feat: make FASTQ analysis optional

data_structures/flag_filter.wdl

@@ -67,6 +67,7 @@ struct FlagFilter {
     String exclude_if_all  # samtools -G
 }
 
+#@ except: EmptyOutputs
 task validate_string_is_12bit_int {
     meta {
         description: "Validates that a string is a octal, decimal, or hexadecimal number and less than 2^12."

data_structures/read_group.wdl

@@ -143,6 +143,7 @@ task get_read_groups {
     }
 }
 
+#@ except: EmptyOutputs
 task validate_read_group {
     meta {
         description: "Validate a `ReadGroup` struct's fields are defined and well-formed"

tools/fq.wdl

@@ -1,6 +1,7 @@
 ## [Homepage](https://github.com/stjude-rust-labs/fq)
 version 1.1
 
+#@ except: EmptyOutputs
 task fqlint {
     meta {
         description: "Performs quality control on the input FASTQs to ensure proper formatting"

tools/samtools.wdl

@@ -3,6 +3,7 @@ version 1.1
 
 import "../data_structures/flag_filter.wdl"
 
+#@ except: EmptyOutputs
 task quickcheck {
     meta {
         description: "Runs Samtools quickcheck on the input BAM file."

tools/util.wdl

@@ -132,6 +132,7 @@ task calc_feature_lengths {
     }
 }
 
+#@ except: EmptyOutputs
 task compression_integrity {
     meta {
         description: "Checks the compression integrity of a bgzipped file"
@@ -358,6 +359,7 @@ task global_phred_scores {
     }
 }
 
+#@ except: EmptyOutputs
 task check_fastq_and_rg_concordance {
     meta {
         description: "Validates FASTQs and read group records are concordant"

workflows/dnaseq/dnaseq-standard.wdl

@@ -133,6 +133,7 @@ workflow dnaseq_standard_experimental {
     }
 }
 
+#@ except: EmptyOutputs
 task parse_input {
     meta {
         description: "Parses and validates the `dnaseq_standard` workflow's provided inputs"

workflows/qc/CHANGELOG.md

@@ -4,6 +4,12 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](http://keepachangelog.com/).
 
+## 2026 May
+
+### Added
+
+- `quality_check_standard` workflow: optional FASTQ analysis via new input `run_fastq_analysis`, allowing callers to skip BAM-to-FASTQ conversion and FASTQ-level tools (Kraken2, fastp, librarian) ([#315](https://github.com/stjudecloud/workflows/pull/315))
+
 ## 2025 September
 
 ### Changed

workflows/qc/quality-check-standard.wdl

@@ -118,6 +118,10 @@ workflow quality_check_standard {
             description: "Only process a random sampling of approximately `n` reads. Any `n <= 0` for processing entire input.",
             warning: "Subsampling is done probabalistically so the exact number of reads in the output will have some variation.",
         }
+        run_fastq_analysis: {
+            description: "Create FASTQs from the input BAM and run FASTQ-level analyses?",
+            help: "If false, the pipeline skips SAMtools bam-to-fastq, fqlint, Kraken2, fastp, librarian, and comparative Kraken2. Also disables qualimap_rnaseq (requires a collated BAM from bam_to_fastq).",
+        }
     }
 
     input {
@@ -153,6 +157,7 @@ workflow quality_check_standard {
         Boolean use_all_cores = false
         Int optical_distance = 0
         Int subsample_n_reads = -1
+        Boolean run_fastq_analysis = true
     }
 
     call parse_input { input:
@@ -164,7 +169,7 @@ workflow quality_check_standard {
     call flag_filter.validate_flag_filter as kraken_filter_validator { input:
         flags = standard_filter,
     }
-    if (run_comparative_kraken) {
+    if (run_comparative_kraken && run_fastq_analysis) {
         call flag_filter.validate_flag_filter as comparative_kraken_filter_validator { input:
             flags = comparative_filter,
         }
@@ -254,109 +259,111 @@ workflow quality_check_standard {
         prefix = post_subsample_prefix,
     }
 
