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5040e54
Fix issues with example formatting.
vsmalladi Feb 20, 2025
971ba7d
Fix expected output.
vsmalladi Feb 20, 2025
fed52c3
Fix missing output that is missing.
vsmalladi Feb 20, 2025
4d1122e
Reverse issues. Should have been excluded.
vsmalladi Feb 20, 2025
0d0313b
Fix syntax on tests.
vsmalladi Feb 25, 2025
0661e13
Fix exclusion of output.
vsmalladi Feb 26, 2025
e6b6bbe
Fix name of task to test so that it gets parse correctly.
vsmalladi Feb 26, 2025
39b2d6c
Fix example.
vsmalladi Feb 28, 2025
932848c
Fix hisat2 example. Close #707.
vsmalladi Mar 4, 2025
2fa563e
Fix some dangling issues.
vsmalladi Mar 4, 2025
c56eec5
Fix some dangling issues.
vsmalladi Mar 4, 2025
f4e86d7
Fix examples for returnCodes to be lower camelcase. Closes #710.
vsmalladi Mar 16, 2025
9355049
Fix task name.
vsmalladi Mar 16, 2025
aff4d38
Add in null optional type. Will not fail if not present. Closes issue…
vsmalladi Apr 8, 2025
618cbf2
Fix spec example.
vsmalladi Apr 8, 2025
a019f44
Fix spec example to meet actually behavior. Seems like example was no…
vsmalladi Apr 8, 2025
81e9ae2
Clean up commits
vsmalladi Jul 7, 2025
813a017
Add additionaly fixes to examples that sprocket testing unvield.
vsmalladi Jul 10, 2025
863d4ed
Add in first round of conformance tests.
vsmalladi Jul 17, 2025
7d7c811
Add in first round of conformance tests.
vsmalladi Jul 17, 2025
fa587d2
Fix running tests.
vsmalladi Jul 17, 2025
13d1fa8
Fix trigger.
vsmalladi Jul 17, 2025
e0afbf9
Fix trigger.
vsmalladi Jul 17, 2025
d3493d7
Fix Python file.
vsmalladi Jul 17, 2025
9e21c3d
Fix path.
vsmalladi Jul 17, 2025
1f193dd
Fix path.
vsmalladi Jul 17, 2025
531134d
Add ignore for 2 long running tests
vsmalladi Jul 18, 2025
d96150a
Update miniwdl-conformance.yml
vsmalladi Jul 18, 2025
0754849
Update miniwdl-conformance.yml
vsmalladi Jul 18, 2025
495496b
Add some testing
vsmalladi Jul 18, 2025
3d15c40
Fix path names
vsmalladi Jul 18, 2025
7b504d7
Fix path names
vsmalladi Jul 18, 2025
ee740ad
Add in results.
vsmalladi Jul 18, 2025
f9db4d8
Fix formatting.
vsmalladi Jul 18, 2025
f7237ef
Fix formatting.
vsmalladi Jul 18, 2025
dc5ce24
Update the size of the machine
vsmalladi Jul 18, 2025
0cd4a77
Test 2 tests
vsmalladi Jul 21, 2025
439681b
Added in miniwdl test as a rename.
vsmalladi Jul 21, 2025
3a1d0ca
Change name and limit to 2 tests.
vsmalladi Jul 21, 2025
091956f
Run all tests and caputre failure file.
vsmalladi Jul 21, 2025
0fa27ec
Fix spelling.
vsmalladi Jul 22, 2025
34343a4
Change path.
vsmalladi Jul 22, 2025
7b563c3
Update miniwdl-test.yml path for file
vsmalladi Jul 23, 2025
1c1e231
Make a sheild
vsmalladi Jul 23, 2025
fccf432
Update README.md with badge
vsmalladi Jul 23, 2025
be4e1ad
Update shields badge for fix-test_1.1
github-actions[bot] Jul 23, 2025
dcaaf69
Remove shields.json.
vsmalladi Jul 25, 2025
90a5c32
Update miniwdl-test.yml
vsmalladi Jul 25, 2025
dd9c6be
Update miniwdl-test.yml
vsmalladi Jul 25, 2025
db26d5a
Update README.md
vsmalladi Jul 25, 2025
217b29a
Merge branch 'fix-test_1.1' of github.com:openwdl/wdl into fix-test_1.1
vsmalladi Jul 25, 2025
3ff09c4
Fix path.
vsmalladi Jul 25, 2025
ea427b7
Update miniwdl shields badge for fix-test_1.1
github-actions[bot] Jul 25, 2025
ed12925
Update README.md
vsmalladi Jul 25, 2025
69d8870
Update miniwdl shields badge for fix-test_1.1
github-actions[bot] Jul 25, 2025
1cde5e7
Fix branch name.
vsmalladi Jul 26, 2025
e392e1e
Add in sprocket to readme.
vsmalladi Jul 26, 2025
1d15320
Update miniwdl shields badge for fix-test_1.1
github-actions[bot] Jul 26, 2025
556563d
Add in sprocket etes.
vsmalladi Jul 26, 2025
878fdb7
Merge branch 'fix-test_1.1' of github.com:openwdl/wdl into fix-test_1.1
vsmalladi Jul 26, 2025
