diff --git a/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml b/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml
index b1bb6da13..4c7542334 100644
--- a/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml
+++ b/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml
@@ -138,7 +138,7 @@
       md5sum: 7c5aba41f53293b712fd86d08ed5b36e
     # clean read screen
     - path: miniwdl_run/call-clean_check_reads/command
-      md5sum: e18830c68993b2837d1da29ce55d2de8
+      md5sum: aeeb107f328ccd7d2d805dc5990b24ac
     - path: miniwdl_run/call-clean_check_reads/inputs.json
       contains: ["read1", "read2", "organism"]
     - path: miniwdl_run/call-clean_check_reads/outputs.json
diff --git a/tests/workflows/theiacov/test_wf_theiacov_illumina_se.yml b/tests/workflows/theiacov/test_wf_theiacov_illumina_se.yml
index 9af5b61c9..0742c19a9 100644
--- a/tests/workflows/theiacov/test_wf_theiacov_illumina_se.yml
+++ b/tests/workflows/theiacov/test_wf_theiacov_illumina_se.yml
@@ -94,7 +94,7 @@
       md5sum: 9a089b8920e55c9cc7bc8cd7d18f9a8e
     # clean read screen
     - path: miniwdl_run/call-clean_check_reads/command
-      md5sum: aec6c57452ddff84c325601a780605d2
+      md5sum: 80a361915a627e86743baacfc383b2b5
     - path: miniwdl_run/call-clean_check_reads/inputs.json
       contains: ["read1", "organism"]
     - path: miniwdl_run/call-clean_check_reads/outputs.json
diff --git a/tests/workflows/theiacov/test_wf_theiacov_ont.yml b/tests/workflows/theiacov/test_wf_theiacov_ont.yml
index 1772e16b4..03027a794 100644
--- a/tests/workflows/theiacov/test_wf_theiacov_ont.yml
+++ b/tests/workflows/theiacov/test_wf_theiacov_ont.yml
@@ -17,7 +17,7 @@
     - wf_theiacov_ont_miniwdl
   files:
     - path: miniwdl_run/call-clean_check_reads/command
-      md5sum: 2517c5cf87db0af66663ffb5e69f6b4f
+      md5sum: 8078e96573428b712ddcb06517333cf5
     - path: miniwdl_run/call-clean_check_reads/inputs.json
     - path: miniwdl_run/call-clean_check_reads/outputs.json
     - path: miniwdl_run/call-clean_check_reads/stderr.txt
@@ -219,7 +219,7 @@
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-pangolin4/work/ont.pangolin_report.csv
     - path: miniwdl_run/call-raw_check_reads/command
-      md5sum: 1858d98f3c15904be0c219b867727048
+      md5sum: 5df9a70c852960f82c84c7da611cd177
     - path: miniwdl_run/call-raw_check_reads/inputs.json
     - path: miniwdl_run/call-raw_check_reads/outputs.json
     - path: miniwdl_run/call-raw_check_reads/stderr.txt
diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
index d2cedb29b..cb21eb7ba 100644
--- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
+++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
@@ -201,7 +201,7 @@
     - path: miniwdl_run/call-cg_pipeline_raw/work/test_readMetrics.tsv
       contains: ["File", "fastq", "coverage"]
     - path: miniwdl_run/call-clean_check_reads/command
-      md5sum: 8235bc815fe3b57471f97474bff3e3f7
+      md5sum: f28c2b4597398988bc9016505425f6f0
     - path: miniwdl_run/call-clean_check_reads/inputs.json
       contains: ["read1", "fastq", "skip_screen", "true"]
     - path: miniwdl_run/call-clean_check_reads/outputs.json
@@ -364,7 +364,7 @@
     - path: miniwdl_run/call-quast/work/transposed_report.txt
       contains: ["Assembly", "length", "contigs", "test"]
     - path: miniwdl_run/call-raw_check_reads/command
-      md5sum: fd8c392c24e4e49859bdd006163db646
+      md5sum: 0e417649675499e2be549ce82e02704c
     - path: miniwdl_run/call-raw_check_reads/inputs.json