-    call samtools.bam_to_fastq after quickcheck after kraken_filter_validator { input:
-        bam = post_subsample_bam,
-        bitwise_filter = standard_filter,
-        prefix = post_subsample_prefix,
-        # RNA needs a collated BAM for Qualimap
-        # DNA can skip the associated storage costs
-        retain_collated_bam = rna,
-        # disabling fast_mode enables writing of secondary and supplementary alignments
-        # to the collated BAM when processing RNA.
-        # Those alignments are used downstream by Qualimap.
-        fast_mode = (!rna),
-        paired_end = true,  # matches default but prevents user from overriding
-        use_all_cores,
-    }
-
-    call fq.fqlint { input:
-        read_one_fastq = select_first([
-            bam_to_fastq.read_one_fastq_gz,
-            "undefined",
-        ]),
-        read_two_fastq = select_first([
-            bam_to_fastq.read_two_fastq_gz,
-            "undefined",
-        ]),
-    }
-    call kraken2.kraken after fqlint { input:
-        read_one_fastq_gz = select_first([
-            bam_to_fastq.read_one_fastq_gz,
-            "undefined",
-        ]),
-        read_two_fastq_gz = select_first([
-            bam_to_fastq.read_two_fastq_gz,
-            "undefined",
-        ]),
-        db = kraken_db,
-        store_sequences = store_kraken_sequences,
-        prefix = post_subsample_prefix,
-        use_all_cores,
-    }
-    if (run_fastp) {
-        call fp.fastp after fqlint { input:
-            read_one_fastq = select_first([
-                bam_to_fastq.read_one_fastq_gz,
-                "undefined",
-            ]),
-            read_two_fastq = select_first([
-                bam_to_fastq.read_two_fastq_gz,
-                "undefined",
-            ]),
-            output_fastq = false,
-        }
-    }
-    if (run_librarian) {
-        call libraran_tasks.librarian after fqlint { input:
-            read_one_fastq = select_first([
-                bam_to_fastq.read_one_fastq_gz,
-                "undefined",
-            ]),
-        }
-    }
-
-    if (run_comparative_kraken) {
-        call samtools.bam_to_fastq as alt_filtered_fastq after quickcheck after comparative_kraken_filter_validator {
-            input:
+    if (run_fastq_analysis) {
+        call samtools.bam_to_fastq after quickcheck after kraken_filter_validator { input:
             bam = post_subsample_bam,
-            bitwise_filter = comparative_filter,
-            prefix = post_subsample_prefix + ".alt_filtered",
-            # matches default but prevents user from overriding
-            # If the user wants a collated BAM, they should save the one
-            # from the first bam_to_fastq call.
-            retain_collated_bam = false,
-            # matches default but prevents user from overriding
-            # Since the only output here is FASTQs, we can disable fast mode.
-            # This discards secondary and supplementary alignments, which should not
-            # be converted to FASTQs. (Is that true?)
-            fast_mode = true,
+            bitwise_filter = standard_filter,
+            prefix = post_subsample_prefix,
+            # RNA needs a collated BAM for Qualimap
+            # DNA can skip the associated storage costs
+            retain_collated_bam = rna,
+            # disabling fast_mode enables writing of secondary and supplementary alignments
+            # to the collated BAM when processing RNA.
+            # Those alignments are used downstream by Qualimap.
+            fast_mode = (!rna),
             paired_end = true,  # matches default but prevents user from overriding
             use_all_cores,
         }
-        call fq.fqlint as alt_filtered_fqlint { input:
+
+        call fq.fqlint { input:
             read_one_fastq = select_first([
-                alt_filtered_fastq.read_one_fastq_gz,
+                bam_to_fastq.read_one_fastq_gz,
                 "undefined",
             ]),
             read_two_fastq = select_first([
-                alt_filtered_fastq.read_two_fastq_gz,
+                bam_to_fastq.read_two_fastq_gz,
                 "undefined",
             ]),
         }
-        call kraken2.kraken as comparative_kraken after alt_filtered_fqlint { input:
+        call kraken2.kraken after fqlint { input:
             read_one_fastq_gz = select_first([
-                alt_filtered_fastq.read_one_fastq_gz,
+                bam_to_fastq.read_one_fastq_gz,
                 "undefined",
             ]),
             read_two_fastq_gz = select_first([
-                alt_filtered_fastq.read_two_fastq_gz,
+                bam_to_fastq.read_two_fastq_gz,
                 "undefined",
             ]),
             db = kraken_db,
             store_sequences = store_kraken_sequences,
-            prefix = post_subsample_prefix + ".alt_filtered",
+            prefix = post_subsample_prefix,
             use_all_cores,
         }
+        if (run_fastp) {
+            call fp.fastp after fqlint { input:
+                read_one_fastq = select_first([
+                    bam_to_fastq.read_one_fastq_gz,
+                    "undefined",
+                ]),
+                read_two_fastq = select_first([
+                    bam_to_fastq.read_two_fastq_gz,
+                    "undefined",
+                ]),
+                output_fastq = false,
+            }
+        }
+        if (run_librarian) {
+            call libraran_tasks.librarian after fqlint { input:
+                read_one_fastq = select_first([
+                    bam_to_fastq.read_one_fastq_gz,
+                    "undefined",
+                ]),
+            }
+        }
+
+        if (run_comparative_kraken) {
+            call samtools.bam_to_fastq as alt_filtered_fastq after quickcheck after comparative_kraken_filter_validator {
+                input:
+                bam = post_subsample_bam,
+                bitwise_filter = comparative_filter,
+                prefix = post_subsample_prefix + ".alt_filtered",
+                # matches default but prevents user from overriding
+                # If the user wants a collated BAM, they should save the one
+                # from the first bam_to_fastq call.
+                retain_collated_bam = false,
+                # matches default but prevents user from overriding
+                # Since the only output here is FASTQs, we can disable fast mode.
+                # This discards secondary and supplementary alignments, which should not
+                # be converted to FASTQs. (Is that true?)
+                fast_mode = true,
+                paired_end = true,  # matches default but prevents user from overriding
+                use_all_cores,
+            }
+            call fq.fqlint as alt_filtered_fqlint { input:
+                read_one_fastq = select_first([
+                    alt_filtered_fastq.read_one_fastq_gz,
+                    "undefined",
+                ]),
+                read_two_fastq = select_first([
+                    alt_filtered_fastq.read_two_fastq_gz,
+                    "undefined",
+                ]),
+            }
+            call kraken2.kraken as comparative_kraken after alt_filtered_fqlint { input:
+                read_one_fastq_gz = select_first([
+                    alt_filtered_fastq.read_one_fastq_gz,
+                    "undefined",
+                ]),
+                read_two_fastq_gz = select_first([
+                    alt_filtered_fastq.read_two_fastq_gz,
+                    "undefined",
+                ]),
+                db = kraken_db,
+                store_sequences = store_kraken_sequences,
+                prefix = post_subsample_prefix + ".alt_filtered",
+                use_all_cores,
+            }
+        }
     }
 
