Merge branch 'dev' into fixes

nf-core · Jan 31, 2024 · f932649 · f932649
2 parents 56a16a3 + ce31465
commit f932649
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Showing 19 changed files with 4 additions and 27 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test
diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test
diff --git a/...rkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_completion.test b/...rkflows/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/.../local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test b/.../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
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
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
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
diff --git 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"