diff --git a/docs/workflows/genomic_characterization/freyja.md b/docs/workflows/genomic_characterization/freyja.md
index b3e2f4b6f..f93428521 100644
--- a/docs/workflows/genomic_characterization/freyja.md
+++ b/docs/workflows/genomic_characterization/freyja.md
@@ -327,12 +327,16 @@ The main output file used in subsequent Freyja workflows is found under the `fre
 | bwa_version | String | Version of BWA used to map read data to the reference genome | PE, SE |
 | fastp_html_report | File | The HTML report made with fastp | PE, SE |
 | fastp_version | String | Version of fastp software used | PE, SE |
+| fastq_scan_clean1_json | File | JSON file output from `fastq-scan` containing summary stats about clean forward read quality and length | PE, SE |
+| fastq_scan_clean2_json | File | JSON file output from `fastq-scan` containing summary stats about clean reverse read quality and length | PE |
 | fastq_scan_num_reads_clean_pairs | String | Number of clean read pairs | PE |
 | fastq_scan_num_reads_clean1 | Int | Number of clean forward reads | PE, SE |
 | fastq_scan_num_reads_clean2 | Int | Number of clean reverse reads | PE |
 | fastq_scan_num_reads_raw_pairs | String | Number of raw read pairs | PE |
 | fastq_scan_num_reads_raw1 | Int | Number of raw forward reads | PE, SE |
 | fastq_scan_num_reads_raw2 | Int | Number of raw reverse reads | PE |
+| fastq_scan_raw1_json | File | JSON file output from `fastq-scan` containing summary stats about raw forward read quality and length | PE, SE |
+| fastq_scan_raw2_json | File | JSON file output from `fastq-scan` containing summary stats about raw reverse read quality and length | PE |
 | fastq_scan_version | String | Version of fastq_scan used for read QC analysis | PE, SE |
 | fastqc_clean1_html | File | Graphical visualization of clean forward read quality from fastqc to open in an internet browser | PE, SE |
 | fastqc_clean2_html | File | Graphical visualization of clean reverse read quality from fastqc to open in an internet browser | PE |
diff --git a/docs/workflows/genomic_characterization/theiacov.md b/docs/workflows/genomic_characterization/theiacov.md
index ba7eac3c4..ffe0993f6 100644
--- a/docs/workflows/genomic_characterization/theiacov.md
+++ b/docs/workflows/genomic_characterization/theiacov.md
@@ -1026,6 +1026,8 @@ All TheiaCoV Workflows (not TheiaCoV_FASTA_Batch)
 | est_percent_gene_coverage_tsv | File | Percent coverage for each gene in the organism being analyzed (depending on the organism input) | CL, ONT, PE, SE |
 | fastp_html_report | File | HTML report for fastp | PE, SE |
 | fastp_version | String | Fastp version used | PE, SE |
+| fastq_scan_clean1_json | File | JSON file output from `fastq-scan` containing summary stats about clean forward read quality and length | PE, SE, CL |
+| fastq_scan_clean2_json | File | JSON file output from `fastq-scan` containing summary stats about clean reverse read quality and length | PE |
 | fastq_scan_num_reads_clean_pairs | String | Number of paired reads after filtering as determined by fastq_scan | PE |
 | fastq_scan_num_reads_clean1 | Int | Number of forward reads after filtering as determined by fastq_scan | CL, PE, SE |
 | fastq_scan_num_reads_clean2 | Int | Number of reverse reads after filtering as determined by fastq_scan | PE |
@@ -1036,6 +1038,8 @@ All TheiaCoV Workflows (not TheiaCoV_FASTA_Batch)
 | fastq_scan_r1_mean_q_raw | Float | Forward read mean quality value before quality trimming and adapter removal |  |
 | fastq_scan_r1_mean_readlength_clean | Float | Forward read mean read length value after quality trimming and adapter removal |  |
 | fastq_scan_r1_mean_readlength_raw | Float | Forward read mean read length value before quality trimming and adapter removal |  |
+| fastq_scan_raw1_json | File | JSON file output from `fastq-scan` containing summary stats about raw forward read quality and length | PE, SE, CL |
+| fastq_scan_raw2_json | File | JSON file output from `fastq-scan` containing summary stats about raw reverse read quality and length | PE |
 | fastq_scan_version | String | Version of fastq_scan used for read QC analysis | CL, PE, SE |
 | fastqc_clean1_html | File | Graphical visualization of clean forward read quality from fastqc to open in an internet browser | PE, SE |
 | fastqc_clean2_html | File | Graphical visualization of clean reverse read quality  from fastqc to open in an internet browser | PE |
diff --git a/docs/workflows/genomic_characterization/theiaeuk.md b/docs/workflows/genomic_characterization/theiaeuk.md
index 19141cd05..bedeac0cf 100644
--- a/docs/workflows/genomic_characterization/theiaeuk.md
+++ b/docs/workflows/genomic_characterization/theiaeuk.md
