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Use the WEBIN from tester and stop hard-coding project accession during testing #112

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Merged
ochkalova merged 6 commits into from
Oct 19, 2026
Merged

Use the WEBIN from tester and stop hard-coding project accession during testing #112

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02acd44
Rename assembly_complete_metadata by adding new ending _fixed_study
aloraine Oct 16, 2026
3ee526f
Stop using fixed study during testing
aloraine Oct 16, 2026
cc7c484
Ignore .venv
aloraine Oct 16, 2026
a8be583
Hard-code project accession (reverting previous edit)
aloraine Oct 16, 2026
601c9f4
Rename test mag_complete_metadata to mag_complete_metadata_fixed_study
aloraine Oct 16, 2026
a24634f
Rename test mag_no_study_complete_metadata to mag_complete_metadata
aloraine Oct 16, 2026
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -11,3 +11,4 @@ null/
.nf-test*
.idea/
test_data
.venv
0 conf/test_assembly_complete_metadata.config → ...mbly_complete_metadata_fixed_study.config
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3 changes: 2 additions & 1 deletion conf/test_assembly_no_coverage_paired_reads.config
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Expand Up @@ -27,7 +27,8 @@ params {
outdir = 'test_output'

mode = "metagenomic_assemblies"
submission_study = "PRJEB98843"
submission_study = null
study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
centre_name = "TEST_CENTER"

}
3 changes: 2 additions & 1 deletion conf/test_assembly_no_coverage_single_reads.config
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Expand Up @@ -27,7 +27,8 @@ params {
outdir = 'test_output'

mode = "metagenomic_assemblies"
submission_study = "PRJEB98843"
submission_study = null
study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
centre_name = "TEST_CENTER"

}
3 changes: 2 additions & 1 deletion conf/test_assembly_one_contig.config
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Expand Up @@ -27,7 +27,8 @@ params {
outdir = 'test_output'

mode = "metagenomic_assemblies"
submission_study = "PRJEB98843"
submission_study = null
study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
centre_name = "TEST_CENTER"

}
3 changes: 2 additions & 1 deletion conf/test_full.config
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Expand Up @@ -18,7 +18,8 @@ params {
input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_multiple_bins_missing_metadata.csv'

mode = "mags"
submission_study = "PRJEB98843"
submission_study = null
study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
centre_name = "TEST_CENTER"

test_upload = true
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0 ...est_mag_no_study_complete_metadata.config → conf/test_mag_complete_metadata.config
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0 conf/test_mag_complete_metadata.conf → ...st_mag_complete_metadata_fixed_study.conf
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3 changes: 2 additions & 1 deletion conf/test_mag_no_coverage_paired_reads.conf
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Expand Up @@ -26,7 +26,8 @@ params {
input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_coverage_paired_reads.csv'

mode = "mags"
submission_study = "PRJEB98843"
submission_study = null
study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
centre_name = "TEST_CENTER"

test_upload = true
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3 changes: 2 additions & 1 deletion conf/test_mag_no_coverage_single_reads.conf
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Expand Up @@ -26,7 +26,8 @@ params {
input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_coverage_single_reads.csv'

mode = "mags"
submission_study = "PRJEB98843"
submission_study = null
study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
centre_name = "TEST_CENTER"

test_upload = true
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3 changes: 2 additions & 1 deletion conf/test_mag_no_quality.conf
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Expand Up @@ -26,7 +26,8 @@ params {
input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_quality.csv'

mode = "mags"
submission_study = "PRJEB98843"
submission_study = null
study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
centre_name = "TEST_CENTER"

test_upload = true
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3 changes: 2 additions & 1 deletion conf/test_mag_no_rna_presence.conf
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Expand Up @@ -26,7 +26,8 @@ params {
input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_rna_presence.csv'

mode = "mags"
submission_study = "PRJEB98843"
submission_study = null
study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
centre_name = "TEST_CENTER"

test_upload = true
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3 changes: 2 additions & 1 deletion conf/test_mag_no_taxonomy.conf
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Expand Up @@ -26,7 +26,8 @@ params {
input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_no_taxonomy.csv'

mode = "mags"
submission_study = "PRJEB98843"
submission_study = null
study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
centre_name = "TEST_CENTER"

test_upload = true
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3 changes: 2 additions & 1 deletion conf/test_mag_one_contig.conf
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Expand Up @@ -26,7 +26,8 @@ params {
input = params.pipelines_testdata_base_path + 'seqsubmit/samplesheets/mag_one_contig.csv'

mode = "mags"
submission_study = "PRJEB98843"
submission_study = null
study_metadata = params.pipelines_testdata_base_path + 'seqsubmit/test_data/study_metadata/study_metadata.json'
centre_name = "TEST_CENTER"

