Merge pull request nf-core#1329 from drpatelh/updates

Remove tags from all nf-test files
maxulysse · Jun 20, 2024 · 53e59a8 · 53e59a8
2 parents 579684a + 9dbdd2c
commit 53e59a8
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -93,6 +93,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1324](https://github.com/nf-core/rnaseq/pull/1324) - Fix tags entries and rename pipeline level tests
 - [PR #1325](https://github.com/nf-core/rnaseq/pull/1325) - Minor fixes to strandedness settings and messaging
 - [PR #1326](https://github.com/nf-core/rnaseq/pull/1326) - Move Conda dependencies for local modules to individual environment file
+- [PR #1329](https://github.com/nf-core/rnaseq/pull/1329) - Remove tags from all nf-test files
 
 ### Parameters
 

diff --git a/modules/local/star_align_igenomes/tests/main.nf.test b/modules/local/star_align_igenomes/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_process {
     name "Test Process STAR_ALIGN_IGENOMES"
     script "../main.nf"
     process "STAR_ALIGN_IGENOMES"
-    tag "STAR_GENOMEGENERATE_IGENOMES"
 
     setup {
         run("STAR_GENOMEGENERATE_IGENOMES") {

diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test b/modules/nf-core/custom/tx2gene/tests/main.nf.test
diff --git a/modules/nf-core/hisat2/align/tests/main.nf.test b/modules/nf-core/hisat2/align/tests/main.nf.test
diff --git a/modules/nf-core/hisat2/build/tests/main.nf.test b/modules/nf-core/hisat2/build/tests/main.nf.test
diff --git a/modules/nf-core/kallisto/quant/tests/main.nf.test b/modules/nf-core/kallisto/quant/tests/main.nf.test
diff --git a/modules/nf-core/rsem/calculateexpression/tests/main.nf.test b/modules/nf-core/rsem/calculateexpression/tests/main.nf.test
diff --git a/modules/nf-core/salmon/quant/tests/main.nf.test b/modules/nf-core/salmon/quant/tests/main.nf.test
diff --git a/modules/nf-core/star/align/tests/main.nf.test b/modules/nf-core/star/align/tests/main.nf.test
diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test
diff --git a/modules/nf-core/tximeta/tximport/tests/main.nf.test b/modules/nf-core/tximeta/tximport/tests/main.nf.test
diff --git a/subworkflows/local/align_star/tests/main.nf.test b/subworkflows/local/align_star/tests/main.nf.test
@@ -4,11 +4,6 @@ nextflow_workflow {
     script "../main.nf"
     workflow "ALIGN_STAR"
     config "./nextflow.config"
-    tag "STAR_GENOMEGENERATE"
-    tag "STAR_GENOMEGENERATE_IGENOMES"
-    tag "STAR_ALIGN"
-    tag "STAR_ALIGN_IGENOMES"
-    tag "BAM_SORT_STATS_SAMTOOLS"
 
     test("star - no igenomes") {
 

diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -4,23 +4,6 @@ nextflow_workflow {
     script "../main.nf"
     workflow "PREPARE_GENOME"
     config "./nextflow.config"
-    tag "BBMAP_BBSPLIT"
-    tag "CUSTOM_CATADDITIONALFASTA"
-    tag "CUSTOM_GETCHROMSIZES"
-    tag "GFFREAD"
-    tag "GTF2BED"
-    tag "GTF_FILTER"
-    tag "GUNZIP"
-    tag "HISAT2_BUILD"
-    tag "HISAT2_EXTRACTSPLICESITES"
-    tag "KALLISTO_INDEX"
-    tag "PREPROCESS_TRANSCRIPTS_FASTA_GENCODE"
-    tag "RSEM_PREPAREREFERENCE"
-    tag "SALMON_INDEX"
-    tag "SORTMERNA"
-    tag "STAR_GENOMEGENERATE"
-    tag "STAR_GENOMEGENERATE_IGENOMES"
-    tag "UNTAR"
 