@@ -484,6 +484,10 @@ The TheiaEuk workflow automatically activates taxa-specific tasks after identifi
 | cg_pipeline_report | File | TSV file of read metrics from raw reads, including average read length, number of reads, and estimated genome coverage |
 | est_coverage_clean | Float | Estimated coverage calculated from   clean reads and genome length |
 | est_coverage_raw | Float | Estimated coverage calculated from  raw reads and genome length |
+| fastq_scan_clean1_json | File | JSON file output from `fastq-scan` containing summary stats about clean forward read quality and length |
+| fastq_scan_clean2_json | File | JSON file output from `fastq-scan` containing summary stats about clean reverse read quality and length |
+| fastq_scan_raw1_json | File | JSON file output from `fastq-scan` containing summary stats about raw forward read quality and length |
+| fastq_scan_raw2_json | File | JSON file output from `fastq-scan` containing summary stats about raw reverse read quality and length |
 | r1_mean_q_clean | Float | Mean quality score of clean forward reads |
 | r1_mean_q_raw | Float | Mean quality score of raw forward reads |
 | r2_mean_q_clean | Float | Mean quality score of clean reverse reads |
diff --git a/docs/workflows/genomic_characterization/theiameta.md b/docs/workflows/genomic_characterization/theiameta.md
index 55c26d9a6..6e9147399 100644
--- a/docs/workflows/genomic_characterization/theiameta.md
+++ b/docs/workflows/genomic_characterization/theiameta.md
@@ -295,12 +295,16 @@ The TheiaMeta_Illumina_PE workflow processes Illumina paired-end (PE) reads ge
 | fastp_html_report | File | Report file for fastp in HTML format |
 | fastp_version | String | Version of fastp used |
 | fastq_scan_docker | String | Docker image of fastq_scan |
+| fastq_scan_clean1_json | File | JSON file output from `fastq-scan` containing summary stats about clean forward read quality and length |
+| fastq_scan_clean2_json | File | JSON file output from `fastq-scan` containing summary stats about clean reverse read quality and length |
 | fastq_scan_num_reads_clean_pairs | String | Number of read pairs after cleaning as calculated by fastq_scan |
 | fastq_scan_num_reads_clean1 | Int | Number of forward reads after cleaning as calculated by fastq_scan |
 | fastq_scan_num_reads_clean2 | Int | Number of reverse reads after cleaning as calculated by fastq_scan |
 | fastq_scan_num_reads_raw_pairs | String | Number of input read pairs as calculated by fastq_scan |
 | fastq_scan_num_reads_raw1 | Int | Number of input forward reads as calculated by fastq_scan |
 | fastq_scan_num_reads_raw2 | Int | Number of input reserve reads as calculated by fastq_scan |
+| fastq_scan_raw1_json | File | JSON file output from `fastq-scan` containing summary stats about raw forward read quality and length |
+| fastq_scan_raw2_json | File | JSON file output from `fastq-scan` containing summary stats about raw reverse read quality and length |
 | fastq_scan_version | String | fastq_scan version |
 | fastqc_clean1_html | File | Graphical visualization of clean forward read quality from fastqc to open in an internet browser |
 | fastqc_clean2_html | File | Graphical visualization of clean reverse read quality from fastqc to open in an internet browser |
diff --git a/docs/workflows/genomic_characterization/theiaprok.md b/docs/workflows/genomic_characterization/theiaprok.md
index 2b5f5308d..6664df6df 100644
--- a/docs/workflows/genomic_characterization/theiaprok.md
+++ b/docs/workflows/genomic_characterization/theiaprok.md
@@ -1731,12 +1731,16 @@ The TheiaProk workflows automatically activate taxa-specific sub-workflows after
 | est_coverage_raw | Float | Estimated coverage calculated from raw reads and genome length | ONT, PE, SE |
 | fastp_html_report | File | The HTML report made with fastp | PE, SE |
 | fastp_version | String | Version of fastp software used | PE, SE |
+| fastq_scan_clean1_json | File | JSON file output from `fastq-scan` containing summary stats about clean forward read quality and length | PE, SE |
+| fastq_scan_clean2_json | File | JSON file output from `fastq-scan` containing summary stats about clean reverse read quality and length | PE |
 | fastq_scan_num_reads_clean_pairs | String | Number of read pairs after cleaning as calculated by fastq_scan | PE |
 | fastq_scan_num_reads_clean1 | Int | Number of forward reads after cleaning as calculated by fastq_scan | PE, SE |
 | fastq_scan_num_reads_clean2 | Int | Number of reverse reads after cleaning as calculated by fastq_scan | PE |
 | fastq_scan_num_reads_raw_pairs | String | Number of input read pairs calculated by fastq_scan | PE |
 | fastq_scan_num_reads_raw1 | Int | Number of input forward reads calculated by fastq_scan | PE, SE |
