stjudecloud · adthrasher · May 29, 2026 · May 29, 2026 · May 29, 2026 · May 29, 2026
diff --git a/data_structures/flag_filter.wdl → data_structures/flag_filter/flag_filter.wdl b/data_structures/flag_filter.wdl → data_structures/flag_filter/flag_filter.wdl
diff --git a/data_structures/flag_filter/module.json b/data_structures/flag_filter/module.json
@@ -0,0 +1,11 @@
+{
+  "name": "flag_filter",
+  "version": "1.0.0",
+  "license": "MIT",
+  "description": "The `flag_filter` WDL module.",
+  "authors": [
+   "Ari Frantz <Ari.Frantz@STJUDE.ORG>"
+  ],
+  "entrypoint": "flag_filter.wdl",
+  "repository": "https://github.com/stjudecloud/workflows.git"
+}
diff --git a/docker/mako/Dockerfile b/docker/mako/Dockerfile
@@ -0,0 +1,3 @@
+FROM rust:1.97
+
+RUN cargo install fg-mako@0.1.3
diff --git a/docker/mako/package.json b/docker/mako/package.json
@@ -0,0 +1,5 @@
+{
+    "name": "mako",
+    "version": "0.1.3",
+    "revision": "0"
+}
diff --git a/tools/bwa.wdl → tools/alignment/bwa.wdl b/tools/bwa.wdl → tools/alignment/bwa.wdl
diff --git a/tools/alignment/module.json b/tools/alignment/module.json
@@ -0,0 +1,31 @@
+{
+    "name": "alignment",
+    "version": "1.0.0",
+    "license": "MIT",
+    "authors": [
+        {
+            "name": "Ari Frantz",
+            "email": "Ari.Frantz@STJUDE.ORG"
+        },
+        {
+            "name": "Andrew Thrasher",
+            "email": "Andrew.Thrasher@STJUDE.ORG"
+        }
+    ],
+    "description": "Module for handling SAM/BAM files",
+    "repository": "https://github.com/stjudecloud/workflows",
+    "tools": [
+        {
+            "name": "bwa",
+            "version": "0.7.17",
+            "license": "MIT",
+            "homepage": "https://github.com/lh3/bwa"
+        },
+        {
+            "name": "star",
+            "version": "2.7.11b",
+            "license": "MIT",
+            "homepage": "https://github.com/alexdobin/STAR"
+        }
+    ]
+}
diff --git a/tools/star.wdl → tools/alignment/star.wdl b/tools/star.wdl → tools/alignment/star.wdl
diff --git a/tools/arriba.wdl → tools/arriba/index.wdl b/tools/arriba.wdl → tools/arriba/index.wdl
diff --git a/tools/arriba/module.json b/tools/arriba/module.json
@@ -0,0 +1,19 @@
+{
+  "name": "arriba",
+  "version": "1.0.0",
+  "license": "MIT",
+  "description": "Module for gene fusion detection in RNA-Seq",
+  "authors": [
+    "Andrew Thrasher <Andrew.Thrasher@STJUDE.org>",
+    "Ari Frantzz <Ari.Frantz@STJUDE.ORG>"
+  ],
+  "repository": "https://github.com/stjudecloud/workflows.git",
+  "tools": [
+      {
+          "name": "arriba",
+          "version": "2.4.0",
+          "license": "MIT",
+          "homepage": "https://github.com/suhrig/arriba"
+      }
+  ]
+}
diff --git a/tools/fq.wdl → tools/fq/fq.wdl b/tools/fq.wdl → tools/fq/fq.wdl
diff --git a/tools/fq/module.json b/tools/fq/module.json
@@ -0,0 +1,20 @@
+{
+    "name": "fq",
+    "version": "1.0.0",
+    "license": "MIT",
+    "authors": [
+        "Ari Frantz <Ari.Frantz@STJUDE.ORG>",
+        "Andrew Thrasher <Andrew.Thrasher@STJUDE.ORG>"
+    ],
+    "description": "Module for handling FASTQ files",
+    "repository": "https://github.com/stjudecloud/workflows",
+    "entrypoint": "fq.wdl",
+    "tools": [
+        {
+            "name": "fq",
+            "version": "0.12.0",
