From e9bbe00299b246b7a88670d12bb73f169f19024d Mon Sep 17 00:00:00 2001 From: Curtis Kapsak Date: Tue, 29 Oct 2024 16:12:44 +0000 Subject: [PATCH] added fastq-scan JSON outputs to read_qc_trim_pe subwf and theiacov_illumina_pe wf --- workflows/theiacov/wf_theiacov_illumina_pe.wdl | 4 ++++ workflows/utilities/wf_read_QC_trim_pe.wdl | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/workflows/theiacov/wf_theiacov_illumina_pe.wdl b/workflows/theiacov/wf_theiacov_illumina_pe.wdl index ece3c201a..17939fdc4 100644 --- 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 index bb79c260d..0d6090036 100644 --- 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