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Replace tags strategy with implicit 'tags in test' strategy #253

Merged
merged 22 commits into from
Jan 29, 2024
Merged

Replace tags strategy with implicit 'tags in test' strategy #253

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61e7662
Replace tag strategy for testing
adamrtalbot Jan 18, 2024
34baed6
Remove all tags.yml files
adamrtalbot Jan 18, 2024
a6c34fc
Tag order changed
adamrtalbot Jan 18, 2024
76095d3
Replace tag logic in Github Action testing workflow
adamrtalbot Jan 18, 2024
c325d8d
Fixup CI
adamrtalbot Jan 18, 2024
fe432bc
Correct UTILS_NEXTFLOW_PIPELINE tag
adamrtalbot Jan 18, 2024
bcae51a
ECLint
adamrtalbot Jan 18, 2024
b1b117d
Use PIPELINE tag
adamrtalbot Jan 19, 2024
7d88962
Add exclusion statments for linting files
adamrtalbot Jan 19, 2024
c36a8aa
Add renamed files as deleted and added
adamrtalbot Jan 19, 2024
412b059
Add another debugging step
adamrtalbot Jan 19, 2024
2f6a78a
Revert "Use PIPELINE tag"
adamrtalbot Jan 19, 2024
f28a336
Use PIPELINE tag
adamrtalbot Jan 19, 2024
401f91d
Add files_yaml stuff for checking all
adamrtalbot Jan 19, 2024
6cdff1c
Add debug step
adamrtalbot Jan 19, 2024
d490e6a
Refine pipeline and 'all' test rules
adamrtalbot Jan 19, 2024
00c2ea0
Add shared tag to pipeline level tests
adamrtalbot Jan 19, 2024
4d2d566
Remove shared yaml anchor because I think it isn't needed
adamrtalbot Jan 19, 2024
6c00433
Use collect and confirm strategy for tests
adamrtalbot Jan 22, 2024
bc25627
Tag tidy based on review comments
adamrtalbot Jan 23, 2024
8946e2d
Merge branch 'dev' into nftest_new_tags_strategy
adamrtalbot Jan 26, 2024
cb4f0e6
Update tags for utils_nfcore_fetchngs_pipeline subworkflow
adamrtalbot Jan 26, 2024
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5 changes: 2 additions & 3 deletions modules/local/multiqc_mappings_config/tests/main.nf.test
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Expand Up @@ -3,9 +3,8 @@ nextflow_process {
name "Test process: MULTIQC_MAPPINGS_CONFIG"
script "../main.nf"
process "MULTIQC_MAPPINGS_CONFIG"
tag "modules"
tag "modules_local"
tag "multiqc_mappings_config"

tag "MULTIQC_MAPPINGS_CONFIG"
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Not for this PR- but if tag is becoming redundant with the process maybe we should talk to the nf-test folks about allowing nf-test to list processes/ workflows rather than tags?

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I think it's similar to what @adamrtalbot meant when creating this issue: askimed/nf-test#178

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Correct, I've suggested it as a feature. This was the behaviour in pytest-workflow as well.

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Gotcha, sorry for the slow uptake


test("Should run without failures") {

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2 changes: 0 additions & 2 deletions modules/local/multiqc_mappings_config/tests/tags.yml
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5 changes: 2 additions & 3 deletions modules/local/sra_fastq_ftp/tests/main.nf.test
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Expand Up @@ -3,9 +3,8 @@ nextflow_process {
name "Test process: SRA_FASTQ_FTP"
script "../main.nf"
process "SRA_FASTQ_FTP"
tag "modules"
tag "modules_local"
tag "sra_fastq_ftp"

tag "SRA_FASTQ_FTP"

test("Should run without failures") {

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2 changes: 0 additions & 2 deletions modules/local/sra_fastq_ftp/tests/tags.yml
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5 changes: 2 additions & 3 deletions modules/local/sra_ids_to_runinfo/tests/main.nf.test
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Expand Up @@ -3,9 +3,8 @@ nextflow_process {
name "Test process: SRA_IDS_TO_RUNINFO"
script "../main.nf"
process "SRA_IDS_TO_RUNINFO"
tag "modules"
tag "modules_local"
tag "sra_ids_to_runinfo"

tag "SRA_IDS_TO_RUNINFO"

