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[WIP] refactor: module support #318

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14eae45
refactor: module support
adthrasher May 29, 2026
3efae8e
chore: update imports
adthrasher May 29, 2026
d4f8a55
refactor: arriba with default entrypoint
adthrasher May 29, 2026
b67bf1d
refactor: combine DNAseq workflows into a single module
adthrasher May 29, 2026
35e791e
chore: add missing module.json
adthrasher Jun 1, 2026
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0 tools/bwa.wdl → tools/alignment/bwa.wdl
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31 changes: 31 additions & 0 deletions tools/alignment/module.json
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{
"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"
}
]
}
0 tools/star.wdl → tools/alignment/star.wdl
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0 tools/arriba.wdl → tools/arriba/index.wdl
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25 changes: 25 additions & 0 deletions tools/arriba/module.json
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{
"name": "arriba",
"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 gene fusion detection in RNA-Seq",
"repository": "https://github.com/stjudecloud/workflows",
"tools": [
{
"name": "arriba",
"version": "2.4.0",
"license": "MIT",
"homepage": "https://github.com/suhrig/arriba"
}
]
}
0 tools/fq.wdl → tools/fq/fq.wdl
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26 changes: 26 additions & 0 deletions tools/fq/module.json
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@@ -0,0 +1,26 @@
{
"name": "fq",
"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 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"
}
]
}
26 changes: 26 additions & 0 deletions tools/samtools/module.json
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{
"name": "samtools",
"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",
"entrypoint": "samtools.wdl",
"tools": [
{
"name": "samtools",
"version": "1.19.2",
"license": "MIT",
"homepage": "https://www.htslib.org/"
}
]
}
0 tools/samtools.wdl → tools/samtools/samtools.wdl
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4 changes: 2 additions & 2 deletions workflows/chipseq/chipseq-standard.wdl
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Expand Up @@ -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"
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2 changes: 1 addition & 1 deletion workflows/dnaseq/dnaseq-core.wdl
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Expand Up @@ -4,7 +4,7 @@ version 1.1
import "../../tools/bwa.wdl"
import "../../tools/fastp.wdl" as fp
import "../../tools/picard.wdl"
import "../../tools/samtools.wdl"
import "../../tools/samtools/samtools.wdl"
import "../../tools/util.wdl"
import "../general/samtools-merge.wdl" as samtools_merge_wf

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2 changes: 1 addition & 1 deletion workflows/dnaseq/dnaseq-standard-fastq.wdl
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Expand Up @@ -2,7 +2,7 @@
version 1.1

import "../../data_structures/read_group.wdl"
import "../../tools/fq.wdl"
import "../../tools/fq/fq.wdl"
import "./dnaseq-core.wdl" as dnaseq_core_wf
import "./dnaseq-standard.wdl" as dnaseq_standard

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4 changes: 2 additions & 2 deletions workflows/dnaseq/dnaseq-standard.wdl
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Expand Up @@ -3,8 +3,8 @@ version 1.1

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 "../../tools/samtools/samtools.wdl"
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 {
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25 changes: 25 additions & 0 deletions workflows/dnaseq/module.json
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{
"name": "dnaseq",
"version": "1.0.0",
"license": "MIT",
"authors": [
{
"name": "Ari Frantz",
"email": "Ari.Frantz@STJUDE.ORG"
},
{
"name": "Andrew Thrasher",
"email": "Andrew.Thrasher@STJUDE.ORG"
}
],
"description": "DNAseq analysis workflow",
"repository": "https://github.com/stjudecloud/workflows",
"dependencies": {
"fastq": {
"path": "./dnaseq-standard-fastq.wdl"
},
"bam": {
"path": "./dnaseq-standard.wdl"
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@adthrasher adthrasher Jun 1, 2026

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I'm not sure this is right. I think it needs a source object wrapping it.

}
}
}
2 changes: 1 addition & 1 deletion workflows/general/alignment-post.wdl
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Expand Up @@ -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

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4 changes: 2 additions & 2 deletions workflows/general/bam-to-fastqs.wdl → ...s/general/bam-to-fastqs/bam-to-fastqs.wdl
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@@ -1,7 +1,7 @@
version 1.1

import "../../tools/fq.wdl"
import "../../tools/samtools.wdl"
import "../../../tools/fq/fq.wdl"
import "../../../tools/samtools/samtools.wdl"

workflow bam_to_fastqs {
meta {
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30 changes: 30 additions & 0 deletions workflows/general/bam-to-fastqs/module.json
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@@ -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"
}
}
}
2 changes: 1 addition & 1 deletion workflows/general/samtools-merge.wdl
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## **WARNING:** this workflow is experimental! Use at your own risk!
version 1.1

import "../../tools/samtools.wdl"
import "../../tools/samtools/samtools.wdl"

workflow samtools_merge {
meta {
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2 changes: 1 addition & 1 deletion workflows/qc/markdups-post.wdl
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Expand Up @@ -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 {
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4 changes: 2 additions & 2 deletions workflows/qc/quality-check-standard.wdl
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Expand Up @@ -2,7 +2,7 @@ version 1.1

import "../../data_structures/flag_filter.wdl"
import "../../tools/fastp.wdl" as fp
import "../../tools/fq.wdl"
import "../../tools/fq/fq.wdl"
import "../../tools/kraken2.wdl"
import "../../tools/librarian.wdl" as libraran_tasks
import "../../tools/md5sum.wdl"
Expand All @@ -11,7 +11,7 @@ import "../../tools/multiqc.wdl" as multiqc_tasks
import "../../tools/ngsderive.wdl"
import "../../tools/picard.wdl"
import "../../tools/qualimap.wdl"
import "../../tools/samtools.wdl"
import "../../tools/samtools/samtools.wdl"
import "../../tools/util.wdl"
import "./markdups-post.wdl" as markdups_post_wf

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2 changes: 1 addition & 1 deletion workflows/reference/gatk-reference.wdl
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version 1.1

import "../../tools/picard.wdl"
import "../../tools/samtools.wdl"
import "../../tools/samtools/samtools.wdl"
import "../../tools/util.wdl"

workflow gatk_reference {
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2 changes: 1 addition & 1 deletion workflows/rnaseq/rnaseq-standard-fastq.wdl
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version 1.1

import "../../data_structures/read_group.wdl"
import "../../tools/fq.wdl"
import "../../tools/fq/fq.wdl"
import "./rnaseq-core.wdl" as rnaseq_core_wf
import "./rnaseq-standard.wdl" as rnaseq_standard

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4 changes: 2 additions & 2 deletions workflows/rnaseq/rnaseq-standard.wdl
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Expand Up @@ -2,8 +2,8 @@ version 1.1

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 "../../tools/samtools/samtools.wdl"
import "../general/bam-to-fastqs/bam-to-fastqs.wdl" as bam_to_fastqs_wf
import "./rnaseq-core.wdl" as rnaseq_core_wf

workflow rnaseq_standard {
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