     test("default options") {
 

diff --git a/subworkflows/local/quantify_rsem/tests/main.nf.test b/subworkflows/local/quantify_rsem/tests/main.nf.test
@@ -4,10 +4,6 @@ nextflow_workflow {
     script "../main.nf"
     workflow "QUANTIFY_RSEM"
     config "./nextflow.config"
-    tag "RSEM_PREPAREREFERENCE"
-    tag "RSEM_CALCULATEEXPRESSION"
-    tag "RSEM_MERGE_COUNTS"
-    tag "BAM_SORT_STATS_SAMTOOLS"
 
     test("homo_sapiens") {
 

diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test
@@ -2,7 +2,6 @@ nextflow_function {
 
     name "Test Functions"
     script "../main.nf"
-    tag "UTILS_NFCORE_RNASEQ_PIPELINE"
 
     test("Test Function checkSamplesAfterGrouping success") {
 

diff --git a/...kflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test b/...kflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test
@@ -3,7 +3,6 @@ nextflow_workflow {
     name "Test Workflow PIPELINE_COMPLETION"
     script "../main.nf"
     workflow "PIPELINE_COMPLETION"
-    tag "UTILS_NFCORE_RNASEQ_PIPELINE"
 
     test("test PIPELINE_COMPLETION successfully completes") {
 

diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test
diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test
diff --git a/subworkflows/nf-core/bam_rseqc/tests/main.nf.test b/subworkflows/nf-core/bam_rseqc/tests/main.nf.test
diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test
diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test
diff --git a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test
diff --git a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test
diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test
diff --git a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
diff --git a/tests/default.nf.test b/tests/default.nf.test
@@ -2,8 +2,6 @@ nextflow_pipeline {
 
     name "Test pipeline with default settings"
     script "../main.nf"
-    tag "RNASEQ"
-    tag "PIPELINE"
 
     test("Params: default") {
 

diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test
@@ -2,8 +2,6 @@ nextflow_pipeline {
 
     name "Test pipeline without a group type for featureCounts"
     script "../main.nf"
-    tag "RNASEQ"
-    tag "PIPELINE"
 
     test("Params: --featurecounts_group_type false") {
 

diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test
@@ -2,8 +2,6 @@ nextflow_pipeline {
 
     name "Test pipeline with Kallisto, skipping both QC and alignment"
     script "../main.nf"
-    tag "RNASEQ"
-    tag "PIPELINE"
 
     test("Params: --pseudo_aligner kallisto --skip_qc --skip_alignment") {
 

diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test
@@ -2,8 +2,6 @@ nextflow_pipeline {
 
     name "Test pipeline with a minimum mapped read threshold of 90"
     script "../main.nf"
-    tag "RNASEQ"
-    tag "PIPELINE"
 
     test("Params: --min_mapped_reads 90") {
 

diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test
@@ -2,8 +2,6 @@ nextflow_pipeline {
 
     name "Test pipeline with ribosomal RNA removal"
     script "../main.nf"
-    tag "RNASEQ"
-    tag "PIPELINE"
 
     test("Params: --remove_ribo_rna") {
 

diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test
@@ -2,8 +2,6 @@ nextflow_pipeline {
 
     name "Test pipeline with Salmon, skipping both QC and alignment"
     script "../main.nf"
-    tag "RNASEQ"
-    tag "PIPELINE"
 
     test("Params: --pseudo_aligner salmon --skip_qc --skip_alignment") {
 

diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test
@@ -2,8 +2,6 @@ nextflow_pipeline {
 
     name "Test pipeline by skipping QC options"
     script "../main.nf"
-    tag "RNASEQ"
-    tag "PIPELINE"
 
     test("Params: --skip_qc") {
 

diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test
@@ -2,8 +2,6 @@ nextflow_pipeline {
 
     name "Test pipeline by skipping trimming options"
     script "../main.nf"
-    tag "RNASEQ"
-    tag "PIPELINE"
 
     test("Params: --skip_trimming") {