test("Should run without failures") {

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2 changes: 0 additions & 2 deletions modules/local/sra_ids_to_runinfo/tests/tags.yml
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5 changes: 2 additions & 3 deletions modules/local/sra_runinfo_to_ftp/tests/main.nf.test
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Expand Up @@ -3,9 +3,8 @@ nextflow_process {
name "Test process: SRA_RUNINFO_TO_FTP"
script "../main.nf"
process "SRA_RUNINFO_TO_FTP"
tag "modules"
tag "modules_local"
tag "sra_runinfo_to_ftp"

tag "SRA_RUNINFO_TO_FTP"

test("Should run without failures") {

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2 changes: 0 additions & 2 deletions modules/local/sra_runinfo_to_ftp/tests/tags.yml
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5 changes: 2 additions & 3 deletions modules/local/sra_to_samplesheet/tests/main.nf.test
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Expand Up @@ -3,9 +3,8 @@ nextflow_process {
name "Test process: SRA_TO_SAMPLESHEET"
script "../main.nf"
process "SRA_TO_SAMPLESHEET"
tag "modules"
tag "modules_local"
tag "sra_to_samplesheet"

tag "SRA_TO_SAMPLESHEET"

test("Should run without failures") {

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2 changes: 0 additions & 2 deletions modules/local/sra_to_samplesheet/tests/tags.yml
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6 changes: 2 additions & 4 deletions modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
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2 changes: 0 additions & 2 deletions modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml
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8 changes: 3 additions & 5 deletions modules/nf-core/sratools/fasterqdump/tests/main.nf.test
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2 changes: 0 additions & 2 deletions modules/nf-core/sratools/fasterqdump/tests/tags.yml
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6 changes: 2 additions & 4 deletions modules/nf-core/sratools/prefetch/tests/main.nf.test
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2 changes: 0 additions & 2 deletions modules/nf-core/sratools/prefetch/tests/tags.yml
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4 changes: 1 addition & 3 deletions modules/nf-core/untar/tests/main.nf.test
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2 changes: 0 additions & 2 deletions modules/nf-core/untar/tests/tags.yml
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11 changes: 5 additions & 6 deletions subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
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2 changes: 0 additions & 2 deletions subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml
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5 changes: 2 additions & 3 deletions subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test
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2 changes: 0 additions & 2 deletions subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
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6 changes: 2 additions & 4 deletions subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
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6 changes: 2 additions & 4 deletions subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
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2 changes: 0 additions & 2 deletions subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
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8 changes: 2 additions & 6 deletions subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
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2 changes: 0 additions & 2 deletions subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
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6 changes: 4 additions & 2 deletions tests/main.nf.test
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Expand Up @@ -2,8 +2,10 @@ nextflow_pipeline {

name "Test pipeline"
script "../main.nf"
tag "pipeline"
tag "pipeline_fetchngs"

tag "SRA"
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why the SRA tag here?

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It's the immediate dependency of the pipeline. Perhaps we just run pipeline level tests at this point?

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OK I've removed it now. It will not test the workflow tests when we launch pipeline level tests anymore.

We can put it back if that behaviour feels weird.


tag "FETCHNGS"
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test("Run with profile test") {

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5 changes: 0 additions & 5 deletions tests/tags.yml
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14 changes: 10 additions & 4 deletions workflows/sra/tests/main.nf.test
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Expand Up @@ -3,10 +3,16 @@ nextflow_workflow {
name "Test workflow: sra/main.nf"
script "../main.nf"
workflow "SRA"
tag "workflows"
tag "workflows_sra"
tag "multiqc_mappings_config"
tag "sra_default_parameters"

// Modules
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Suggested change
// Modules
// Dependencies

I'd rather we be explicit there and say dependencies, as any at this level "workflow" can contain modules and/or subworkflows

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Good idea.

tag "MULTIQC_MAPPINGS_CONFIG"
tag "SRA_FASTQ_FTP"
tag "SRA_IDS_TO_RUNINFO"
tag "SRA_RUNINFO_TO_FTP"
tag "SRA_TO_SAMPLESHEET"
Comment on lines +9 to +13
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Hmmm...we have to be explicit with all of the workflow dependencies here now?

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Could be quite easy to lose track of these as you update the pipeline / workflow....

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Yes we do. Not ideal, but hard to do automatically. See askimed/nf-test#179 for relevant ticket.

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I had exactly the same thought as Harshil, don't think people will be very good at keeping these lists up to date. But I see the difficulties.

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No magic bullet so far. I've proposed automatically testing dependencies, but I also think nf-test can only go so far and it might just have to be the resposibility of the pipeline developer.