535410f
Fix syntax.
vsmalladi Jul 26, 2025
d0ad68f
Update Sprocket shields badge for fix-test_1.1
github-actions[bot] Jul 26, 2025
b59bb5b
Update sprocket-test.yml
vsmalladi Jul 27, 2025
e87a1f5
Update sprocket-test.yml
vsmalladi Jul 27, 2025
516139a
Change the test failure mode.
vsmalladi Aug 5, 2025
5d9d86c
Fix syntax.
vsmalladi Aug 5, 2025
f5f027b
Update Sprocket shields badge for fix-test_1.1
github-actions[bot] Aug 5, 2025
ac5d8aa
Scrub readme.
vsmalladi Aug 5, 2025
ae5ec9c
Update Sprocket shields badge for fix-test_1.1
github-actions[bot] Aug 5, 2025
3e07f57
Fix paths.
vsmalladi Aug 5, 2025
2afc6fe
Fix paths again.
vsmalladi Aug 5, 2025
1c54b81
Fix yaml.
vsmalladi Aug 5, 2025
6991c51
Update miniwdl shields badge for fix-test_1.1
github-actions[bot] Aug 5, 2025
e868c1c
update paths.
vsmalladi Aug 5, 2025
b0d1f99
Update miniwdl shields badge for fix-test_1.1
github-actions[bot] Aug 5, 2025
9ef54c0
Fix paths and name of a test.
vsmalladi Aug 5, 2025
aa0f6fb
Update Sprocket shields badge for fix-test_1.1
github-actions[bot] Aug 5, 2025
a48b646
Fix test outputs.
vsmalladi Aug 13, 2025
a1b5c9a
Update miniwdl shields badge for fix-test_1.1
github-actions[bot] Aug 13, 2025
072f4c1
Fix for missing files
vsmalladi Aug 13, 2025
49e4d42
Fix variable instead of text
vsmalladi Aug 13, 2025
22032a4
Update Sprocket shields badge for fix-test_1.1
github-actions[bot] Aug 13, 2025
6b01ed4
Update names of badges and tests.
vsmalladi Aug 19, 2025
758f7a7
Update badge names
vsmalladi Aug 19, 2025
0d61f0a
Update miniwdl shields badge for fix-test_1.1
github-actions[bot] Aug 19, 2025
9786801
Update Sprocket shields badge for fix-test_1.1
github-actions[bot] Aug 19, 2025
63df4ff
Add in toil tests.
vsmalladi Aug 21, 2025
57fcea7
Fix from 1.2 to 1.1.
vsmalladi Aug 21, 2025
5ab2871
Update Toil WDL shields badge for fix-test_1.1
github-actions[bot] Aug 21, 2025
82bd4ac
Update Toil WDL shields badge for fix-test_1.1
github-actions[bot] Aug 21, 2025
8a92472
Change label.
vsmalladi Aug 21, 2025
5d8e761
Merge branch 'fix-test_1.1' of github.com:openwdl/wdl into fix-test_1.1
vsmalladi Aug 22, 2025
be1610a
First try at cromwell tests. Must use development version.
vsmalladi Aug 23, 2025
87ccd45
Update miniwdl shields badge for fix-test_1.1
github-actions[bot] Aug 23, 2025
1e2f2e5
Update cromwell-test.yml
vsmalladi Aug 23, 2025
bc83904
Update cromwell-test.yml
vsmalladi Aug 23, 2025
01eeffd
Update cromwell-test.yml
vsmalladi Aug 23, 2025
574c7aa
Update cromwell-test.yml
vsmalladi Aug 23, 2025
2f3dbac
Fix output path.
vsmalladi Aug 23, 2025
ed0c708
Update Cromwell shields badge for fix-test_1.1
github-actions[bot] Aug 23, 2025
03dbbe8
Update README.md
vsmalladi Aug 23, 2025
59fb876
Update README.md
vsmalladi Aug 23, 2025
15cd95e
Fix updates to badges.
vsmalladi Aug 23, 2025
c469abb
Update Cromwell shields badge for fix-test_1.1
github-actions[bot] Aug 23, 2025
1b822bb
Merge branch 'wdl-1.1' into fix-test_1.1
vsmalladi Aug 23, 2025
0d3b041
Update tests to link to latest run.
vsmalladi Aug 26, 2025
2b42c91
Merge branch 'fix-test_1.1' of github.com:openwdl/wdl into fix-test_1.1
vsmalladi Aug 26, 2025
d576927
Fix pattern matching.
vsmalladi Aug 26, 2025
4451286
Fix pattern matching.
vsmalladi Aug 26, 2025
6c9f336
Fix spec to skip certain tests due to limitations of github actions.
vsmalladi Aug 28, 2025
b135db9
Fix json syntax.
vsmalladi Aug 28, 2025
0fcfb9d
Update miniwdl shields badge for fix-test_1.1
github-actions[bot] Aug 28, 2025
2837051
Update Sprocket shields badge for fix-test_1.1
github-actions[bot] Aug 28, 2025
7bb89d3
Update Toil WDL shields badge for fix-test_1.1
github-actions[bot] Aug 28, 2025
4bdb35e
Update Cromwell shields badge for fix-test_1.1