+            "license": "MIT",
+            "homepage": "https://github.com/stjude-rust-labs/fq"
+        }
+    ]
+}
diff --git a/tools/test/fq.yaml → tools/fq/test/fq.yaml b/tools/test/fq.yaml → tools/fq/test/fq.yaml
diff --git a/tools/mako.wdl b/tools/mako.wdl
@@ -0,0 +1,69 @@
+version 1.4
+
+enum SortOrder[String] {
+    queryname = "queryname",
+    coordinate = "coordinate",
+    queryname_natural = "queryname::natural",
+    template_coordinate = "template-coordinate",
+}
+
+task sort {
+    meta {
+        description: "Sorts the input BAM file"
+        outputs: {
+            sorted_bam: "The input BAM after it has been sorted according to `sort_order`",
+        }
+    }
+
+    parameter_meta {
+        bam: "Input BAM format file to sort"
+        sort_order: {
+            description: "Order by which to sort the input BAM",
+            choices: [
+                "queryname",
+                "coordinate",
+                "queryname::natural",
+                "template-coordinate",
+            ],
+            group: "Common",
+        }
+        prefix: "Prefix for the sorted BAM file and accessory files. The extension `.bam` will be added."
+        verify: "Only verify sort order. Does not sort the BAM file."
+        memory_gb: "RAM to allocate for task, specified in GB"
+        modify_disk_size_gb: "Add to or subtract from dynamic disk space allocation. Default disk size is determined by the size of the inputs. Specified in GB."
+    }
+
+    input {
+        File bam
+        String sort_order = "coordinate"
+        String prefix = basename(bam, ".bam") + ".sorted"
+        Boolean verify = false
+        Int memory_gb = 25
+        Int modify_disk_size_gb = 0
+    }
+
+    Float bam_size = size(bam, "GB")
+    Int disk_size_gb = ceil(bam_size * 4) + 10 + modify_disk_size_gb
+
+    String outfile_name = prefix + ".bam"
+
+    command <<<
+        set -euo pipefail
+
+        mako sort \
+            -i "~{bam}" \
+            ~{if verify then "--verify" else "-o \"~{outfile_name}\""} \
+            --order "~{sort_order}"
+    >>>
+
+    output {
+        File sorted_bam = outfile_name
+    }
+
+    requirements {
+        memory: "~{memory_gb} GB"
+        disks: "~{disk_size_gb} GB"
+        container: "ghcr.io/stjudecloud/mako:0.1.3-0"
+        maxRetries: 1
+    }
+}
diff --git a/tools/samtools/module.json b/tools/samtools/module.json
@@ -0,0 +1,25 @@
+{
+    "name": "samtools",
+    "version": "1.0.0",
+    "license": "MIT",
+    "authors": [
+        "Ari Frantz <Ari.Frantz@STJUDE.ORG>",
+        "Andrew Thrasher <Andrew.Thrasher@STJUDE.ORG>"
+    ],
+    "description": "Module for handling SAM/BAM files",
+    "repository": "https://github.com/stjudecloud/workflows",
+    "entrypoint": "samtools.wdl",
+    "tools": [
+        {
+            "name": "samtools",
+            "version": "1.19.2",
+            "license": "MIT",
+            "homepage": "https://www.htslib.org/"
+        }
+    ],
+    "dependencies": {
+      "flag_filter": {
+          "path": "../../data_structures/flag_filter"
+      }
+    }
+}
diff --git a/tools/samtools.wdl → tools/samtools/samtools.wdl b/tools/samtools.wdl → tools/samtools/samtools.wdl
@@ -1,7 +1,8 @@
 ## [Homepage](http://samtools.sourceforge.net/)
-version 1.1
+version 1.4
 