 | fastq_scan_num_reads_raw2 | Int | Number of input reverse reads calculated by fastq_scan | PE |
+| fastq_scan_raw1_json | File | JSON file output from `fastq-scan` containing summary stats about raw forward read quality and length | PE, SE |
+| fastq_scan_raw2_json | File | JSON file output from `fastq-scan` containing summary stats about raw reverse read quality and length | PE |
 | fastq_scan_version | String | Version of fastq-scan software used | PE, SE |
 | fastqc_clean1_html | File | Graphical visualization of clean forward read quality from fastqc to open in an internet browser | PE, SE |
 | fastqc_clean2_html | File | Graphical visualization of clean reverse read quality from fastqc to open in an internet browser | PE |
diff --git a/tasks/quality_control/basic_statistics/task_fastq_scan.wdl b/tasks/quality_control/basic_statistics/task_fastq_scan.wdl
index 029b94917..e2f4a2d4d 100644
--- a/tasks/quality_control/basic_statistics/task_fastq_scan.wdl
+++ b/tasks/quality_control/basic_statistics/task_fastq_scan.wdl
@@ -6,14 +6,16 @@ task fastq_scan_pe {
     File read2
     String read1_name = basename(basename(basename(read1, ".gz"), ".fastq"), ".fq")
     String read2_name = basename(basename(basename(read2, ".gz"), ".fastq"), ".fq")
-    Int disk_size = 100
-    String docker = "quay.io/biocontainers/fastq-scan:0.4.4--h7d875b9_1"
+    Int disk_size = 50
+    String docker = "us-docker.pkg.dev/general-theiagen/biocontainers/fastq-scan:1.0.1--h4ac6f70_3"
     Int memory = 2
-    Int cpu = 2
+    Int cpu = 1
   }
   command <<<
-    # capture date and version
-    date | tee DATE
+    # exit task in case anything fails in one-liners or variables are unset
+    set -euo pipefail
+
+    # capture version
     fastq-scan -v | tee VERSION
 
     # set cat command based on compression
@@ -24,11 +26,21 @@ task fastq_scan_pe {
     fi
 
     # capture forward read stats
+    echo "DEBUG: running fastq-scan on $(basename ~{read1})"
     eval "${cat_reads} ~{read1}" | fastq-scan | tee ~{read1_name}_fastq-scan.json
-    cat ~{read1_name}_fastq-scan.json | jq .qc_stats.read_total | tee READ1_SEQS
+    # using simple redirect so STDOUT is not confusing
+    jq .qc_stats.read_total ~{read1_name}_fastq-scan.json > READ1_SEQS
+    echo "DEBUG: number of reads in $(basename ~{read1}): $(cat READ1_SEQS)"
     read1_seqs=$(cat READ1_SEQS)
+    echo
+
+    # capture reverse read stats
+    echo "DEBUG: running fastq-scan on $(basename ~{read2})"
     eval "${cat_reads} ~{read2}" | fastq-scan | tee ~{read2_name}_fastq-scan.json
-    cat ~{read2_name}_fastq-scan.json | jq .qc_stats.read_total | tee READ2_SEQS
+
+    # using simple redirect so STDOUT is not confusing
+    jq .qc_stats.read_total ~{read2_name}_fastq-scan.json > READ2_SEQS
+    echo "DEBUG: number of reads in $(basename ~{read2}): $(cat READ2_SEQS)"
     read2_seqs=$(cat READ2_SEQS)
 
     # capture number of read pairs
@@ -37,17 +49,18 @@ task fastq_scan_pe {
     else
       read_pairs="Uneven pairs: R1=${read1_seqs}, R2=${read2_seqs}"
     fi
-
-    echo $read_pairs | tee READ_PAIRS
+    
+    # use simple redirect so STDOUT is not confusing
+    echo "$read_pairs" > READ_PAIRS
+    echo "DEBUG: number of read pairs: $(cat READ_PAIRS)"
   >>>
   output {
-    File read1_fastq_scan_report = "~{read1_name}_fastq-scan.json"
-    File read2_fastq_scan_report = "~{read2_name}_fastq-scan.json"
+    File read1_fastq_scan_json = "~{read1_name}_fastq-scan.json"
+    File read2_fastq_scan_json = "~{read2_name}_fastq-scan.json"
     Int read1_seq = read_int("READ1_SEQS")
     Int read2_seq = read_int("READ2_SEQS")
     String read_pairs = read_string("READ_PAIRS")
     String version = read_string("VERSION")
-    String pipeline_date = read_string("DATE")
     String fastq_scan_docker = docker
   }
   runtime {
@@ -55,8 +68,8 @@ task fastq_scan_pe {
     memory: memory + " GB"
     cpu: cpu
     disks:  "local-disk " + disk_size + " SSD"
-    disk: disk_size + " GB" # TES
-    preemptible: 0
+    disk: disk_size + " GB"
+    preemptible: 1
     maxRetries: 3
   }
 }
@@ -65,14 +78,16 @@ task fastq_scan_se {
   input {
     File read1
     String read1_name = basename(basename(basename(read1, ".gz"), ".fastq"), ".fq")
-    Int disk_size = 100
+    Int disk_size = 50
     Int memory = 2
-    Int cpu = 2
-    String docker = "quay.io/biocontainers/fastq-scan:0.4.4--h7d875b9_1"
+    Int cpu = 1
+    String docker = "us-docker.pkg.dev/general-theiagen/biocontainers/fastq-scan:1.0.1--h4ac6f70_3"
   }
   command <<<
-    # capture date and version
-    date | tee DATE
+    # exit task in case anything fails in one-liners or variables are unset
+    set -euo pipefail
