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Updated workflow tests to exclude multiqc_report
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@CarsonJM
CarsonJM committed Mar 19, 2024
1 parent 2aedae2 commit a442554
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2 changes: 1 addition & 1 deletion workflows/readsimulator/tests/test_amplicon.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@ nextflow_workflow {
assertAll(
{ assert workflow.success },
{ assert snapshot(
workflow.out
workflow.out.get(0).findAll { it != "multiqc_report" }
).match() }
)
}
Expand Down
146 changes: 38 additions & 108 deletions workflows/readsimulator/tests/test_amplicon.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,119 +1,49 @@
{
"amplicon = true": {
"content": [
{
"0": [
[
{
"id": "first",
"seed": 40,
"outdir": "art_illumina",
"datatype": "amplicon_illumina"
},
[
"first1.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
"first2.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
[
{
"id": "second",
"seed": 41,
"outdir": "art_illumina",
"datatype": "amplicon_illumina"
},
[
"second1.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
"second2.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
[
{
"id": "third",
"seed": 42,
"outdir": "art_illumina",
"datatype": "amplicon_illumina"
},
[
"third1.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
"third2.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"1": [
[
{
"id": "amplicon_illumina"
},
"amplicon_illumina_samplesheet.csv:md5,2f0440b621dd2de3c89cda85c81e5be7"
]
],
"2": [
[
"multiqc_report.html:md5,788578636e6f53ba65a66cecf8172f3a"
[
[
{
"id": "first",
"seed": 40,
"outdir": "art_illumina",
"datatype": "amplicon_illumina"
},
[
"first1.fq.gz:md5,5dfb2de5a3d547b4a1cbdfe8fe33eb78",
"first2.fq.gz:md5,3ff099ec08c9d1f1f87f7bcd1455aad3"
]
],
"3": [
"versions.yml:md5,7282f5159b374e936cdb2a26261c07dd",
"versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c"
],
"multiqc_report": [
[
"multiqc_report.html:md5,788578636e6f53ba65a66cecf8172f3a"
[
{
"id": "second",
"seed": 41,
"outdir": "art_illumina",
"datatype": "amplicon_illumina"
},
[
"second1.fq.gz:md5,fdb32a77b5d100efd77f9b253475b354",
"second2.fq.gz:md5,97b1101a3a2a3814f301ccd90b5c2f30"
]
],
"samplesheet": [
[
{
"id": "amplicon_illumina"
},
"amplicon_illumina_samplesheet.csv:md5,2f0440b621dd2de3c89cda85c81e5be7"
[
{
"id": "third",
"seed": 42,
"outdir": "art_illumina",
"datatype": "amplicon_illumina"
},
[
"third1.fq.gz:md5,62ab3b38160c81c9d9fa972871f896d3",
"third2.fq.gz:md5,912ae27dc22fea5b3d2f8f3a5dd4fa08"
]
],
"simulated_reads": [
[
{
"id": "first",
"seed": 40,
"outdir": "art_illumina",
"datatype": "amplicon_illumina"
},
[
"first1.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
"first2.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
[
{
"id": "second",
"seed": 41,
"outdir": "art_illumina",
"datatype": "amplicon_illumina"
},
[
"second1.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
"second2.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
[
{
"id": "third",
"seed": 42,
"outdir": "art_illumina",
"datatype": "amplicon_illumina"
},
[
"third1.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
"third2.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
"versions": [
"versions.yml:md5,7282f5159b374e936cdb2a26261c07dd",
"versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c"
]
}
]
],
"timestamp": "2024-01-19T19:15:08.881730553"
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-03-19T14:38:49.385639018"
}
}
}
2 changes: 1 addition & 1 deletion workflows/readsimulator/tests/test_metagenome.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ nextflow_workflow {