       contains: ["read1", "fastq", "skip_screen", "true"]
     - path: miniwdl_run/call-raw_check_reads/outputs.json
@@ -581,7 +581,7 @@
     - path: miniwdl_run/wdl/tasks/quality_control/basic_statistics/task_quast.wdl
       contains: ["version", "quast", "output"]
     - path: miniwdl_run/wdl/tasks/quality_control/comparisons/task_screen.wdl
-      md5sum: 75631c4db89792a939e4d872adc05b86
+      md5sum: adb43c5bf0a83b9e2ef7669ed2d1760f
     - path: miniwdl_run/wdl/tasks/quality_control/read_filtering/task_trimmomatic.wdl
       contains: ["version", "trimmomatic", "output"]
     - path: miniwdl_run/wdl/tasks/species_typing/escherichia_shigella/task_ectyper.wdl
diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
index d19f1319e..e4076ec77 100644
--- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
+++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
@@ -194,7 +194,7 @@
     - path: miniwdl_run/call-cg_pipeline_raw/work/test_readMetrics.tsv
       contains: ["File", "fastq", "coverage"]
     - path: miniwdl_run/call-clean_check_reads/command
-      md5sum: 1ed4ae1859ade5045c01c92dfe54899c
+      md5sum: 51f799af8609c440d51e0046ebc030e8
     - path: miniwdl_run/call-clean_check_reads/inputs.json
       contains: ["read1", "fastq", "skip_screen", "true"]
     - path: miniwdl_run/call-clean_check_reads/outputs.json
@@ -203,7 +203,7 @@
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-clean_check_reads/stderr.txt.offset
     - path: miniwdl_run/call-clean_check_reads/stdout.txt
-      md5sum: 9e807ce699271c3f647c7594df2b5b0a
+      md5sum: 73809db947c875bf81acccaad76a57d5
     - path: miniwdl_run/call-clean_check_reads/task.log
       contains: ["wdl", "theiaprok_illumina_se", "check_reads", "done"]
     - path: miniwdl_run/call-clean_check_reads/work/EST_GENOME_LENGTH
@@ -355,7 +355,7 @@
     - path: miniwdl_run/call-quast/work/transposed_report.txt
       contains: ["Assembly", "length", "contigs", "test"]
     - path: miniwdl_run/call-raw_check_reads/command
-      md5sum: 3f6bf93b769ef9b152f005195cf2502e
+      md5sum: 7594079920cccbcf01d027547f54ccc2
     - path: miniwdl_run/call-raw_check_reads/inputs.json
       contains: ["read1", "fastq", "skip_screen", "true"]
     - path: miniwdl_run/call-raw_check_reads/outputs.json
@@ -364,7 +364,7 @@
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: miniwdl_run/call-raw_check_reads/stderr.txt.offset
     - path: miniwdl_run/call-raw_check_reads/stdout.txt
-      md5sum: 9e807ce699271c3f647c7594df2b5b0a
+      md5sum: 73809db947c875bf81acccaad76a57d5
     - path: miniwdl_run/call-raw_check_reads/task.log
       contains: ["wdl", "theiaprok_illumina_se", "check_reads", "done"]
     - path: miniwdl_run/call-raw_check_reads/work/EST_GENOME_LENGTH
@@ -526,7 +526,7 @@
     - 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: 284ce680b52e7e1c1753537b344fa161
+      md5sum: 3b9e04569d7e856dcc649b7726b306b7
     - 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
@@ -544,7 +544,7 @@
     - path: miniwdl_run/wdl/tasks/quality_control/basic_statistics/task_quast.wdl
       contains: ["version", "quast", "output"]
     - path: miniwdl_run/wdl/tasks/quality_control/comparisons/task_screen.wdl
-      md5sum: 75631c4db89792a939e4d872adc05b86
+      md5sum: adb43c5bf0a83b9e2ef7669ed2d1760f
     - path: miniwdl_run/wdl/tasks/quality_control/read_filtering/task_trimmomatic.wdl
       contains: ["version", "trimmomatic", "output"]
     - path: miniwdl_run/wdl/tasks/species_typing/escherichia_shigella/task_ectyper.wdl