+    
+    # capture version
     fastq-scan -v | tee VERSION
 
     # set cat command based on compression
@@ -83,14 +98,16 @@ task fastq_scan_se {
     fi
 
     # capture forward read stats
+    echo "DEBUG: running fastq-scan on $(basename ~{read1})"
     eval "${cat_reads} ~{read1}" | fastq-scan | tee ~{read1_name}_fastq-scan.json
-    cat ~{read1_name}_fastq-scan.json | jq .qc_stats.read_total | tee READ1_SEQS
+    # using simple redirect so STDOUT is not confusing
+    jq .qc_stats.read_total ~{read1_name}_fastq-scan.json > READ1_SEQS
+    echo "DEBUG: number of reads in $(basename ~{read1}): $(cat READ1_SEQS)"
   >>>
   output {
-    File fastq_scan_report = "~{read1_name}_fastq-scan.json"
+    File fastq_scan_json = "~{read1_name}_fastq-scan.json"
     Int read1_seq = read_int("READ1_SEQS")
     String version = read_string("VERSION")
-    String pipeline_date = read_string("DATE")
     String fastq_scan_docker = docker
   }
   runtime {
@@ -98,8 +115,8 @@ task fastq_scan_se {
     memory: memory + " GB"
     cpu: cpu
     disks:  "local-disk " + disk_size + " SSD"
-    disk: disk_size + " GB" # TES
-    preemptible: 0
+    disk: disk_size + " GB"
+    preemptible: 1
     maxRetries: 3
   }
 }
diff --git a/tasks/utilities/data_export/task_broad_terra_tools.wdl b/tasks/utilities/data_export/task_broad_terra_tools.wdl
index 5292ccbc9..8a54d6bad 100644
--- a/tasks/utilities/data_export/task_broad_terra_tools.wdl
+++ b/tasks/utilities/data_export/task_broad_terra_tools.wdl
@@ -35,6 +35,10 @@ task export_taxon_tables {
     Int? num_reads_raw2
     String? num_reads_raw_pairs
     String? fastq_scan_version
+    File? fastq_scan_raw1_json
+    File? fastq_scan_raw2_json
+    File? fastq_scan_clean1_json
+    File? fastq_scan_clean2_json
     Int? num_reads_clean1
     Int? num_reads_clean2
     String? num_reads_clean_pairs
@@ -391,7 +395,7 @@ task export_taxon_tables {
   }
   command <<<
     set -euo pipefail
-    
+
     # capture taxon and corresponding table names from input taxon_tables
     taxon_array=($(cut -f1 ~{taxon_tables} | tail +2))
     echo "Taxon array: ${taxon_array[*]}"
@@ -447,6 +451,10 @@ 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}",
@@ -779,7 +787,7 @@ task export_taxon_tables {
       "agrvate_version": "~{agrvate_version}",
       "agrvate_docker": "~{agrvate_docker}",
       "srst2_vibrio_detailed_tsv": "~{srst2_vibrio_detailed_tsv}",
-      "srst2_vibrio_version": "~{srst2_vibrio_version}",~
+      "srst2_vibrio_version": "~{srst2_vibrio_version}",
       "srst2_vibrio_docker": "~{srst2_vibrio_docker}",
       "srst2_vibrio_database": "~{srst2_vibrio_database}",
       "srst2_vibrio_ctxA": "~{srst2_vibrio_ctxA}",
diff --git a/tests/config/environment.yml b/tests/config/environment.yml
index 0aed07151..c4016d3ae 100644
--- a/tests/config/environment.yml
+++ b/tests/config/environment.yml
@@ -2,7 +2,6 @@ name: pytest-env-CI
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - python >=3.7
   - cromwell=86
diff --git a/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml b/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml
index fe20263a2..a7108f67f 100644
--- a/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml
+++ b/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml
@@ -115,17 +115,16 @@
     - path: miniwdl_run/call-fastq_scan_clean_reads/inputs.json
       contains: ["read1", "clearlabs"]
     - path: miniwdl_run/call-fastq_scan_clean_reads/outputs.json
-      contains: ["fastq_scan_se", "pipeline_date", "read1_seq"]
+      contains: ["fastq_scan_se", "read1_seq"]
     - path: miniwdl_run/call-fastq_scan_clean_reads/stderr.txt
     - path: miniwdl_run/call-fastq_scan_clean_reads/stderr.txt.offset
     - path: miniwdl_run/call-fastq_scan_clean_reads/stdout.txt
     - path: miniwdl_run/call-fastq_scan_clean_reads/task.log
       contains: ["wdl", "theiacov_clearlabs", "fastq_scan_clean_reads", "done"]
-    - path: miniwdl_run/call-fastq_scan_clean_reads/work/DATE
     - path: miniwdl_run/call-fastq_scan_clean_reads/work/READ1_SEQS
       md5sum: 097e79b36919c8377c56088363e3d8b7
     - path: miniwdl_run/call-fastq_scan_clean_reads/work/VERSION
-      md5sum: 8e4e9cdfbacc9021a3175ccbbbde002b
+      md5sum: a59bb42644e35c09b8fa8087156fa4c2
     - path: miniwdl_run/call-fastq_scan_clean_reads/work/_miniwdl_inputs/0/clearlabs_R1_dehosted.fastq.gz
     - path: miniwdl_run/call-fastq_scan_clean_reads/work/clearlabs_R1_dehosted_fastq-scan.json
       md5sum: 869dd2e934c600bba35f30f08e2da7c9
@@ -134,17 +133,16 @@
     - path: miniwdl_run/call-fastq_scan_raw_reads/inputs.json
       contains: ["read1", "clearlabs"]
     - path: miniwdl_run/call-fastq_scan_raw_reads/outputs.json