// Subworkflows
tag "SRA"
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test("Parameters: default") {

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14 changes: 10 additions & 4 deletions workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
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Expand Up @@ -3,10 +3,16 @@ nextflow_workflow {
name "Test workflow: sra/main.nf"
script "../main.nf"
workflow "SRA"
tag "workflows"
tag "workflows_sra"
tag "multiqc_mappings_config"
tag "sra_custom_ena_metadata_fields"

// Modules
tag "MULTIQC_MAPPINGS_CONFIG"
tag "SRA_FASTQ_FTP"
tag "SRA_IDS_TO_RUNINFO"
tag "SRA_RUNINFO_TO_FTP"
tag "SRA_TO_SAMPLESHEET"

// Subworkflows
tag "SRA"

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

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14 changes: 10 additions & 4 deletions workflows/sra/tests/sra_force_sratools_download.nf.test
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Expand Up @@ -3,10 +3,16 @@ nextflow_workflow {
name "Test workflow: sra/main.nf"
script "../main.nf"
workflow "SRA"
tag "workflows"
tag "workflows_sra"
tag "multiqc_mappings_config"
tag "sra_force_sratools_download"

// Modules
tag "MULTIQC_MAPPINGS_CONFIG"
tag "SRA_FASTQ_FTP"
tag "SRA_IDS_TO_RUNINFO"
tag "SRA_RUNINFO_TO_FTP"
tag "SRA_TO_SAMPLESHEET"

// Subworkflows
tag "SRA"

test("Parameters: --force_sratools_download") {

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14 changes: 10 additions & 4 deletions workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test
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Expand Up @@ -3,10 +3,16 @@ nextflow_workflow {
name "Test workflow: sra/main.nf"
script "../main.nf"
workflow "SRA"
tag "workflows"
tag "workflows_sra"
tag "multiqc_mappings_config"
tag "sra_nf_core_pipeline_atacseq"

// Modules
tag "MULTIQC_MAPPINGS_CONFIG"
tag "SRA_FASTQ_FTP"
tag "SRA_IDS_TO_RUNINFO"
tag "SRA_RUNINFO_TO_FTP"
tag "SRA_TO_SAMPLESHEET"

// Subworkflows
tag "SRA"

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

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14 changes: 10 additions & 4 deletions workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test
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Expand Up @@ -3,10 +3,16 @@ nextflow_workflow {
name "Test workflow: sra/main.nf"
script "../main.nf"
workflow "SRA"
tag "workflows"
tag "workflows_sra"
tag "multiqc_mappings_config"
tag "sra_nf_core_pipeline_rnaseq"

// Modules
tag "MULTIQC_MAPPINGS_CONFIG"
tag "SRA_FASTQ_FTP"
tag "SRA_IDS_TO_RUNINFO"
tag "SRA_RUNINFO_TO_FTP"
tag "SRA_TO_SAMPLESHEET"

// Subworkflows
tag "SRA"

test("Parameters: --nf_core_pipeline rnaseq") {

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14 changes: 10 additions & 4 deletions workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test
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Expand Up @@ -3,10 +3,16 @@ nextflow_workflow {
name "Test workflow: sra/main.nf"
script "../main.nf"
workflow "SRA"
tag "workflows"
tag "workflows_sra"
tag "multiqc_mappings_config"
tag "sra_nf_core_pipeline_taxprofiler"

// Modules
tag "MULTIQC_MAPPINGS_CONFIG"
tag "SRA_FASTQ_FTP"
tag "SRA_IDS_TO_RUNINFO"
tag "SRA_RUNINFO_TO_FTP"
tag "SRA_TO_SAMPLESHEET"

// Subworkflows
tag "SRA"

test("Parameters: --nf_core_pipeline taxprofiler") {

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14 changes: 10 additions & 4 deletions workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test
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Expand Up @@ -3,10 +3,16 @@ nextflow_workflow {
name "Test workflow: sra/main.nf"
script "../main.nf"
workflow "SRA"
tag "workflows"
tag "workflows_sra"
tag "multiqc_mappings_config"
tag "sra_nf_core_pipeline_viralrecon"

// Modules
tag "MULTIQC_MAPPINGS_CONFIG"
tag "SRA_FASTQ_FTP"
tag "SRA_IDS_TO_RUNINFO"
tag "SRA_RUNINFO_TO_FTP"
tag "SRA_TO_SAMPLESHEET"

// Subworkflows
tag "SRA"

test("Parameters: --nf_core_pipeline viralrecon") {

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