github-actions[bot] Aug 28, 2025
1717688
Fix sex pattern.
vsmalladi Aug 28, 2025
72fe444
Update miniwdl shields badge for fix-test_1.1
github-actions[bot] Aug 28, 2025
3f50364
Update Sprocket shields badge for fix-test_1.1
github-actions[bot] Aug 28, 2025
53e085f
Update Toil WDL shields badge for fix-test_1.1
github-actions[bot] Aug 28, 2025
467df7d
Update Cromwell shields badge for fix-test_1.1
github-actions[bot] Aug 28, 2025
c5f5770
Update CHANGELOG.md
vsmalladi Sep 2, 2025
53ae1f2
Update miniwdl shields badge for fix-test_1.1
github-actions[bot] Sep 2, 2025
99d3a20
Update Sprocket shields badge for fix-test_1.1
github-actions[bot] Sep 2, 2025
08cdcd7
Update Toil WDL shields badge for fix-test_1.1
github-actions[bot] Sep 2, 2025
4ddcc53
Update Cromwell shields badge for fix-test_1.1
github-actions[bot] Sep 2, 2025
c9a1d00
Update fixes to test scripts.
vsmalladi Sep 19, 2025
6400a21
Update spec with suggested changes.
vsmalladi Sep 19, 2025
82de728
Fix syntax.
vsmalladi Sep 19, 2025
cb9fb73
chore: updates MiniWDL shields badge for `fix-test_1.1`
github-actions[bot] Sep 19, 2025
17be498
chore: updates MiniWDL shields badge for `fix-test_1.1`
github-actions[bot] Sep 19, 2025
163b924
chore: updates Toil WDL shields badge for `fix-test_1.1`
github-actions[bot] Sep 19, 2025
15b099b
chore: updates Toil WDL shields badge for `fix-test_1.1`
github-actions[bot] Sep 19, 2025
56a4b9f
chore: updates Cromwell shields badge for `fix-test_1.1`
github-actions[bot] Sep 19, 2025
7041f7d
Migrate changes for more robust from 1.2 test updates.
vsmalladi Oct 4, 2025
b1c9fbb
Fix bam file name.
vsmalladi Oct 4, 2025
348abdb
chore: updates Sprocket shields badge for `fix-test_1.1`
github-actions[bot] Oct 4, 2025
efa9ffe
chore: updates MiniWDL shields badge for `fix-test_1.1`
github-actions[bot] Oct 4, 2025
6086c2c
chore: updates Sprocket shields badge for `fix-test_1.1`
github-actions[bot] Oct 4, 2025
3ea4070
chore: updates Toil WDL shields badge for `fix-test_1.1`
github-actions[bot] Oct 4, 2025
d2e6aeb
chore: updates Toil WDL shields badge for `fix-test_1.1`
github-actions[bot] Oct 4, 2025
7e3a7ed
chore: updates Cromwell shields badge for `fix-test_1.1`
github-actions[bot] Oct 4, 2025
f5f8b63
chore: updates Cromwell shields badge for `fix-test_1.1`
github-actions[bot] Oct 4, 2025
83d8681
Remove files that we downloaded and update test.
vsmalladi Oct 6, 2025
78e9bdc
chore: updates Sprocket shields badge for `fix-test_1.1`
github-actions[bot] Oct 6, 2025
869b808
chore: updates MiniWDL shields badge for `fix-test_1.1`
github-actions[bot] Oct 6, 2025
0a63d0d
chore: updates Toil WDL shields badge for `fix-test_1.1`
github-actions[bot] Oct 6, 2025
65cf4f0
chore: updates Cromwell shields badge for `fix-test_1.1`
github-actions[bot] Oct 6, 2025
88416a4
Fix regex.
vsmalladi Oct 6, 2025
11e291c
Merge branch 'fix-test_1.1' of github.com:openwdl/wdl into fix-test_1.1
vsmalladi Oct 6, 2025
11cdf0e
chore: updates Sprocket shields badge for `fix-test_1.1`
github-actions[bot] Oct 6, 2025
c227418
chore: updates MiniWDL shields badge for `fix-test_1.1`
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f66f8ec
chore: updates Toil WDL shields badge for `fix-test_1.1`
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chore: updates Cromwell shields badge for `fix-test_1.1`
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112 changes: 70 additions & 42 deletions SPEC.md
Original file line number Diff line number Diff line change
Expand Up @@ -1161,12 +1161,23 @@ Example output:
"account_number": "123456",
"routing_number": 300211325,
"balance": 3.5,
"pin_digits": [1, 2, 3, 4]
"pin_digits": [1, 2, 3, 4],
"username": null
}
},
"test_struct.has_account": true
}
```

Test config:

```json
{
"optional_output": "username"
}
```


</p>
</details>

Expand Down Expand Up @@ -1446,9 +1457,9 @@ workflow map_to_struct {

# What are the keys to this Struct?
Words map_coercion = {
a: 10,
b: 11,
c: 12
"a": 10,
"b": 11,
"c": 12
}
}
}
Expand All @@ -1471,9 +1482,9 @@ Example output:
"c": 12
},
"map_to_struct.map_coercion": {
"beware": 10,
"key": 11,
"lookup": 12
"a": 10,
"b": 11,
"c": 12
}
}
```
Expand Down Expand Up @@ -3730,7 +3741,7 @@ Test config:

```json
{
"exclude_output": "csvs"
"exclude_output": "outputs.csvs"
}
```
</p>
Expand Down Expand Up @@ -3839,7 +3850,7 @@ Test config:

```json
{
"exclude_output": "outfiles"
"exclude_output": "glob.outfiles"
}
```
</p>
Expand Down Expand Up @@ -3890,7 +3901,7 @@ Test config:

```json
{
"exclude_output": "bashrc"
"exclude_output": "relative_and_absolute.bashrc"
}
```
</p>
Expand Down Expand Up @@ -3943,6 +3954,15 @@ Example output:
"optional_output.file_array": ["example1.txt", null]
}
```

Test config:

```json
{
"exclude_output": "optional_output.file_array"
}
```

</p>
</details>

Expand Down Expand Up @@ -4443,7 +4463,7 @@ task single_return_code {
>>>

runtime {
return_codes: 1
returnCodes: 1
}
}
```
Expand All @@ -4465,7 +4485,7 @@ Test config:

```json
{
"return_code": 1
"returnCodes": 0
}
```
</p>
Expand All @@ -4484,7 +4504,7 @@ task multi_return_code {
>>>

runtime {
return_codes: [1, 2, 5, 10]
returnCodes: [1, 2, 5, 10]
}
}
```
Expand All @@ -4507,7 +4527,7 @@ Test config:
```json
{
"fail": true,
"return_code": 42
"returnCodes": 42
}
```
</p>
Expand All @@ -4520,13 +4540,13 @@ Example: all_return_codes_task.wdl
```wdl
version 1.1

task multi_return_code_task {
task all_return_codes {
command <<<
exit 42
>>>

runtime {
return_codes: "*"
returnCodes: "*"
}
}
```
Expand All @@ -4548,7 +4568,7 @@ Test config:

```json
{
"return_code": 42
"returnCodes": 0
}
```
</p>
Expand Down Expand Up @@ -4874,7 +4894,9 @@ version 1.1
task hisat2 {
input {
File index_tar_gz
String sra_acc
File fastq1
File fastq2
String sample_name
Int? max_reads
Int threads = 8
Float memory_gb = 16
Expand All @@ -4885,16 +4907,17 @@ task hisat2 {

command <<<
mkdir "~{index_id}"
tar -C "~{index_id}" --strip-components 2 -xzf "~{index_tar_gz}"
tar -C "~{index_id}" --strip-components 1 -xzf "~{index_tar_gz}"
hisat2 \
-p ~{threads} \
~{if defined(max_reads) then "-u ~{select_first([max_reads])}" else ""} \
-x "~{index_id}" \
--sra-acc ~{sra_acc} > ~{sra_acc}.sam
-1 ~{fastq1} -2 ~{fastq2} \
-x "~{index_id}"/genome \
> ~{sample_name}.sam
>>>

output {
File sam = "output.sam"
File sam = "~{sample_name}.sam"
}

runtime {
Expand All @@ -4910,7 +4933,9 @@ task hisat2 {

parameter_meta {
index_tar_gz: "Gzipped tar file with HISAT2 index files"
sra_acc: "SRA accession number or reads to align"
fastq1: "The first-end FastQ file."
fastq2: "The second-end FastQ file."
sample_name: "Name of the sample"
}
}
```
Expand All @@ -4920,17 +4945,19 @@ Example input:

```json
{
"hisat2.index_tar_gz": "https://genome-idx.s3.amazonaws.com/hisat/grch38_genome.tar.gz",
"hisat2.sra_acc": "SRR3440404",
"hisat2.max_reads": 10
"index_tar_gz": "https://genome-idx.s3.amazonaws.com/hisat/grch38_genome.tar.gz",
"fastq1": "https://storage.googleapis.com/genomics-public-data/gatk-examples/example1/NA20274/ERR250968_1.filt.fastq.gz",
"fastq2":"https://storage.googleapis.com/genomics-public-data/gatk-examples/example1/NA20274/ERR250968_2.filt.fastq.gz",
"sample_name": "NA20274",
"max_reads": 10
}
```

