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Use default snapshot for all workflows
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@drpatelh
drpatelh committed Aug 17, 2023
1 parent 73ea3ca commit de46456
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Showing 23 changed files with 150 additions and 190 deletions.
2 changes: 1 addition & 1 deletion modules/local/multiqc_mappings_config/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert snapshot(process.out).match() }
)
}
}
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27 changes: 26 additions & 1 deletion modules/local/multiqc_mappings_config/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,31 @@
]
}
],
"timestamp": "2023-07-05T15:01:18+0000"
"timestamp": "2023-08-17T12:02:35+0000"
},
"Should run without failures": {
"content": [
{
"0": [
[
"multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
"versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
]
],
"1": [
"versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
],
"versions": [
"versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
],
"yml": [
[
"multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
"versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
]
]
}
],
"timestamp": "2023-08-17T12:02:35+0000"
}
}
2 changes: 1 addition & 1 deletion modules/local/sra_fastq_ftp/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert snapshot(process.out).match() }
)
}
}
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2 changes: 1 addition & 1 deletion modules/local/sra_ids_to_runinfo/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert snapshot(process.out).match() }
)
}
}
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2 changes: 1 addition & 1 deletion modules/local/sra_merge_samplesheet/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert snapshot(process.out).match() }
)
}
}
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2 changes: 1 addition & 1 deletion modules/local/sra_runinfo_to_ftp/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert snapshot(process.out).match() }
)
}
}
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2 changes: 1 addition & 1 deletion modules/local/sra_to_samplesheet/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert snapshot(process.out).match() }
)
}
}
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21 changes: 1 addition & 20 deletions workflows/sra/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -17,26 +17,7 @@ nextflow_pipeline {
then {
assertAll(
{ assert workflow.success },
{ assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
{ assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
{ assert snapshot(
path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata")
},
{ assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
{ assert snapshot(
path("$outputDir/samplesheet/id_mappings.csv"),
path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet")
},
{ assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
{ assert snapshot(process.out).match() }
)
}
}
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16 changes: 12 additions & 4 deletions workflows/sra/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,4 +1,12 @@
{
"Parameters: default": {
"content": [
{

}
],
"timestamp": "2023-08-17T12:09:45+0000"
},
"metadata": {
"content": [
"DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
Expand All @@ -12,20 +20,20 @@
"SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
"SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
],
"timestamp": "2023-08-06T23:48:50+0000"
"timestamp": "2023-08-17T12:09:45+0000"
},
"samplesheet": {
"content": [
"id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
"multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
],
"timestamp": "2023-08-06T23:48:50+0000"
"timestamp": "2023-08-17T12:09:45+0000"
},
"software_versions": {
"content": [
"{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
],
"timestamp": "2023-08-06T23:48:50+0000"
"timestamp": "2023-08-17T12:09:45+0000"
},
"fastq": {
"content": [
Expand Down Expand Up @@ -75,6 +83,6 @@
"SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
]
],
"timestamp": "2023-08-06T23:48:50+0000"
"timestamp": "2023-08-17T12:09:45+0000"
}
}
19 changes: 2 additions & 17 deletions workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ nextflow_pipeline {
tag "workflows_sra"
tag "sra_custom_ena_metadata_fields"

test("Parameters: '--nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...'") {
test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") {

when {
params {
Expand All @@ -20,22 +20,7 @@ nextflow_pipeline {
then {
assertAll(
{ assert workflow.success },
{ assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
{ assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
{ assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") },
{ assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
{ assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
{ assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
{ assert snapshot(process.out).match() }
)
}
}
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16 changes: 12 additions & 4 deletions workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -12,20 +12,28 @@
"SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1",
"SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236"
],
"timestamp": "2023-07-03T23:38:27+0000"
"timestamp": "2023-08-17T12:11:42+0000"
},
"samplesheet": {
"content": [
"id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f",
"multiqc_config.yml:md5,6f6189ee58855de81eaf82ad86e21040"
],
"timestamp": "2023-07-03T23:38:27+0000"
"timestamp": "2023-08-17T12:11:42+0000"
},
"software_versions": {
"content": [
"{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
],
"timestamp": "2023-07-03T23:38:27+0000"
"timestamp": "2023-08-17T12:11:42+0000"
},
"Parameters: '--nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...'": {
"content": [
{