-      contains: ["fastq_scan_se", "pipeline_date", "read1_seq"]
+      contains: ["fastq_scan_se", "read1_seq"]
     - path: miniwdl_run/call-fastq_scan_raw_reads/stderr.txt
     - path: miniwdl_run/call-fastq_scan_raw_reads/stderr.txt.offset
     - path: miniwdl_run/call-fastq_scan_raw_reads/stdout.txt
     - path: miniwdl_run/call-fastq_scan_raw_reads/task.log
       contains: ["wdl", "theiacov_clearlabs", "fastq_scan_raw_reads", "done"]
-    - path: miniwdl_run/call-fastq_scan_raw_reads/work/DATE
     - path: miniwdl_run/call-fastq_scan_raw_reads/work/READ1_SEQS
       md5sum: 097e79b36919c8377c56088363e3d8b7
     - path: miniwdl_run/call-fastq_scan_raw_reads/work/VERSION
-      md5sum: 8e4e9cdfbacc9021a3175ccbbbde002b
+      md5sum: a59bb42644e35c09b8fa8087156fa4c2
     - path: miniwdl_run/call-fastq_scan_raw_reads/work/_miniwdl_inputs/0/clearlabs.fastq.gz
     - path: miniwdl_run/call-fastq_scan_raw_reads/work/clearlabs_fastq-scan.json
       md5sum: 869dd2e934c600bba35f30f08e2da7c9
diff --git a/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml b/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml
index dfef9c994..1ff0b33b8 100644
--- a/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml
+++ b/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml
@@ -60,11 +60,11 @@
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     # fastq scan raw
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/command
-      md5sum: 9b2cc0107f1a90972482d7b3a658d242
+      md5sum: 56bcc1ba5d2a9c94f4704fc4b8e6b7ba
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/inputs.json
       contains: ["read1", "read2", "illumina_pe"]
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/outputs.json
-      contains: ["fastq_scan_pe", "pipeline_date", "read1_seq", "read2_seq"]
+      contains: ["fastq_scan_pe", "read1_seq", "read2_seq"]
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/stderr.txt
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/stderr.txt.offset
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/stdout.txt
@@ -74,7 +74,6 @@
       md5sum: 2a77387b247176aa5fcc9aed228699c9
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/SRR13687078_2_fastq-scan.json
       md5sum: d0eebdd4e14cf0a0b371fee1338474c9
-    - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/DATE
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/READ1_SEQS
       md5sum: 4e4a08422dbf7001fd09ad5126e13b44
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/READ2_SEQS
diff --git a/tests/workflows/theiacov/test_wf_theiacov_illumina_se.yml b/tests/workflows/theiacov/test_wf_theiacov_illumina_se.yml
index 22453bdd5..99668f641 100644
--- a/tests/workflows/theiacov/test_wf_theiacov_illumina_se.yml
+++ b/tests/workflows/theiacov/test_wf_theiacov_illumina_se.yml
@@ -56,11 +56,11 @@
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     # fastq scan raw
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/command
-      md5sum: 56f66a4ef82d3ae03c17db6a26f59528
+      md5sum: f96c3103490fff3560fc930a84bd459d
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/inputs.json
       contains: ["read1", "illumina_se"]
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/outputs.json
-      contains: ["fastq_scan_se", "pipeline_date", "read1_seq"]
+      contains: ["fastq_scan_se", "read1_seq"]
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/stderr.txt
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/stderr.txt.offset
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/stdout.txt
@@ -68,7 +68,6 @@
       contains: ["wdl", "theiacov_illumina_se", "fastq_scan_raw", "done"]
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/ERR6319327_fastq-scan.json
       md5sum: 66b2f7c60b74de654f590d77bdd2231e
-    - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/DATE
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/READ1_SEQS
       md5sum: 87f1a9ed69127009aa0c173cd74c9d31
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/VERSION
diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
index ce057f3ed..aad099a4e 100644
--- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
+++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
@@ -416,14 +416,13 @@
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/inputs.json
       contains: ["read", "fastq"]
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/outputs.json
-      contains: ["read", "fastq", "fastq_scan_report"]
+      contains: ["read", "fastq", "fastq_scan_json"]
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/stderr.txt
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/stderr.txt.offset
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/stdout.txt
