diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 12343148..1395c844 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -13,7 +13,7 @@ on: env: NXF_ANSI_LOG: false - NFT_VER: "0.8.3" + NFT_VER: "0.8.4" NFT_WORKDIR: "~" NFT_DIFF: "pdiff" NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" diff --git a/CHANGELOG.md b/CHANGELOG.md index a91320c1..856667de 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -32,6 +32,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #258](https://github.com/nf-core/fetchngs/pull/258) - Fixes for [PR #253](https://github.com/nf-core/fetchngs/pull/253) - [PR #259](https://github.com/nf-core/fetchngs/pull/259) - Add Aspera CLI download support to pipeline ([#68](https://github.com/nf-core/fetchngs/issues/68)) - [PR #261](https://github.com/nf-core/fetchngs/pull/261) - Revert sratools fasterqdump version ([#221](https://github.com/nf-core/fetchngs/issues/221)) +- [PR #262](https://github.com/nf-core/fetchngs/pull/262) - Use nf-test version v0.8.4 and remove implicit tags ### Software dependencies diff --git a/modules/local/aspera_cli/tests/main.nf.test b/modules/local/aspera_cli/tests/main.nf.test index 3858e2c3..b2f5f1bd 100644 --- a/modules/local/aspera_cli/tests/main.nf.test +++ b/modules/local/aspera_cli/tests/main.nf.test @@ -4,8 +4,6 @@ nextflow_process { script "../main.nf" process "ASPERA_CLI" - tag "ASPERA_CLI" - test("Should run without failures") { when { diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test index e782116e..106f3248 100644 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test @@ -4,8 +4,6 @@ nextflow_process { script "../main.nf" process "MULTIQC_MAPPINGS_CONFIG" - tag "MULTIQC_MAPPINGS_CONFIG" - test("Should run without failures") { when { diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test index 27329cd9..f58aaae2 100644 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test @@ -4,8 +4,6 @@ nextflow_process { script "../main.nf" process "SRA_FASTQ_FTP" - tag "SRA_FASTQ_FTP" - test("Should run without failures") { when { diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test index cc0d6de9..2e510ea1 100644 --- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test +++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test @@ -4,8 +4,6 @@ nextflow_process { script "../main.nf" process "SRA_IDS_TO_RUNINFO" - tag "SRA_IDS_TO_RUNINFO" - test("Should run without failures") { when { diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test index 1060b394..4b03249c 100644 --- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test +++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test @@ -4,8 +4,6 @@ nextflow_process { script "../main.nf" process "SRA_RUNINFO_TO_FTP" - tag "SRA_RUNINFO_TO_FTP" - test("Should run without failures") { when { diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test index 999864b8..4458858e 100644 --- a/modules/local/sra_to_samplesheet/tests/main.nf.test +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test @@ -4,8 +4,6 @@ nextflow_process { script "../main.nf" process "SRA_TO_SAMPLESHEET" - tag "SRA_TO_SAMPLESHEET" - test("Should run without failures") { when { diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test index 6fde77c6..11899742 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test +++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test @@ -4,9 +4,7 @@ nextflow_process { script "../main.nf" process "CUSTOM_SRATOOLSNCBISETTINGS" config "modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config" - - tag "CUSTOM_SRATOOLSNCBISETTINGS" - + test("Should run without failures") { when { diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test index b3107336..c64f6fc1 100644 --- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test +++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test @@ -3,7 +3,6 @@ nextflow_process { script "../main.nf" config "./nextflow.config" process "SRATOOLS_FASTERQDUMP" - tag "SRATOOLS_FASTERQDUMP" tag "UNTAR" diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test index 7319108c..b0f5ffa2 100644 --- a/modules/nf-core/sratools/prefetch/tests/main.nf.test +++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test @@ -2,7 +2,6 @@ nextflow_process { name "Test Process SRATOOLS_PREFETCH" script "../main.nf" process "SRATOOLS_PREFETCH" - tag "SRATOOLS_PREFETCH" test("sratools/prefetch") { diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test index 0eb25d3c..05134043 100644 --- a/modules/nf-core/untar/tests/main.nf.test +++ b/modules/nf-core/untar/tests/main.nf.test @@ -3,8 +3,7 @@ nextflow_process { name "Test Process UNTAR" script "../main.nf" process "UNTAR" - tag "UNTAR" - + test("test_untar") { when { diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test index a1814bf6..cfbfab4c 100644 --- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test +++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test @@ -3,7 +3,6 @@ nextflow_workflow { name "Test Workflow PIPELINE_COMPLETION" script "subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf" workflow "PIPELINE_COMPLETION" - tag "PIPELINE_COMPLETION" test("Should run") { diff --git a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test index d8dc3963..611eaee7 100644 --- a/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test +++ b/subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test @@ -3,7 +3,6 @@ nextflow_workflow { name "Test Workflow PIPELINE_INITIALISATION" script "subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf" workflow "PIPELINE_INITIALISATION" - tag 'PIPELINE_INITIALISATION' test("Should run") { diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test index 9ff65074..7293a792 100644 --- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test @@ -3,7 +3,6 @@ nextflow_workflow { name "Test workflow: fastq_download_prefetch_fasterqdump_sratools/main.nf" script "../main.nf" workflow "FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS" - tag "FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS" tag "CUSTOM_SRATOOLSNCBISETTINGS" tag "SRATOOLS_PREFETCH" diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index b1b3a2c3..94e7198c 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -4,7 +4,6 @@ nextflow_workflow { script "../main.nf" config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" workflow "UTILS_NEXTFLOW_PIPELINE" - tag "UTILS_NEXTFLOW_PIPELINE" test("Should run no inputs") { diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test index cb7376c0..3df54055 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test @@ -4,7 +4,6 @@ nextflow_workflow { script "../main.nf" config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" workflow "UTILS_NFCORE_PIPELINE" - tag "UTILS_NFCORE_PIPELINE" test("Should run without failures") { diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test index b13e7e6e..5649654e 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test @@ -3,7 +3,6 @@ nextflow_workflow { name "Test Workflow UTILS_NFVALIDATION_PLUGIN" script "../main.nf" workflow "UTILS_NFVALIDATION_PLUGIN" - tag "UTILS_NFVALIDATION_PLUGIN" test("Should run nothing") { diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 062d6886..c08f345a 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -3,7 +3,6 @@ nextflow_workflow { name "Test workflow: sra/main.nf" script "../main.nf" workflow "SRA" - tag "SRA" // Dependencies tag "MULTIQC_MAPPINGS_CONFIG"