samobermiller · Jun 26, 2026 · Jun 24, 2026 · Jun 25, 2026 · Jun 26, 2026 · Jun 26, 2026
diff --git a/README.md b/README.md
@@ -74,3 +74,6 @@ The main QC fastq output is named by prefix_filtered.fastq.gz.
 
 ## Link to Doc Site
 Please refer [here](https://docs.microbiomedata.org/workflows/chapters/3_Metagenome_Reads_QC/) for more information.
+
+## Required Testing
+Contributions to this repository must undergo direct testing via jaws, using the test jsons in the required_tests folder.
diff --git a/required_tests/README b/required_tests/README
@@ -0,0 +1,15 @@
+# Required Testing
+
+Jsons in this folder cover the various data types handled by this workflow, as detailed in the below table. 
+
+Each PR to ReadsQC MUST come with successful jaws tests using the below jsons, in addition to any other relevant testing. Provide the jaws ids in a comment on your PR. If additional data types become available, you are REQUIRED TO ADD A TEST JSON to this folder. Beyond having a status of 'succeeded', you MUST MANUALLY CHECK that the output of these tests:
+1) have a correctly annotated fastq, indicating which reads are 1 or 2 if they are non-interleaved
+2) have correctly populated stats that match those existing in mongodb
+
+
+| Use Case                                               | Last successful run on NERSC in prod | ReadsQC Json                                  | DG Id                                               |
+|--------------------------------------------------------|--------------------------------------|-----------------------------------------------|-----------------------------------------------------|
+| Short Read - Non Interleave - SRA - Non Manifest       | n/a                                  | single_accession.json                         | n/a                                                 |
+| Short Read - Non Interleave - non SRA - Non Manifest   | 1/12/26                              | rqcfilter_nonint_direct.json                  | nmdc:dgns-11-kc8d3v87                               |
+| Short Read - Non Interleave - non SRA - Manifest       | 5/23/26                              | rqcfilter_paired_recent_manifest_direct.json  | nmdc:dgns-15-6m4kha03, nmdc:omprc-11-2vny0554       |
+| Short Read - Interleave - non SRA - Non Manifest       | 1/26/24                              | rqcfilter_int_recent.json                     | nmdc:omprc-11-x221tr39                              |
diff --git a/required_tests/rqcfilter_int_recent.json b/required_tests/rqcfilter_int_recent.json
@@ -0,0 +1,6 @@
+{
+  "rqcfilter.input_files": ["https://portal.nersc.gov/project/m3408/submission_data/80f5752b-e8d3-453f-9a47-f48210ed6ffc/HS177_72.fastq.gz"],
+  "rqcfilter.proj": "nmdc:xxxxxxx",
+  "rqcfilter.interleaved": true,
+  "rqcfilter.shortRead": true
+}
diff --git a/required_tests/rqcfilter_nonint_direct.json b/required_tests/rqcfilter_nonint_direct.json
@@ -0,0 +1,7 @@
+{
+  "rqcfilter.input_fq1": ["https://storage.googleapis.com/neon-microbial-raw-seq-files/2023/BMI_HLGJLBGX5_mms_R1/BMI_HLGJLBGX5_Tube34_R1.fastq.gz"],
+  "rqcfilter.input_fq2": ["https://storage.googleapis.com/neon-microbial-raw-seq-files/2023/BMI_HLGJLBGX5_mms_R2/BMI_HLGJLBGX5_Tube34_R2.fastq.gz"],
+  "rqcfilter.proj": "nmdc:xxxxxxx",
+  "rqcfilter.interleaved": false,
+  "rqcfilter.shortRead": true
+}
diff --git a/required_tests/rqcfilter_paired_recent_manifest_direct.json b/required_tests/rqcfilter_paired_recent_manifest_direct.json
@@ -0,0 +1,13 @@
+{
+  "rqcfilter.input_fq1": [
+    "https://storage.googleapis.com/neon-microbial-raw-seq-files/2023/BMI_H7FFKBGX5_mms_R1/BMI_H7FFKBGX5_Plate10WellA2_R1.fastq.gz",
+    "https://storage.googleapis.com/neon-microbial-raw-seq-files/2023/BMI_HLGJLBGX5_mms_R1/BMI_HLGJLBGX5_Plate10WellA2_R1.fastq.gz"
+  ],
+  "rqcfilter.input_fq2": [
+    "https://storage.googleapis.com/neon-microbial-raw-seq-files/2023/BMI_H7FFKBGX5_mms_R2/BMI_H7FFKBGX5_Plate10WellA2_R2.fastq.gz",
+    "https://storage.googleapis.com/neon-microbial-raw-seq-files/2023/BMI_HLGJLBGX5_mms_R2/BMI_HLGJLBGX5_Plate10WellA2_R2.fastq.gz"
+  ],
+  "rqcfilter.shortRead": true,
+  "rqcfilter.interleaved": false,
+  "rqcfilter.proj": "nmdc:xxxxxxx"
+}
diff --git a/required_tests/single_accession.json b/required_tests/single_accession.json
@@ -0,0 +1,8 @@
+{
+  "rqcfilter.accessions": [
+    "ERX4811336"
+  ],
+  "rqcfilter.proj": "nmdc:xxxxxxx",
+  "rqcfilter.interleaved": false,
+  "rqcfilter.shortRead": true
+}
diff --git a/shortReadsqc.wdl b/shortReadsqc.wdl
@@ -155,7 +155,7 @@ task stage_interleave {
             cat $fq2_name  >> ~{target_reads_2}
         done
 
-        reformat.sh -Xmx~{memory}G trimreaddescription=t in1=~{target_reads_1} in2=~{target_reads_2} out=~{output_interleaved} 
+        reformat.sh -Xmx~{memory}G in1=~{target_reads_1} in2=~{target_reads_2} out=~{output_interleaved} 
 
         # Validate that the read1 and read2 files are sorted correctly
         reformat.sh -Xmx~{memory}G verifypaired=t in=~{output_interleaved}
@@ -237,6 +237,9 @@ task rqcfilter {
             > >(tee -a  ~{filename_outlog}) \
             2> >(tee -a ~{filename_errlog}  >&2)
 
+        # Validate the filtered output is paired if not interleaved
+            reformat.sh -Xmx~{memory}G verifypaired=t in=filtered/raw.anqdpht.fastq.gz
+
     >>>
 
     output {

diff --git a/test/Ecoli_10x.1.fastq.gz b/test/Ecoli_10x.1.fastq.gz
diff --git a/test/Ecoli_10x.2.fastq.gz b/test/Ecoli_10x.2.fastq.gz
diff --git a/test/README.md b/test/README.md
diff --git a/test/incorrect_pairs_R1.fastq.gz b/test/incorrect_pairs_R1.fastq.gz
diff --git a/test/incorrect_pairs_R2.fastq.gz b/test/incorrect_pairs_R2.fastq.gz
diff --git a/test/large_test_filterStats.json b/test/large_test_filterStats.json
diff --git a/test/longreads_input.json b/test/longreads_input.json
diff --git a/test/rqc_test.wdl b/test/rqc_test.wdl
diff --git a/test/shortread_interleave_input.json b/test/shortread_interleave_input.json
diff --git a/test/shortread_noninterleaved_input.json b/test/shortread_noninterleaved_input.json
diff --git a/test/small_test_filterStats.json b/test/small_test_filterStats.json
diff --git a/version.txt b/version.txt
@@ -1 +1 @@
-v1.0.27
+v1.0.28