       contains: ["fastq", "qc_stats", "read_lengths"]
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/task.log
       contains: ["wdl", "theiaprok_illumina_pe", "fastq_scan_clean", "done"]
-    - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/DATE
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/READ1_SEQS
       md5sum: 5fcafec683df465a99878ceaffe8a294
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/READ2_SEQS
@@ -431,7 +430,7 @@
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/READ_PAIRS
       md5sum: 5fcafec683df465a99878ceaffe8a294
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/VERSION
-      md5sum: 8e4e9cdfbacc9021a3175ccbbbde002b
+      md5sum: a59bb42644e35c09b8fa8087156fa4c2
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/_miniwdl_inputs/0/test_1.clean.fastq.gz
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/_miniwdl_inputs/0/test_2.clean.fastq.gz
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/test_1.clean_fastq-scan.json
@@ -443,14 +442,13 @@
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/inputs.json
       contains: ["read", "fastq"]
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/outputs.json
-      contains: ["read", "fastq", "fastq_scan_report"]
+      contains: ["read", "fastq", "fastq_scan_json"]
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/stderr.txt
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/stderr.txt.offset
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/stdout.txt
       contains: ["fastq", "qc_stats", "read_lengths"]
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/task.log
       contains: ["wdl", "theiaprok_illumina_pe", "fastq_scan_raw", "done"]
-    - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/DATE
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/READ1_SEQS
       md5sum: 75fa2f47fecb5dec8d244366881e76ec
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/READ2_SEQS
@@ -462,7 +460,7 @@
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/SRR2838702_R2_fastq-scan.json
       md5sum: e81f34050c11995771de79182f06d793
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/VERSION
-      md5sum: 8e4e9cdfbacc9021a3175ccbbbde002b
+      md5sum: a59bb42644e35c09b8fa8087156fa4c2
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/_miniwdl_inputs/0/SRR2838702_R1.fastq.gz
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/_miniwdl_inputs/0/SRR2838702_R2.fastq.gz
     - path: miniwdl_run/call-read_QC_trim/call-trimmomatic_pe/command
@@ -561,7 +559,7 @@
     - path: miniwdl_run/wdl/tasks/gene_typing/drug_resistance/task_resfinder.wdl
       md5sum: 27528633723303b462d095b642649453
     - path: miniwdl_run/wdl/tasks/gene_typing/variant_detection/task_snippy_variants.wdl
-      md5sum: 3b9e04569d7e856dcc649b7726b306b7
+      md5sum: 440a620a10ccdafe612f0b33ef05f86d
     - path: miniwdl_run/wdl/tasks/quality_control/read_filtering/task_bbduk.wdl
       md5sum: aec6ef024d6dff31723f44290f6b9cf5
     - path: miniwdl_run/wdl/tasks/quality_control/advanced_metrics/task_busco.wdl
@@ -631,7 +629,7 @@
     - path: miniwdl_run/wdl/tasks/utilities/data_export/task_broad_terra_tools.wdl
       md5sum: 850ad97598aca5c28eb36e6a5c13c2fc
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
-      md5sum: 3cb5c86b15e931b0c0b98ed784386438
+      md5sum: d8db687487a45536d4837a540ed2a135
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
       md5sum: ea5cff6eff8c2c42046cf2eae6f16b6f
     - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_pe.wdl
diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
index fbbd7d4fe..6a7e2a86a 100644
--- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
+++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
@@ -400,18 +400,17 @@
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/inputs.json
       contains: ["read", "fastq"]
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/outputs.json
-      contains: ["read", "fastq", "fastq_scan_report"]
+      contains: ["read", "fastq", "fastq_scan_json"]
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/stderr.txt
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/stderr.txt.offset
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/stdout.txt
       contains: ["fastq", "qc_stats", "read_lengths"]
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/task.log
       contains: ["wdl", "theiaprok_illumina_se", "fastq_scan_clean", "done"]
-    - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/DATE
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/READ1_SEQS
       md5sum: 499f7af0d267a13f5523ec9a60ec46e3
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/VERSION