test_upload = true
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6 changes: 3 additions & 3 deletions nextflow.config
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Expand Up @@ -241,15 +241,15 @@ profiles {
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
test_mag_complete_metadata { includeConfig 'conf/test_mag_complete_metadata.conf' }
test_mag_no_study_complete_metadata { includeConfig 'conf/test_mag_no_study_complete_metadata.config' }
test_mag_complete_metadata_fixed_study { includeConfig 'conf/test_mag_complete_metadata_fixed_study.conf' }
test_mag_complete_metadata { includeConfig 'conf/test_mag_complete_metadata.config' }
test_mag_no_coverage_single_reads { includeConfig 'conf/test_mag_no_coverage_single_reads.conf' }
test_mag_no_coverage_paired_reads { includeConfig 'conf/test_mag_no_coverage_paired_reads.conf' }
test_mag_no_quality { includeConfig 'conf/test_mag_no_quality.conf' }
test_mag_one_contig { includeConfig 'conf/test_mag_one_contig.conf' }
test_mag_no_rna_presence { includeConfig 'conf/test_mag_no_rna_presence.conf' }
test_mag_no_taxonomy { includeConfig 'conf/test_mag_no_taxonomy.conf' }
test_assembly_complete_metadata { includeConfig 'conf/test_assembly_complete_metadata.config' }
test_assembly_complete_metadata_fixed_study { includeConfig 'conf/test_assembly_complete_metadata_fixed_study.config' }
test_assembly_no_study_complete_metadata { includeConfig 'conf/test_assembly_no_study_complete_metadata.config' }
test_assembly_no_coverage_single_reads { includeConfig 'conf/test_assembly_no_coverage_single_reads.config' }
test_assembly_no_coverage_paired_reads { includeConfig 'conf/test_assembly_no_coverage_paired_reads.config' }
Expand Down
6 changes: 3 additions & 3 deletions tests/assembly_complete_metadata.nf.test → ...bly_complete_metadata_fixed_study.nf.test
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Expand Up @@ -4,10 +4,10 @@ nextflow_pipeline {
script "../main.nf"
tag "pipeline"
tag "mode_assembly"
tag "test_assembly_complete_metadata"
profile "test_assembly_complete_metadata"
tag "test_assembly_complete_metadata_fixed_study"
profile "test_assembly_complete_metadata_fixed_study"

test("-profile test_assembly_complete_metadata") {
test("-profile test_assembly_complete_metadata_fixed_study") {

