From 178c45a9c06cf12a123b1f4461ef81b175e95b86 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 20 Jun 2024 14:27:20 +0100 Subject: [PATCH 1/2] Remove tags from all nf-test files --- .../star_align_igenomes/tests/main.nf.test | 1 - .../nf-core/custom/tx2gene/tests/main.nf.test | 1 - modules/nf-core/hisat2/align/tests/main.nf.test | 2 -- modules/nf-core/hisat2/build/tests/main.nf.test | 1 - .../nf-core/kallisto/quant/tests/main.nf.test | 1 - .../rsem/calculateexpression/tests/main.nf.test | 1 - modules/nf-core/salmon/quant/tests/main.nf.test | 1 - modules/nf-core/star/align/tests/main.nf.test | 1 - .../summarizedexperiment/tests/main.nf.test | 3 --- .../nf-core/tximeta/tximport/tests/main.nf.test | 2 -- .../local/align_star/tests/main.nf.test | 5 ----- .../local/prepare_genome/tests/main.nf.test | 17 ----------------- .../local/quantify_rsem/tests/main.nf.test | 4 ---- .../tests/main.function.nf.test | 1 - .../main.pipeline_completion.workflow.nf.test | 1 - .../tests/main.nf.test | 3 --- .../tests/main.nf.test | 3 --- .../nf-core/bam_rseqc/tests/main.nf.test | 8 -------- .../bam_sort_stats_samtools/tests/main.nf.test | 3 --- .../bam_stats_samtools/tests/main.nf.test | 3 --- .../tests/main.nf.test | 2 -- .../fastq_align_hisat2/tests/main.nf.test | 4 ---- .../tests/main.nf.test | 3 --- .../tests/main.nf.test | 3 --- .../tests/main.nf.test | 3 --- .../tests/main.nf.test | 7 ------- .../tests/main.function.nf.test | 1 - .../tests/main.function.nf.test | 3 +-- tests/default.nf.test | 2 -- tests/featurecounts_group_type.nf.test | 2 -- tests/kallisto.nf.test | 2 -- tests/min_mapped_reads.nf.test | 2 -- tests/remove_ribo_rna.nf.test | 2 -- tests/salmon.nf.test | 2 -- tests/skip_qc.nf.test | 2 -- tests/skip_trimming.nf.test | 2 -- 36 files changed, 1 insertion(+), 103 deletions(-) diff --git a/modules/local/star_align_igenomes/tests/main.nf.test b/modules/local/star_align_igenomes/tests/main.nf.test index 91be69f01..8255c1732 100644 --- 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 index a3f0d0d64..8a7a6d1b2 100644 --- a/modules/nf-core/custom/tx2gene/tests/main.nf.test +++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test @@ -3,7 +3,6 @@ nextflow_process { name "Test Process CUSTOM_TX2GENE" script "../main.nf" process "CUSTOM_TX2GENE" - tag "UNTAR" setup { diff --git a/modules/nf-core/hisat2/align/tests/main.nf.test b/modules/nf-core/hisat2/align/tests/main.nf.test index 660647edb..251fd711e 100644 --- a/modules/nf-core/hisat2/align/tests/main.nf.test +++ b/modules/nf-core/hisat2/align/tests/main.nf.test @@ -3,8 +3,6 @@ nextflow_process { name "Test Process HISAT2_ALIGN" script "../main.nf" process "HISAT2_ALIGN" - tag "HISAT2_BUILD" - tag "HISAT2_EXTRACTSPLICESITES" test("Single-End") { diff --git a/modules/nf-core/hisat2/build/tests/main.nf.test b/modules/nf-core/hisat2/build/tests/main.nf.test index 05b71f08c..240b73de1 100644 --- a/modules/nf-core/hisat2/build/tests/main.nf.test +++ b/modules/nf-core/hisat2/build/tests/main.nf.test @@ -3,7 +3,6 @@ nextflow_process { name "Test Process HISAT2_BUILD" script "../main.nf" process "HISAT2_BUILD" - tag "HISAT2_EXTRACTSPLICESITES" test("Should run without failures") { diff --git a/modules/nf-core/kallisto/quant/tests/main.nf.test b/modules/nf-core/kallisto/quant/tests/main.nf.test index dec8b8d4b..cb7e480a1 100644 --- a/modules/nf-core/kallisto/quant/tests/main.nf.test +++ b/modules/nf-core/kallisto/quant/tests/main.nf.test @@ -3,7 +3,6 @@ nextflow_process { name "Test Process KALLISTO_QUANT" script "../main.nf" process "KALLISTO_QUANT" - tag "KALLISTO_INDEX" setup { run("KALLISTO_INDEX") { diff --git a/modules/nf-core/rsem/calculateexpression/tests/main.nf.test b/modules/nf-core/rsem/calculateexpression/tests/main.nf.test index 445e58d85..3ab43eb1a 100644 --- a/modules/nf-core/rsem/calculateexpression/tests/main.nf.test +++ b/modules/nf-core/rsem/calculateexpression/tests/main.nf.test @@ -3,7 +3,6 @@ nextflow_process { name "Test Process RSEM_CALCULATEEXPRESSION" script "../main.nf" process "RSEM_CALCULATEEXPRESSION" - tag "RSEM_PREPAREREFERENCE" config "./nextflow.config" test("homo_sapiens") { diff --git a/modules/nf-core/salmon/quant/tests/main.nf.test b/modules/nf-core/salmon/quant/tests/main.nf.test index dbaebedfc..1bd264e96 100644 --- a/modules/nf-core/salmon/quant/tests/main.nf.test +++ b/modules/nf-core/salmon/quant/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "SALMON_QUANT" config "./nextflow.config" - tag "SALMON_INDEX" setup { run("SALMON_INDEX") { diff --git a/modules/nf-core/star/align/tests/main.nf.test b/modules/nf-core/star/align/tests/main.nf.test index 8b34ae793..4cd6f2a52 100644 --- a/modules/nf-core/star/align/tests/main.nf.test +++ b/modules/nf-core/star/align/tests/main.nf.test @@ -3,7 +3,6 @@ nextflow_process { name "Test Process STAR_ALIGN" script "../main.nf" process "STAR_ALIGN" - tag "STAR_GENOMEGENERATE" setup { run("STAR_GENOMEGENERATE") { diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test index 4dda21181..8faa18afb 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test @@ -3,9 +3,6 @@ nextflow_process { name "Test Process SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT" script "../main.nf" process "SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT" - tag "UNTAR" - tag "CUSTOM_TX2GENE" - tag "TXIMETA_TXIMPORT" setup { diff --git a/modules/nf-core/tximeta/tximport/tests/main.nf.test b/modules/nf-core/tximeta/tximport/tests/main.nf.test index 8f27bc928..782030fb8 100644 --- a/modules/nf-core/tximeta/tximport/tests/main.nf.test +++ b/modules/nf-core/tximeta/tximport/tests/main.nf.test @@ -3,8 +3,6 @@ nextflow_process { name "Test Process TXIMETA_TXIMPORT" script "../main.nf" process "TXIMETA_TXIMPORT" - tag "UNTAR" - tag "CUSTOM_TX2GENE" test("saccharomyces_cerevisiae - kallisto - gtf") { diff --git a/subworkflows/local/align_star/tests/main.nf.test b/subworkflows/local/align_star/tests/main.nf.test index b5ceece0b..2b98dffbf 100644 --- 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 index 8291d9c41..8c5cc5b6b 100644 --- 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 index ab62162d0..818282af3 100644 --- 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 index 2e71f9990..c809b2117 100644 --- 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/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test index c7e862c38..ea784ea01 100644 --- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test +++ b/subworkflows/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 index c91f6c180..1ef1f7fe7 100644 --- 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 @@ -3,9 +3,6 @@ nextflow_workflow { name "Test Workflow BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS" script "../main.nf" workflow "BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS" - tag "UMITOOLS_DEDUP" - tag "SAMTOOLS_INDEX" - tag "BAM_STATS_SAMTOOLS" test("sarscov2_bam_bai") { diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test index 85c4b03c0..7ecf3fe40 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test @@ -3,9 +3,6 @@ nextflow_workflow { name "Test Workflow BAM_MARKDUPLICATES_PICARD" script "../main.nf" workflow "BAM_MARKDUPLICATES_PICARD" - tag "PICARD_MARKDUPLICATES" - tag "SAMTOOLS_INDEX" - tag "BAM_STATS_SAMTOOLS" test("sarscov2 - bam") { diff --git a/subworkflows/nf-core/bam_rseqc/tests/main.nf.test b/subworkflows/nf-core/bam_rseqc/tests/main.nf.test index 32e48d338..eb87c27c9 100644 --- a/subworkflows/nf-core/bam_rseqc/tests/main.nf.test +++ b/subworkflows/nf-core/bam_rseqc/tests/main.nf.test @@ -3,14 +3,6 @@ nextflow_workflow { name "Test Workflow BAM_RSEQC" script "../main.nf" workflow "BAM_RSEQC" - tag "RSEQC_BAMSTAT" - tag "RSEQC_INNERDISTANCE" - tag "RSEQC_INFEREXPERIMENT" - tag "RSEQC_JUNCTIONANNOTATION" - tag "RSEQC_JUNCTIONSATURATION" - tag "RSEQC_READDISTRIBUTION" - tag "RSEQC_READDUPLICATION" - tag "RSEQC_TIN" test("sarscov2 paired-end [bam]") { 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 index 957effa3a..2045512c8 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test @@ -3,9 +3,6 @@ nextflow_workflow { name "Test Workflow BAM_SORT_STATS_SAMTOOLS" script "../main.nf" workflow "BAM_SORT_STATS_SAMTOOLS" - tag "SAMTOOLS_SORT" - tag "SAMTOOLS_INDEX" - tag "BAM_STATS_SAMTOOLS" test("test_bam_sort_stats_samtools_single_end") { diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test index d2c9752bb..1eabc2b36 100644 --- a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test +++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test @@ -3,9 +3,6 @@ nextflow_workflow { name "Test Workflow BAM_STATS_SAMTOOLS" script "../main.nf" workflow "BAM_STATS_SAMTOOLS" - tag "SAMTOOLS_STATS" - tag "SAMTOOLS_IDXSTATS" - tag "SAMTOOLS_FLAGSTAT" test("test_bam_stats_samtools_single_end") { diff --git a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test