-import "../data_structures/flag_filter.wdl"
+#import "../../data_structures/flag_filter.wdl"
+import * from flag_filter
 
 task quickcheck {
     meta {

diff --git a/tools/test/samtools.yaml → tools/samtools/test/samtools.yaml b/tools/test/samtools.yaml → tools/samtools/test/samtools.yaml
diff --git a/workflows/chipseq/chipseq-standard.wdl b/workflows/chipseq/chipseq-standard.wdl
@@ -5,9 +5,9 @@ import "../../tools/deeptools.wdl"
 import "../../tools/fastp.wdl" as fp
 import "../../tools/md5sum.wdl"
 import "../../tools/picard.wdl"
-import "../../tools/samtools.wdl"
+import "../../tools/samtools/samtools.wdl"
 import "../../tools/util.wdl"
-import "../general/bam-to-fastqs.wdl" as b2fq
+import "../general/bam-to-fastqs/bam-to-fastqs.wdl" as b2fq
 import "https://raw.githubusercontent.com/stjude/seaseq/2.3/workflows/workflows/mapping.wdl"
     as seaseq_map
 import "https://raw.githubusercontent.com/stjude/seaseq/3.0/workflows/tasks/samtools.wdl"

diff --git a/workflows/dnaseq/dnaseq-core.wdl b/workflows/dnaseq/dnaseq-core.wdl
@@ -1,10 +1,10 @@
 ## **WARNING:** this workflow is experimental! Use at your own risk!
-version 1.1
+version 1.4
 
-import "../../tools/bwa.wdl"
+import "../../tools/alignment/bwa.wdl"
 import "../../tools/fastp.wdl" as fp
 import "../../tools/picard.wdl"
-import "../../tools/samtools.wdl"
+import {index} from samtools
 import "../../tools/util.wdl"
 import "../general/samtools-merge.wdl" as samtools_merge_wf
 
@@ -138,7 +138,7 @@ workflow dnaseq_core_experimental {
         use_all_cores,
     }
 
-    call samtools.index { input:
+    call index { input:
         bam = merge.merged_bam,
     }
 

diff --git a/workflows/dnaseq/dnaseq-standard-fastq.wdl b/workflows/dnaseq/dnaseq-standard-fastq.wdl
@@ -1,8 +1,8 @@
 ## **WARNING:** this workflow is experimental! Use at your own risk!
-version 1.1
+version 1.4
 
 import "../../data_structures/read_group.wdl"
-import "../../tools/fq.wdl"
+import {fqlint, subsample} from fq
 import "./dnaseq-core.wdl" as dnaseq_core_wf
 import "./dnaseq-standard.wdl" as dnaseq_standard
 
@@ -77,7 +77,7 @@ workflow dnaseq_standard_fastq_experimental {
 
     if (validate_input) {
         scatter (reads in zip(read_one_fastqs_gz, read_two_fastqs_gz)) {
-            call fq.fqlint after read_group_to_string { input:
+            call fqlint after read_group_to_string { input:
                 read_one_fastq = reads.left,
                 read_two_fastq = reads.right,
             }
@@ -87,7 +87,7 @@ workflow dnaseq_standard_fastq_experimental {
     if (subsample_n_reads > 0) {
         Int reads_per_pair = ceil(subsample_n_reads / length(read_one_fastqs_gz))
         scatter (reads in zip(read_one_fastqs_gz, read_two_fastqs_gz)) {
-            call fq.subsample after fqlint { input:
+            call subsample after fqlint { input:
                 read_one_fastq = reads.left,
                 read_two_fastq = reads.right,
                 record_count = reads_per_pair,

diff --git a/workflows/dnaseq/dnaseq-standard.wdl b/workflows/dnaseq/dnaseq-standard.wdl
@@ -1,10 +1,10 @@
 ## **WARNING:** this workflow is experimental! Use at your own risk!
-version 1.1
+version 1.4
 
 import "../../data_structures/read_group.wdl"
 import "../../tools/picard.wdl"
-import "../../tools/samtools.wdl"
-import "../general/bam-to-fastqs.wdl" as bam_to_fastqs_wf
+import {subsample} from samtools
+import "../general/bam-to-fastqs/bam-to-fastqs.wdl" as bam_to_fastqs_wf
 import "./dnaseq-core.wdl" as dnaseq_core_wf
 
 workflow dnaseq_standard_experimental {
@@ -64,7 +64,7 @@ workflow dnaseq_standard_experimental {
     }
 