     call mosdepth.coverage as wg_coverage after quickcheck { input:
@@ -392,18 +399,20 @@ workflow quality_check_standard {
             ]),
             outfile_name = post_subsample_prefix + ".strandedness.tsv",
         }
-        call qualimap.rnaseq as qualimap_rnaseq { input:
-            bam = select_first([
-                bam_to_fastq.collated_bam,
-                "undefined",
-            ]),
-            prefix = post_subsample_prefix + ".qualimap_rnaseq_results",
-            gtf = select_first([
-                gtf,
-                "undefined",
-            ]),
-            name_sorted = true,
-            paired_end = true,  # matches default but prevents user from overriding
+        if (run_fastq_analysis) {
+            call qualimap.rnaseq as qualimap_rnaseq { input:
+                bam = select_first([
+                    bam_to_fastq.collated_bam,
+                    "undefined",
+                ]),
+                prefix = post_subsample_prefix + ".qualimap_rnaseq_results",
+                gtf = select_first([
+                    gtf,
+                    "undefined",
+                ]),
+                name_sorted = true,
+                paired_end = true,  # matches default but prevents user from overriding
+            }
         }
     }
     if (mark_duplicates) {

workflows/rnaseq/rnaseq-standard.wdl

@@ -141,6 +141,7 @@ workflow rnaseq_standard {
     }
 }
 
+#@ except: EmptyOutputs
 task parse_input {
     meta {
         description: "Parses and validates the `rnaseq_standard[_fastq]` workflows' provided inputs"