do the same for theiacov_ont

theiagen · Nov 7, 2024 · 2b055a4 · 2b055a4
1 parent 2983982
commit 2b055a4
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Showing 2 changed files with 12 additions and 3 deletions.
diff --git a/tests/inputs/theiacov/wf_theiacov_ont.json b/tests/inputs/theiacov/wf_theiacov_ont.json
@@ -3,5 +3,6 @@
     "theiacov_ont.read1": "tests/data/theiacov/fastqs/ont/ont.fastq.gz",
     "theiacov_ont.primer_bed": "tests/data/theiacov/primers/artic-v3.primers.bed",
     "theiacov_ont.reference_genome": "tests/data/theiacov/reference/MN908947.fasta",
-    "theiacov_ont.reference_gene_locations_bed": "tests/inputs/sc2_gene_locations.bed"
+    "theiacov_ont.reference_gene_locations_bed": "tests/inputs/sc2_gene_locations.bed",
+    "theiacov_ont.read_qc_trim.kraken_db": "tests/data/theiacov/databases/github_kraken2_test_db.tar.gz"
 }
diff --git a/workflows/utilities/wf_read_QC_trim_ont.wdl b/workflows/utilities/wf_read_QC_trim_ont.wdl
@@ -56,7 +56,11 @@ workflow read_QC_trim_ont {
       input:
         samplename = samplename,
         read1 = read1,
-        target_organism = target_organism
+        target_organism = target_organism,
+        kraken2_db = kraken_db,
+        disk_size = kraken_disk_size,
+        memory = kraken_memory,
+        cpu = kraken_cpu
     }
     call kraken2.kraken2_parse_classified as kraken2_recalculate_abundances_raw {
       input:
@@ -69,7 +73,11 @@ workflow read_QC_trim_ont {
       input:
         samplename = samplename,
         read1 = ncbi_scrub_se.read1_dehosted,
-        target_organism = target_organism
+        target_organism = target_organism,
+        kraken2_db = kraken_db,
+        disk_size = kraken_disk_size,
+        memory = kraken_memory,
+        cpu = kraken_cpu
     }
     call kraken2.kraken2_parse_classified as kraken2_recalculate_abundances_dehosted {
       input: