From 55fbbde55235573f57621936a66800d07fc923ce Mon Sep 17 00:00:00 2001 From: Curtis Kapsak Date: Mon, 4 Nov 2024 14:47:32 +0000 Subject: [PATCH] added fastq-scan JSON outputs to export_taxon_tables task and added as inputs to theiaprok_illumina_pe and se workflows. need to test in terra --- tasks/utilities/data_export/task_broad_terra_tools.wdl | 8 ++++++++ workflows/theiaprok/wf_theiaprok_illumina_pe.wdl | 4 ++++ workflows/theiaprok/wf_theiaprok_illumina_se.wdl | 2 ++ 3 files changed, 14 insertions(+) diff --git a/tasks/utilities/data_export/task_broad_terra_tools.wdl b/tasks/utilities/data_export/task_broad_terra_tools.wdl index 3a3fba0fd..12e79348c 100644 --- 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 index d71c5e324..718415206 100644 --- 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 index 1c3eee081..bcf1132b7 100644 --- 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,