     if (subsample_n_reads > 0) {
-        call samtools.subsample after validate_input_bam { input:
+        call subsample after validate_input_bam { input:
             bam,
             desired_reads = subsample_n_reads,
             use_all_cores,

diff --git a/workflows/dnaseq/module.json b/workflows/dnaseq/module.json
@@ -0,0 +1,22 @@
+{
+    "name": "dnaseq",
+    "version": "1.0.0",
+    "license": "MIT",
+    "authors": [
+      "Ari Frantz <Ari.Frantz@STJUDE.ORG>",
+      "Andrew Thrasher <Andrew.Thrasher@STJUDE.ORG>"
+    ],
+    "description": "DNAseq analysis workflow",
+    "repository": "https://github.com/stjudecloud/workflows",
+    "dependencies": {
+        "samtools": {
+            "path": "../../tools/samtools"
+        },
+        "fq": {
+            "path": "../../tools/fq"
+        }
+    },
+    "exclude": [
+        "dnaseq-core.wdl"
+    ]
+}
diff --git a/workflows/general/alignment-post.wdl b/workflows/general/alignment-post.wdl
@@ -2,7 +2,7 @@ version 1.1
 
 import "../../tools/md5sum.wdl"
 import "../../tools/picard.wdl"
-import "../../tools/samtools.wdl"
+import "../../tools/samtools/samtools.wdl"
 import "https://raw.githubusercontent.com/stjude/XenoCP/4.0.0-alpha/wdl/workflows/xenocp.wdl"
     as xenocp_wf
 

diff --git a/workflows/general/bam-to-fastqs.wdl → ...s/general/bam-to-fastqs/bam-to-fastqs.wdl b/workflows/general/bam-to-fastqs.wdl → ...s/general/bam-to-fastqs/bam-to-fastqs.wdl
@@ -1,7 +1,7 @@
-version 1.1
+version 1.4
 
-import "../../tools/fq.wdl"
-import "../../tools/samtools.wdl"
+import "../../../tools/fq/fq.wdl"
+import "../../../tools/samtools/samtools.wdl"
 
 workflow bam_to_fastqs {
     meta {

diff --git a/workflows/general/bam-to-fastqs/module.json b/workflows/general/bam-to-fastqs/module.json
@@ -0,0 +1,30 @@
+{
+    "name": "bam-to-fastqs",
+    "version": "1.0.0",
+    "license": "MIT",
+    "authors": [
+        {
+            "name": "Ari Frantz",
+            "email": "Ari.Frantz@STJUDE.ORG"
+        },
+        {
+            "name": "Andrew Thrasher",
+            "email": "Andrew.Thrasher@STJUDE.ORG"
+        }
+    ],
+    "description": "Convert BAM files to FASTQ(s) with Samtools",
+    "repository": "https://github.com/stjudecloud/workflows",
+    "entrypoint": "bam-to-fastqs.wdl",
+    "dependencies": {
+        "fq": {
+            "git": "https://github.com/stjudecloud/workflows",
+            "branch": "main",
+            "path": "tools/fq"
+        },
+        "samtools": {
+            "git": "https://github.com/stjudecloud/workflows",
+            "branch": "main",
+            "path": "tools/samtools"
+        }
+    }
+}
diff --git a/workflows/general/samtools-merge.wdl b/workflows/general/samtools-merge.wdl
@@ -1,7 +1,7 @@
 ## **WARNING:** this workflow is experimental! Use at your own risk!
-version 1.1
+version 1.4
 
-import "../../tools/samtools.wdl"
+import "../../tools/samtools/samtools.wdl"
 
 workflow samtools_merge {
     meta {

diff --git a/workflows/qc/markdups-post.wdl b/workflows/qc/markdups-post.wdl
@@ -9,7 +9,7 @@ version 1.1
 
 import "../../tools/mosdepth.wdl"
 import "../../tools/picard.wdl"
-import "../../tools/samtools.wdl"
+import "../../tools/samtools/samtools.wdl"
 
 workflow markdups_post {
     meta {
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		FROM rust:1.97

		RUN cargo install fg-mako@0.1.3