assertAll(
{ assert workflow.success },
{ assert snapshot(
workflow.out
workflow.out.get(0).findAll { it != "multiqc_report" }
).match() }
)
}
Expand Down
146 changes: 38 additions & 108 deletions workflows/readsimulator/tests/test_metagenome.nf.test.snap
View file
Original file line number Diff line number Diff line change
@@ -1,119 +1,49 @@
{
"metagenome = true": {
"content": [
{
"0": [
[
{
"id": "first",
"seed": 40,
"outdir": "insilicoseq",
"datatype": "metagenomic_illumina"
},
[
"first_R1.fastq.gz:md5,2a324062e0afb4d3eab8134479f317d4",
"first_R2.fastq.gz:md5,9e0c86c0ff15091734fe7d52039f7727"
]
],
[
{
"id": "second",
"seed": 41,
"outdir": "insilicoseq",
"datatype": "metagenomic_illumina"
},
[
"second_R1.fastq.gz:md5,3536190205e1a6ba3609fe6a1567e0c7",
"second_R2.fastq.gz:md5,a91ff7cf5ea2069d541fc7d081c82bfb"
]
],
[
{
"id": "third",
"seed": 42,
"outdir": "insilicoseq",
"datatype": "metagenomic_illumina"
},
[
"third_R1.fastq.gz:md5,137d1f3ced4783a0a45f6d7aed6da743",
"third_R2.fastq.gz:md5,3a78f893f1c12af70d13fe3df59eaa84"
]
]
],
"1": [
[
{
"id": "metagenomic_illumina"
},
"metagenomic_illumina_samplesheet.csv:md5,8064936eff731e7c4c879916eb8b2edb"
]
],
"2": [
[
"multiqc_report.html:md5,ebcfd57013f73d2afd52650543a88aee"
[
[
{
"id": "first",
"seed": 40,
"outdir": "insilicoseq",
"datatype": "metagenomic_illumina"
},
[
"first_R1.fastq.gz:md5,2a324062e0afb4d3eab8134479f317d4",
"first_R2.fastq.gz:md5,9e0c86c0ff15091734fe7d52039f7727"
]
],
"3": [
"versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c",
"versions.yml:md5,c8240bb3edb947511ec99bd2ef740b8a"
],
"multiqc_report": [
[
"multiqc_report.html:md5,ebcfd57013f73d2afd52650543a88aee"
[
{
"id": "second",
"seed": 41,
"outdir": "insilicoseq",
"datatype": "metagenomic_illumina"
},
[
"second_R1.fastq.gz:md5,3536190205e1a6ba3609fe6a1567e0c7",
"second_R2.fastq.gz:md5,a91ff7cf5ea2069d541fc7d081c82bfb"
]
],
"samplesheet": [
[
{
"id": "metagenomic_illumina"
},
"metagenomic_illumina_samplesheet.csv:md5,8064936eff731e7c4c879916eb8b2edb"
[
{
"id": "third",
"seed": 42,
"outdir": "insilicoseq",
"datatype": "metagenomic_illumina"
},
[
"third_R1.fastq.gz:md5,137d1f3ced4783a0a45f6d7aed6da743",
"third_R2.fastq.gz:md5,3a78f893f1c12af70d13fe3df59eaa84"
]
],
"simulated_reads": [
[
{
"id": "first",
"seed": 40,
"outdir": "insilicoseq",
"datatype": "metagenomic_illumina"
},
[
"first_R1.fastq.gz:md5,2a324062e0afb4d3eab8134479f317d4",
"first_R2.fastq.gz:md5,9e0c86c0ff15091734fe7d52039f7727"
]
],
[
{
"id": "second",
"seed": 41,
"outdir": "insilicoseq",
"datatype": "metagenomic_illumina"
},
[
"second_R1.fastq.gz:md5,3536190205e1a6ba3609fe6a1567e0c7",
"second_R2.fastq.gz:md5,a91ff7cf5ea2069d541fc7d081c82bfb"
]
],
[
{
"id": "third",
"seed": 42,
"outdir": "insilicoseq",
"datatype": "metagenomic_illumina"
},
[
"third_R1.fastq.gz:md5,137d1f3ced4783a0a45f6d7aed6da743",
"third_R2.fastq.gz:md5,3a78f893f1c12af70d13fe3df59eaa84"
]
]
],
"versions": [
"versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c",
"versions.yml:md5,c8240bb3edb947511ec99bd2ef740b8a"
]
}
]
],
"timestamp": "2024-01-19T00:09:35.115953915"
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-03-19T14:51:11.751345459"
}
}
}
2 changes: 1 addition & 1 deletion workflows/readsimulator/tests/test_target_capture.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ nextflow_workflow {
assertAll(
{ assert workflow.success },
{ assert snapshot(
workflow.out
workflow.out.get(0).findAll { it != "multiqc_report" }
).match() }
)
}
Expand Down
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