}
],
"timestamp": "2023-08-17T12:11:42+0000"
},
"fastq": {
"content": [
Expand Down Expand Up @@ -75,6 +83,6 @@
"SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
]
],
"timestamp": "2023-07-03T23:38:27+0000"
"timestamp": "2023-08-17T12:11:42+0000"
}
}
19 changes: 2 additions & 17 deletions workflows/sra/tests/sra_force_sratools_download.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ nextflow_pipeline {
tag "workflows_sra"
tag "sra_force_sratools_download"

test("Parameters: '--force_sratools_download'") {
test("Parameters: --force_sratools_download") {

when {
params {
Expand All @@ -18,22 +18,7 @@ nextflow_pipeline {
then {
assertAll(
{ assert workflow.success },
{ assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
{ assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
{ assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") },
{ assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
{ assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
{ assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
{ assert snapshot(process.out).match() }
)
}
}
Expand Down
16 changes: 12 additions & 4 deletions workflows/sra/tests/sra_force_sratools_download.nf.test.snap
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,12 @@
{
"Parameters: '--force_sratools_download'": {
"content": [
{

}
],
"timestamp": "2023-08-17T12:15:55+0000"
},
"metadata": {
"content": [
"DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f",
Expand All @@ -12,20 +20,20 @@
"SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
"SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
],
"timestamp": "2023-08-06T23:43:45+0000"
"timestamp": "2023-08-17T12:15:55+0000"
},
"samplesheet": {
"content": [
"id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
"multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
],
"timestamp": "2023-08-06T23:43:45+0000"
"timestamp": "2023-08-17T12:15:55+0000"
},
"software_versions": {
"content": [
"{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
],
"timestamp": "2023-08-06T23:43:45+0000"
"timestamp": "2023-08-17T12:15:55+0000"
},
"fastq": {
"content": [
Expand Down Expand Up @@ -54,6 +62,6 @@
"SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7",
"SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af"
],
"timestamp": "2023-08-06T23:43:45+0000"
"timestamp": "2023-08-17T12:15:55+0000"
}
}
19 changes: 2 additions & 17 deletions workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ nextflow_pipeline {
tag "workflows_sra"
tag "sra_nf_core_pipeline_atacseq"

test("Parameters: '--nf_core_pipeline atacseq'") {
test("Parameters: --nf_core_pipeline atacseq") {

when {
params {
Expand All @@ -18,22 +18,7 @@ nextflow_pipeline {
then {
assertAll(
{ assert workflow.success },
{ assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") },
{ assert snapshot(path("$outputDir/fastq/").list()).match("fastq") },
{ assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"),
path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"),
path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"),
path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"),
path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"),
path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") },
{ assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() },
{ assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"),
path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") },
{ assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }
{ assert snapshot(process.out).match() }
)
}
}
Expand Down
16 changes: 12 additions & 4 deletions workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,20 +12,28 @@
"SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1",
"SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be"
],
"timestamp": "2023-08-06T23:38:47+0000"
"timestamp": "2023-08-17T12:21:36+0000"
},
"samplesheet": {
"content": [
"id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565",
"multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548"
],
"timestamp": "2023-08-06T23:38:47+0000"
"timestamp": "2023-08-17T12:21:36+0000"
},
"software_versions": {
"content": [
"{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}"
],
"timestamp": "2023-08-06T23:38:47+0000"
"timestamp": "2023-08-17T12:21:36+0000"
},
"Parameters: '--nf_core_pipeline atacseq'": {
"content": [
{

}
],
"timestamp": "2023-08-17T12:21:36+0000"
},
"fastq": {
"content": [
Expand Down Expand Up @@ -75,6 +83,6 @@
"SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945"
]
],
"timestamp": "2023-08-06T23:38:47+0000"
"timestamp": "2023-08-17T12:21:36+0000"
}
}
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