_kb_extract_reads {
     }
 
     output {
-        File summary_tsv_zst = summarize.summary_tsv_zst
+        File kallisto_read_classifications = summarize.summary_tsv_zst
     }
 }

Original file line number	Diff line number	Diff line change
`@@ -29,6 +29,6 @@ workflow classify_reads_by_contig {`
`29`	`29`	`}`
`30`	`30`
`31`	`31`	`output {`
`32`		`- File read_classifications = classify_reads.read_classifications`
	`32`	`+ File virnucpro_reads_classifications = classify_reads.read_classifications`
`33`	`33`	`}`
`34`	`34`	`}`
Original file line number	Diff line number	Diff line change
`@@ -31,6 +31,6 @@ workflow classify_virnucpro_contigs {`
`31`	`31`	`}`
`32`	`32`
`33`	`33`	`output {`
`34`		`- File contig_classifications = classify_contigs.contig_classifications`
	`34`	`+ File virnucpro_contigs_classifications = classify_contigs.contig_classifications`
`35`	`35`	`}`
`36`	`36`	`}`
Original file line number	Diff line number	Diff line change
`@@ -28,6 +28,6 @@ workflow join_read_classifications {`
`28`	`28`	`}`
`29`	`29`
`30`	`30`	`output {`
`31`		`- File classifications_parquet = join_reads.classifications_parquet`
	`31`	`+ File classifications_summary = join_reads.classifications_parquet`
`32`	`32`	`}`
`33`	`33`	`}`
Original file line number	Diff line number	Diff line change
`@@ -26,6 +26,6 @@ workflow parse_kraken2_reads {`
`26`	`26`	`}`
`27`	`27`
`28`	`28`	`output {`
`29`		`- File read_taxonomy = parse_reads.read_taxonomy`
	`29`	`+ File kraken2_reads_classified = parse_reads.read_taxonomy`
`30`	`30`	`}`
`31`	`31`	`}`
Original file line number	Diff line number	Diff line change
`@@ -24,6 +24,6 @@ workflow summarize_kb_extract_reads {`
`24`	`24`	`}`
`25`	`25`
`26`	`26`	`output {`
`27`		`- File summary_tsv_zst = summarize.summary_tsv_zst`
	`27`	`+ File kallisto_read_classifications = summarize.summary_tsv_zst`
`28`	`28`	`}`
`29`	`29`	`}`