added fastq-scan JSON outputs to export_taxon_tables task and added a…

…s inputs to theiaprok_illumina_pe and se workflows. need to test in terra
theiagen · Nov 4, 2024 · 55fbbde · 55fbbde
1 parent 5f37276
commit 55fbbde
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diff --git a/tasks/utilities/data_export/task_broad_terra_tools.wdl b/tasks/utilities/data_export/task_broad_terra_tools.wdl
@@ -35,6 +35,10 @@ task export_taxon_tables {
     Int? num_reads_raw2
     String? num_reads_raw_pairs
     String? fastq_scan_version
+    File? fastq_scan_raw1_json
+    File? fastq_scan_raw2_json
+    File? fastq_scan_clean1_json
+    File? fastq_scan_clean2_json
     Int? num_reads_clean1
     Int? num_reads_clean2
     String? num_reads_clean_pairs
@@ -446,6 +450,10 @@ task export_taxon_tables {
       "num_reads_raw2": "~{num_reads_raw2}",
       "num_reads_raw_pairs": "~{num_reads_raw_pairs}",
       "fastq_scan_version": "~{fastq_scan_version}",
+      "fastq_scan_raw1_json": "~{fastq_scan_raw1_json}",
+      "fastq_scan_raw2_json": "~{fastq_scan_raw2_json}",
+      "fastq_scan_clean1_json": "~{fastq_scan_clean1_json}",
+      "fastq_scan_clean2_json": "~{fastq_scan_clean2_json}",
       "num_reads_clean1": "~{num_reads_clean1}",
       "num_reads_clean2": "~{num_reads_clean2}",
       "num_reads_clean_pairs": "~{num_reads_clean_pairs}",

diff --git a/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl b/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
@@ -277,6 +277,10 @@ workflow theiaprok_illumina_pe {
               num_reads_clean1 = read_QC_trim.fastq_scan_clean1,
               num_reads_clean2 = read_QC_trim.fastq_scan_clean2,
               num_reads_clean_pairs = read_QC_trim.fastq_scan_clean_pairs,
+              fastq_scan_raw1_json = read_QC_trim.fastq_scan_raw1_json,
+              fastq_scan_raw2_json = read_QC_trim.fastq_scan_raw2_json,
+              fastq_scan_clean1_json = read_QC_trim.fastq_scan_clean1_json,
+              fastq_scan_clean2_json = read_QC_trim.fastq_scan_clean2_json,
               trimmomatic_version = read_QC_trim.trimmomatic_version,
               fastp_version = read_QC_trim.fastp_version,
               bbduk_docker = read_QC_trim.bbduk_docker,

diff --git a/workflows/theiaprok/wf_theiaprok_illumina_se.wdl b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
@@ -254,6 +254,8 @@ workflow theiaprok_illumina_se {
               num_reads_raw1 = read_QC_trim.fastq_scan_raw1,
               fastq_scan_version = read_QC_trim.fastq_scan_version,
               num_reads_clean1 = read_QC_trim.fastq_scan_clean1,
+              fastq_scan_raw1_json = read_QC_trim.fastq_scan_raw1_json,
+              fastq_scan_clean1_json = read_QC_trim.fastq_scan_clean1_json,
               trimmomatic_version = read_QC_trim.trimmomatic_version,
               fastp_version = read_QC_trim.fastp_version,
               bbduk_docker = read_QC_trim.bbduk_docker,