-      md5sum: 8e4e9cdfbacc9021a3175ccbbbde002b
+      md5sum: a59bb42644e35c09b8fa8087156fa4c2
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/_miniwdl_inputs/0/test_1.clean.fastq.gz
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/test_1.clean_fastq-scan.json
       md5sum: eb30273b3f19578fec5360da8b255e28
@@ -420,20 +419,19 @@
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/inputs.json
       contains: ["read", "fastq"]
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/outputs.json
-      contains: ["read", "fastq", "fastq_scan_report"]
+      contains: ["read", "fastq", "fastq_scan_json"]
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/stderr.txt
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/stderr.txt.offset
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/stdout.txt
       contains: ["fastq", "qc_stats", "read_lengths"]
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/task.log
       contains: ["wdl", "theiaprok_illumina_se", "fastq_scan_raw", "done"]
-    - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/DATE
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/READ1_SEQS
       md5sum: 75fa2f47fecb5dec8d244366881e76ec
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/SRR2838702_R1_fastq-scan.json
       md5sum: c4a64c8fd27fa357206e0d41b74866e2
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/VERSION
-      md5sum: 8e4e9cdfbacc9021a3175ccbbbde002b
+      md5sum: a59bb42644e35c09b8fa8087156fa4c2
     - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/_miniwdl_inputs/0/SRR2838702_R1.fastq.gz
     - path: miniwdl_run/call-read_QC_trim/call-trimmomatic_se/command
       md5sum: a317f1a2182fe1a3b26812b54eff088e
@@ -526,7 +524,7 @@
     - path: miniwdl_run/wdl/tasks/gene_typing/drug_resistance/task_resfinder.wdl
       md5sum: 27528633723303b462d095b642649453
     - path: miniwdl_run/wdl/tasks/gene_typing/variant_detection/task_snippy_variants.wdl
-      md5sum: 3b9e04569d7e856dcc649b7726b306b7
+      md5sum: 440a620a10ccdafe612f0b33ef05f86d
     - path: miniwdl_run/wdl/tasks/quality_control/read_filtering/task_bbduk.wdl
       md5sum: aec6ef024d6dff31723f44290f6b9cf5
     - path: miniwdl_run/wdl/tasks/quality_control/advanced_metrics/task_busco.wdl
@@ -594,10 +592,10 @@
     - path: miniwdl_run/wdl/tasks/utilities/data_export/task_broad_terra_tools.wdl
       md5sum: 850ad97598aca5c28eb36e6a5c13c2fc
     - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
-      md5sum: fdb66b59ac886501a4ae90a25cefd633
+      md5sum: 4111a758490174325ae8ea52a95319e9
     - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
       md5sum: ea5cff6eff8c2c42046cf2eae6f16b6f
     - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_se.wdl
-      md5sum: d11bfe33fdd96eab28892be5a01c1c7d
+      md5sum: a7ef5a7a38dd60ff2edf699ae6808ebb
     - path: miniwdl_run/workflow.log
       contains: ["wdl", "theiaprok_illumina_se", "NOTICE", "done"]
diff --git a/workflows/freyja/wf_freyja_fastq.wdl b/workflows/freyja/wf_freyja_fastq.wdl
index 9a4446bf8..7b46a204c 100644
--- a/workflows/freyja/wf_freyja_fastq.wdl
+++ b/workflows/freyja/wf_freyja_fastq.wdl
@@ -116,10 +116,14 @@ workflow freyja_fastq {
     String fastq_scan_num_reads_raw1 = select_first([read_QC_trim_pe.fastq_scan_raw1, read_QC_trim_se.fastq_scan_raw1, ""])
     Int? fastq_scan_num_reads_raw2 = read_QC_trim_pe.fastq_scan_raw2
     String? fastq_scan_num_reads_raw_pairs = read_QC_trim_pe.fastq_scan_raw_pairs
+    String fastq_scan_raw1_json = select_first([read_QC_trim_pe.fastq_scan_raw1_json, read_QC_trim_se.fastq_scan_raw1_json, ""])
+    File? fastq_scan_raw2_json = read_QC_trim_pe.fastq_scan_raw2_json
     String fastq_scan_version = select_first([read_QC_trim_pe.fastq_scan_version, read_QC_trim_se.fastq_scan_version, ""])
     String fastq_scan_num_reads_clean1 = select_first([read_QC_trim_pe.fastq_scan_clean1, read_QC_trim_se.fastq_scan_clean1, ""])
     Int? fastq_scan_num_reads_clean2 = read_QC_trim_pe.fastq_scan_clean2
     String? fastq_scan_num_reads_clean_pairs = read_QC_trim_pe.fastq_scan_clean_pairs
+    String fastq_scan_clean1_json = select_first([read_QC_trim_pe.fastq_scan_clean1_json, read_QC_trim_se.fastq_scan_clean1_json, ""])
+    File? fastq_scan_clean2_json = read_QC_trim_pe.fastq_scan_clean2_json
     # Read QC - fastqc outputs - Illumina PE and SE
     String fastqc_num_reads_raw1 = select_first([read_QC_trim_pe.fastqc_raw1, read_QC_trim_se.fastqc_raw1, ""])
     Int? fastqc_num_reads_raw2 = read_QC_trim_pe.fastqc_raw2
diff --git a/workflows/theiacov/wf_theiacov_clearlabs.wdl b/workflows/theiacov/wf_theiacov_clearlabs.wdl
index 0368bef95..5774e02f7 100644
--- a/workflows/theiacov/wf_theiacov_clearlabs.wdl
