added fastq-scan JSON outputs to read_qc_trim_pe subwf and theiacov_i…

…llumina_pe wf
theiagen · Oct 29, 2024 · e9bbe00 · e9bbe00
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commit e9bbe00
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diff --git a/workflows/theiacov/wf_theiacov_illumina_pe.wdl b/workflows/theiacov/wf_theiacov_illumina_pe.wdl
@@ -260,6 +260,10 @@ workflow theiacov_illumina_pe {
     Int? fastq_scan_num_reads_clean1 = read_QC_trim.fastq_scan_clean1
     Int? fastq_scan_num_reads_clean2 = read_QC_trim.fastq_scan_clean2
     String? fastq_scan_num_reads_clean_pairs = read_QC_trim.fastq_scan_clean_pairs
+    File? fastq_scan_raw1_json = read_QC_trim.fastq_scan_raw1_json
+    File? fastq_scan_raw2_json = read_QC_trim.fastq_scan_raw2_json
+    File? fastq_scan_clean1_json = read_QC_trim.fastq_scan_clean1_json
+    File? fastq_scan_clean2_json = read_QC_trim.fastq_scan_clean2_json
     # Read QC - fastqc outputs
     Int? fastqc_num_reads_raw1 = read_QC_trim.fastqc_raw1
     Int? fastqc_num_reads_raw2 = read_QC_trim.fastqc_raw2

diff --git a/workflows/utilities/wf_read_QC_trim_pe.wdl b/workflows/utilities/wf_read_QC_trim_pe.wdl
@@ -174,6 +174,10 @@ workflow read_QC_trim_pe {
     String? fastq_scan_clean_pairs = fastq_scan_clean.read_pairs
     String? fastq_scan_version = fastq_scan_raw.version
     String? fastq_scan_docker = fastq_scan_raw.fastq_scan_docker
+    File? fastq_scan_raw1_json = fastq_scan_raw.read1_fastq_scan_json
+    File? fastq_scan_raw2_json = fastq_scan_raw.read2_fastq_scan_json
+    File? fastq_scan_clean1_json = fastq_scan_clean.read1_fastq_scan_json
+    File? fastq_scan_clean2_json = fastq_scan_clean.read2_fastq_scan_json
 
     # fastqc
     Int? fastqc_raw1 = fastqc_raw.read1_seq