index fa1f2364c..94b66019e 100644 --- a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test +++ b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test @@ -4,8 +4,6 @@ nextflow_workflow { script "../main.nf" workflow "BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG" config "./nextflow.config" - tag "UCSC_BEDCLIP" - tag "UCSC_BEDGRAPHTOBIGWIG" test("sarscov2 [bedgraph] [genome_sizes]") { diff --git a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test index ab09c6ca2..b04fc1162 100644 --- a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test @@ -4,10 +4,6 @@ nextflow_workflow { script "../main.nf" workflow "FASTQ_ALIGN_HISAT2" config "./nextflow.config" - tag "HISAT2_EXTRACTSPLICESITES" - tag "HISAT2_BUILD" - tag "HISAT2_ALIGN" - tag "BAM_SORT_STATS_SAMTOOLS" setup { run("HISAT2_EXTRACTSPLICESITES") { 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 index 72029590e..165dc7675 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test @@ -4,9 +4,6 @@ nextflow_workflow { script "../main.nf" workflow "FASTQ_FASTQC_UMITOOLS_FASTP" config './nextflow.config' - tag "FASTQC" - tag "UMITOOLS_EXTRACT" - tag "FASTP" test("sarscov2 paired-end [fastq]") { 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 index d409bfe6f..6d01cbbd1 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test @@ -4,9 +4,6 @@ nextflow_workflow { script "../main.nf" workflow "FASTQ_FASTQC_UMITOOLS_TRIMGALORE" config './nextflow.config' - tag "FASTQC" - tag "UMITOOLS_EXTRACT" - tag "TRIMGALORE" test("test single end read with UMI") { 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 index 98d5615f5..0a4b29706 100644 --- a/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test @@ -4,9 +4,6 @@ nextflow_workflow { script "../main.nf" workflow "FASTQ_SUBSAMPLE_FQ_SALMON" config "./nextflow.config" - tag "SALMON_INDEX" - tag "FQ_SUBSAMPLE" - tag "SALMON_QUANT" test("homo_sapiens paired-end [fastq]") { diff --git a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test index d53fb4ea8..21004870a 100644 --- a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test +++ b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test @@ -3,13 +3,6 @@ nextflow_workflow { name "Test Workflow QUANTIFY_PSEUDO_ALIGNMENT" script "../main.nf" workflow "QUANTIFY_PSEUDO_ALIGNMENT" - tag "SALMON_INDEX" - tag "KALLISTO_INDEX" - tag "SALMON_QUANT" - tag "KALLISTO_QUANT" - tag "CUSTOM_TX2GENE" - tag "TXIMETA_TXIMPORT" - tag "SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT" test("salmon") { 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 index 8b838192f..f66d9954f 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test @@ -4,7 +4,6 @@ nextflow_function { name "Test Functions" script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf" config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" - tag "UTILS_NEXTFLOW_PIPELINE" test("Test Function getWorkflowVersion") { 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 index 41b8d19e2..3de07f37a 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test @@ -3,8 +3,7 @@ nextflow_function { name "Test Functions" script "../main.nf" - config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" - tag "UTILS_NFCORE_PIPELINE" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" test("Test Function checkConfigProvided") { diff --git a/tests/default.nf.test b/tests/default.nf.test index 2d3323175..b086c6db3 100644 --- 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 index d847bd60c..69de358f5 100644 --- 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 index 517f20156..a6a578a77 100644 --- 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 index 95e8e7028..9dcc7408c 100644 --- 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 index a439588de..d414d1484 100644 --- 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 index 36373dd9d..cf0a2d93e 100644 --- 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 index bd5918083..db718462e 100644 --- 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 index 4f656d016..28452df5c 100644 --- 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") { From 9dbdd2c16b524a83efc54d020c3fdf9ed6b9a117 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 20 Jun 2024 14:34:32 +0100 Subject: [PATCH 2/2] Update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8bc61304d..130819513 100644 --- 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