Example output:

```json
{
"hisat2.sam": "SRR3440404.sam"
"hisat2.sam": "NA20274.sam"
}
```

Expand Down Expand Up @@ -4981,6 +5008,7 @@ task gatk_haplotype_caller {
ln -s ~{reference.fasta} ref/~{reference.id}.fasta
ln -s ~{reference.index} ref/~{reference.id}.fasta.fai
ln -s ~{reference.dict} ref/~{reference.id}.dict
samtools index ~{bam}
gatk --java-options "-Xmx~{memory_gb}g" HaplotypeCaller \
~{if defined(interval) then "-L ~{select_first([interval])}" else ""} \
-R ref/~{reference.id}.fasta \
Expand Down Expand Up @@ -5018,22 +5046,22 @@ Example input:

```json
{
"gatk_haplotype_caller.bam": "ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/NIST_NA12878_HG001_HiSeq_300x/RMNISTHS_30xdownsample.bam",
"gatk_haplotype_caller.reference": {
"id":"Homo_sapiens_assembly38",
"fasta": "https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta",
"index": "https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"dict": "https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dict"
},
"gatk_haplotype_caller.interval": "chr1:1000000-1010000"
"bam": "https://storage.googleapis.com/genomics-public-data/1000-genomes/bam/HG00107.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.bam",
"reference": {
"id":"Homo_sapiens_assembly19_1000genomes_decoy",
"fasta": "https://storage.googleapis.com/genomics-public-data/references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta",
"index": "https://storage.googleapis.com/genomics-public-data/references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta.fai",
"dict": "https://storage.googleapis.com/genomics-public-data/references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.dict"
},
"interval": "1:12505000-12506000"
}
```

Example output:

```json
{
"gatk_haplotype_caller.vcf": "HG002.vcf"
"gatk_haplotype_caller.vcf": "HG00107.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.vcf"
}
```

Expand Down Expand Up @@ -5193,7 +5221,7 @@ When a [call statement](#call-statement) needs to refer to a task or workflow in

<details>
<summary>
Example: call_imported_task.wdl
Example: call_imported.wdl

```wdl
version 1.1
Expand Down Expand Up @@ -6340,7 +6368,7 @@ Example output:

```json
{
"test_round.all_true": [true, false]
"test_round.all_true": [true, true]
}
```
</p>
Expand Down Expand Up @@ -6511,7 +6539,7 @@ workflow test_sub {
String chocoearly = sub(chocolike, "late", "early") # I like chocoearly when\nit's early
String chocolate = sub(chocolike, "late$", "early") # I like chocolate when\nit's early
String chocoearlylate = sub(chocolike, "[^ ]late", "early") # I like chocearly when\nit's late
String choco4 = sub(chocolike, " [:alpha:]{4} ", " 4444 ") # I 4444 chocolate when\nit's late
String choco4 = sub(chocolike, " [[:alpha:]]{4} ", " 4444 ") # I 4444 chocolate when\nit's late
String no_newline = sub(chocolike, "\\n", " ") # "I like chocolate when it's late"
}
}
Expand Down Expand Up @@ -6592,7 +6620,7 @@ Test config:

```json
{
"exclude_output": ["data_file"]
"exclude_output": ["change_extension.data_file"]
}
```
</p>
Expand Down Expand Up @@ -6728,7 +6756,7 @@ Test config:

```json
{
"exclude_output": ["files"]
"exclude_output": ["gen_files.files"]
}
```
</p>
Expand Down Expand Up @@ -10113,7 +10141,7 @@ Example output:
```json
{
"serde_pair.tails_of_two": {
"Houston": "Chicago"
"Chicago": "Piscataway"
}
}
```
Expand Down