when {
params {
Expand Down
20 changes: 5 additions & 15 deletions ...s/assembly_complete_metadata.nf.test.snap → ...omplete_metadata_fixed_study.nf.test.snap
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@@ -1,5 +1,5 @@
{
"-profile test_assembly_complete_metadata": {
"-profile test_assembly_complete_metadata_fixed_study": {
"content": [
7,
{
Expand Down Expand Up @@ -51,16 +51,6 @@
"multiqc/multiqc_data/multiqc_data.json",
"multiqc/multiqc_data/multiqc_software_versions.txt",
"multiqc/multiqc_data/multiqc_sources.txt",
"multiqc/multiqc_plots",
"multiqc/multiqc_plots/pdf",
"multiqc/multiqc_plots/pdf/Assemblies assigned accessions.pdf",
"multiqc/multiqc_plots/pdf/assembly_metadata.pdf",
"multiqc/multiqc_plots/png",
"multiqc/multiqc_plots/png/Assemblies assigned accessions.png",
"multiqc/multiqc_plots/png/assembly_metadata.png",
"multiqc/multiqc_plots/svg",
"multiqc/multiqc_plots/svg/Assemblies assigned accessions.svg",
"multiqc/multiqc_plots/svg/assembly_metadata.svg",
"multiqc/multiqc_report.html",
"pipeline_info",
"pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml"
Expand All @@ -71,10 +61,10 @@
"multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
]
],
"timestamp": "2026-10-16T11:08:01.267709",
"meta": {
"nf-test": "0.9.2",
"nextflow": "26.04.1"
},
"timestamp": "2026-05-13T13:17:16.523674"
"nf-test": "0.9.5",
"nextflow": "26.10.0"
}
}
}
23 changes: 8 additions & 15 deletions tests/assembly_no_coverage_paired_reads.nf.test.snap
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@@ -1,7 +1,7 @@
{
"-profile test_assembly_no_coverage_paired_reads": {
"content": [
8,
9,
{
"CONCAT_ACCESSIONS": {
"coreutils": 9.4,
Expand All @@ -25,6 +25,9 @@
"GENERATE_ASSEMBLY_MANIFEST": {
"assembly_uploader": "1.3.5"
},
"REGISTERSTUDY": {
"mgnify-pipelines-toolkit": "1.5.1"
},
"SUBMIT": {
"ena-webin-cli": "9.0.3",
"mgnify-pipelines-toolkit": "1.5.1",
Expand Down Expand Up @@ -56,16 +59,6 @@
"multiqc/multiqc_data/multiqc_data.json",
"multiqc/multiqc_data/multiqc_software_versions.txt",
"multiqc/multiqc_data/multiqc_sources.txt",
"multiqc/multiqc_plots",
"multiqc/multiqc_plots/pdf",
"multiqc/multiqc_plots/pdf/Assemblies assigned accessions.pdf",
"multiqc/multiqc_plots/pdf/assembly_metadata.pdf",
"multiqc/multiqc_plots/png",
"multiqc/multiqc_plots/png/Assemblies assigned accessions.png",
"multiqc/multiqc_plots/png/assembly_metadata.png",
"multiqc/multiqc_plots/svg",
"multiqc/multiqc_plots/svg/Assemblies assigned accessions.svg",
"multiqc/multiqc_plots/svg/assembly_metadata.svg",
"multiqc/multiqc_report.html",
"pipeline_info",
"pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml"
Expand All @@ -77,10 +70,10 @@
"multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
]
],
"timestamp": "2026-10-15T15:39:15.438257",
"meta": {
"nf-test": "0.9.2",
"nextflow": "26.04.1"
},
"timestamp": "2026-05-13T13:18:47.77148"
"nf-test": "0.9.5",
"nextflow": "26.10.0"
}
}
}
23 changes: 8 additions & 15 deletions tests/assembly_no_coverage_single_reads.nf.test.snap
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@@ -1,7 +1,7 @@
{
"-profile test_assembly_no_coverage_single_reads": {
"content": [
8,
9,
{
"CONCAT_ACCESSIONS": {
"coreutils": 9.4,
Expand All @@ -25,6 +25,9 @@
"GENERATE_ASSEMBLY_MANIFEST": {
"assembly_uploader": "1.3.5"
},
"REGISTERSTUDY": {
"mgnify-pipelines-toolkit": "1.5.1"
},
"SUBMIT": {
"ena-webin-cli": "9.0.3",
"mgnify-pipelines-toolkit": "1.5.1",
Expand Down Expand Up @@ -56,16 +59,6 @@
"multiqc/multiqc_data/multiqc_data.json",
"multiqc/multiqc_data/multiqc_software_versions.txt",
"multiqc/multiqc_data/multiqc_sources.txt",
"multiqc/multiqc_plots",
"multiqc/multiqc_plots/pdf",
"multiqc/multiqc_plots/pdf/Assemblies assigned accessions.pdf",
"multiqc/multiqc_plots/pdf/assembly_metadata.pdf",
"multiqc/multiqc_plots/png",
"multiqc/multiqc_plots/png/Assemblies assigned accessions.png",
"multiqc/multiqc_plots/png/assembly_metadata.png",
"multiqc/multiqc_plots/svg",
"multiqc/multiqc_plots/svg/Assemblies assigned accessions.svg",
"multiqc/multiqc_plots/svg/assembly_metadata.svg",
"multiqc/multiqc_report.html",
"pipeline_info",
"pipeline_info/nf_core_seqsubmit_software_mqc_versions.yml"
Expand All @@ -77,10 +70,10 @@
"multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
]
],
"timestamp": "2026-10-15T16:34:10.672881",
"meta": {
"nf-test": "0.9.2",
"nextflow": "26.04.1"
},
"timestamp": "2026-05-13T13:19:25.904346"
"nf-test": "0.9.5",
"nextflow": "26.10.0"
}
}
}
13 changes: 8 additions & 5 deletions tests/assembly_one_contig.nf.test.snap
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@@ -1,8 +1,11 @@
{
"-profile test_assembly_one_contig": {
"content": [
1,
2,
{
"REGISTERSTUDY": {
"mgnify-pipelines-toolkit": "1.5.1"
},
Comment on lines +6 to +8

@ochkalova ochkalova Oct 16, 2026

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It shouldn't be there. That a bug described in #113
I'll fix it later, in the different branch

"Workflow": {
"nf-core/seqsubmit": "v1.0.0"
}
Expand All @@ -28,10 +31,10 @@
"multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
]
],
"timestamp": "2026-10-15T16:17:10.488596",
"meta": {
"nf-test": "0.9.2",
"nextflow": "26.04.1"
},
"timestamp": "2026-05-14T10:39:20.087785"
"nf-test": "0.9.5",
"nextflow": "26.10.0"
}
}
}
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