+++ b/workflows/theiacov/wf_theiacov_clearlabs.wdl
@@ -171,6 +171,8 @@ workflow theiacov_clearlabs {
     Int fastq_scan_num_reads_raw1 = fastq_scan_raw_reads.read1_seq
     Int fastq_scan_num_reads_clean1 = fastq_scan_clean_reads.read1_seq
     String fastq_scan_version = fastq_scan_raw_reads.version
+    File fastq_scan_raw1_json = fastq_scan_raw_reads.fastq_scan_json
+    File fastq_scan_clean1_json = fastq_scan_clean_reads.fastq_scan_json
     # Read QC - kraken outputs
     String kraken_version = kraken2_raw.version
     Float kraken_human = kraken2_raw.percent_human
diff --git a/workflows/theiacov/wf_theiacov_illumina_pe.wdl b/workflows/theiacov/wf_theiacov_illumina_pe.wdl
index 5f5e5b651..29585659e 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/theiacov/wf_theiacov_illumina_se.wdl b/workflows/theiacov/wf_theiacov_illumina_se.wdl
index 4ae59f5dc..0de516664 100644
--- a/workflows/theiacov/wf_theiacov_illumina_se.wdl
+++ b/workflows/theiacov/wf_theiacov_illumina_se.wdl
@@ -215,6 +215,8 @@ workflow theiacov_illumina_se {
     Int? fastq_scan_num_reads_raw1 = read_QC_trim.fastq_scan_raw1
     String? fastq_scan_version = read_QC_trim.fastq_scan_version
     Int? fastq_scan_num_reads_clean1 = read_QC_trim.fastq_scan_clean1
+    File? fastq_scan_raw1_json = read_QC_trim.fastq_scan_raw1_json
+    File? fastq_scan_clean1_json = read_QC_trim.fastq_scan_clean1_json
     # Read QC - fastqc outputs
     Int? fastqc_num_reads_raw1 = read_QC_trim.fastqc_raw1
     Int? fastqc_num_reads_clean1 = read_QC_trim.fastqc_clean1
diff --git a/workflows/theiaeuk/wf_theiaeuk_illumina_pe.wdl b/workflows/theiaeuk/wf_theiaeuk_illumina_pe.wdl
index 67c5c5464..3e792345d 100644
--- a/workflows/theiaeuk/wf_theiaeuk_illumina_pe.wdl
+++ b/workflows/theiaeuk/wf_theiaeuk_illumina_pe.wdl
@@ -208,6 +208,10 @@ workflow theiaeuk_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 - trimmomatic outputs
     String? trimmomatic_version = read_QC_trim.trimmomatic_version
     String? trimmomatic_docker = read_QC_trim.trimmomatic_docker
diff --git a/workflows/theiameta/wf_theiameta_illumina_pe.wdl b/workflows/theiameta/wf_theiameta_illumina_pe.wdl
index 51f1a0054..2a6a23488 100644
--- a/workflows/theiameta/wf_theiameta_illumina_pe.wdl
+++ b/workflows/theiameta/wf_theiameta_illumina_pe.wdl
@@ -207,6 +207,10 @@ workflow theiameta_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/theiaprok/wf_theiaprok_illumina_pe.wdl b/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
index d71c5e324..32271224e 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,
@@ -615,6 +619,10 @@ workflow theiaprok_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/theiaprok/wf_theiaprok_illumina_se.wdl b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
index 1c3eee081..e743ecbce 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,
@@ -571,6 +573,8 @@ workflow theiaprok_illumina_se {
     Int? fastq_scan_num_reads_raw1 = read_QC_trim.fastq_scan_raw1
     String? fastq_scan_version = read_QC_trim.fastq_scan_version
     Int? fastq_scan_num_reads_clean1 = read_QC_trim.fastq_scan_clean1
+    File? fastq_scan_raw1_json = read_QC_trim.fastq_scan_raw1_json
+    File? fastq_scan_clean1_json = read_QC_trim.fastq_scan_clean1_json
     # Read QC - fastqc outputs
     Int? fastqc_num_reads_raw1 = read_QC_trim.fastqc_raw1
     Int? fastqc_num_reads_clean1 = read_QC_trim.fastqc_clean1
diff --git a/workflows/utilities/wf_read_QC_trim_ont.wdl b/workflows/utilities/wf_read_QC_trim_ont.wdl
index c03141251..5b84562aa 100644
--- a/workflows/utilities/wf_read_QC_trim_ont.wdl
+++ b/workflows/utilities/wf_read_QC_trim_ont.wdl
@@ -9,7 +9,7 @@ import "../../tasks/utilities/task_rasusa.wdl" as rasusa_task
 
 workflow read_QC_trim_ont {
   meta {
-    description: "Runs basic QC on Oxford Nanopore (ONT) reads with (1) fastq_scan, (2) nanoplot, (3) rasusa downsampling, (4) tiptoft plasmid detection, and (5) nanoq filtering"
+    description: "Runs basic QC on Oxford Nanopore (ONT) reads with nanoplot, rasusa downsampling, tiptoft plasmid detection, and nanoq filtering"
   }
   input {
     String samplename
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
diff --git a/workflows/utilities/wf_read_QC_trim_se.wdl b/workflows/utilities/wf_read_QC_trim_se.wdl
index d652014ce..af147b512 100644
--- a/workflows/utilities/wf_read_QC_trim_se.wdl
+++ b/workflows/utilities/wf_read_QC_trim_se.wdl
@@ -149,6 +149,8 @@ workflow read_QC_trim_se {
     Int? fastq_scan_clean1 = fastq_scan_clean.read1_seq
     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.fastq_scan_json
+    File? fastq_scan_clean1_json = fastq_scan_clean.fastq_scan_json
 
     # fastqc
     Int? fastqc_raw1 = fastqc_raw.read1_seq