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Merge pull request #1329 from drpatelh/updates
Remove tags from all nf-test files
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‎CHANGELOG.md

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@@ -93,6 +93,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
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- [PR #1324](https://github.com/nf-core/rnaseq/pull/1324) - Fix tags entries and rename pipeline level tests
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- [PR #1325](https://github.com/nf-core/rnaseq/pull/1325) - Minor fixes to strandedness settings and messaging
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- [PR #1326](https://github.com/nf-core/rnaseq/pull/1326) - Move Conda dependencies for local modules to individual environment file
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- [PR #1329](https://github.com/nf-core/rnaseq/pull/1329) - Remove tags from all nf-test files
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### Parameters
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‎modules/local/star_align_igenomes/tests/main.nf.test

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@@ -3,7 +3,6 @@ nextflow_process {
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name "Test Process STAR_ALIGN_IGENOMES"
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script "../main.nf"
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process "STAR_ALIGN_IGENOMES"
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tag "STAR_GENOMEGENERATE_IGENOMES"
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setup {
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run("STAR_GENOMEGENERATE_IGENOMES") {

‎modules/nf-core/custom/tx2gene/tests/main.nf.test

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‎modules/nf-core/hisat2/align/tests/main.nf.test

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‎modules/nf-core/hisat2/build/tests/main.nf.test

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‎modules/nf-core/kallisto/quant/tests/main.nf.test

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‎modules/nf-core/rsem/calculateexpression/tests/main.nf.test

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‎modules/nf-core/salmon/quant/tests/main.nf.test

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‎modules/nf-core/star/align/tests/main.nf.test

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‎modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test

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‎modules/nf-core/tximeta/tximport/tests/main.nf.test

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‎subworkflows/local/align_star/tests/main.nf.test

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@@ -4,11 +4,6 @@ nextflow_workflow {
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script "../main.nf"
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workflow "ALIGN_STAR"
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config "./nextflow.config"
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tag "STAR_GENOMEGENERATE"
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tag "STAR_GENOMEGENERATE_IGENOMES"
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tag "STAR_ALIGN"
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tag "STAR_ALIGN_IGENOMES"
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tag "BAM_SORT_STATS_SAMTOOLS"
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test("star - no igenomes") {
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‎subworkflows/local/prepare_genome/tests/main.nf.test

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

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script "../main.nf"
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workflow "QUANTIFY_RSEM"
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config "./nextflow.config"
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tag "RSEM_PREPAREREFERENCE"
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tag "RSEM_CALCULATEEXPRESSION"
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tag "RSEM_MERGE_COUNTS"
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tag "BAM_SORT_STATS_SAMTOOLS"
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test("homo_sapiens") {
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‎subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.function.nf.test

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

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@@ -3,7 +3,6 @@ nextflow_workflow {
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name "Test Workflow PIPELINE_COMPLETION"
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script "../main.nf"
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workflow "PIPELINE_COMPLETION"
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tag "UTILS_NFCORE_RNASEQ_PIPELINE"
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test("test PIPELINE_COMPLETION successfully completes") {
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‎subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test

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‎subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test

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‎subworkflows/nf-core/bam_rseqc/tests/main.nf.test

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‎subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test

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‎subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test

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‎subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test

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‎subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test

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‎subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test

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‎subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test

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‎subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test

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‎subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test

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‎subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test

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‎subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test

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‎tests/default.nf.test

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name "Test pipeline with default settings"
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script "../main.nf"
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tag "RNASEQ"
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tag "PIPELINE"
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test("Params: default") {
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‎tests/featurecounts_group_type.nf.test

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name "Test pipeline without a group type for featureCounts"
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script "../main.nf"
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tag "RNASEQ"
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tag "PIPELINE"
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test("Params: --featurecounts_group_type false") {
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‎tests/kallisto.nf.test

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name "Test pipeline with Kallisto, skipping both QC and alignment"
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script "../main.nf"
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tag "RNASEQ"
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tag "PIPELINE"
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test("Params: --pseudo_aligner kallisto --skip_qc --skip_alignment") {
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‎tests/min_mapped_reads.nf.test

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name "Test pipeline with a minimum mapped read threshold of 90"
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script "../main.nf"
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tag "RNASEQ"
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tag "PIPELINE"
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test("Params: --min_mapped_reads 90") {
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‎tests/remove_ribo_rna.nf.test

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name "Test pipeline with ribosomal RNA removal"
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script "../main.nf"
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tag "RNASEQ"
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tag "PIPELINE"
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test("Params: --remove_ribo_rna") {
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‎tests/salmon.nf.test

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name "Test pipeline with Salmon, skipping both QC and alignment"
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script "../main.nf"
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tag "RNASEQ"
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tag "PIPELINE"
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test("Params: --pseudo_aligner salmon --skip_qc --skip_alignment") {
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‎tests/skip_qc.nf.test

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name "Test pipeline by skipping QC options"
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script "../main.nf"
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tag "RNASEQ"
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tag "PIPELINE"
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test("Params: --skip_qc") {
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‎tests/skip_trimming.nf.test

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name "Test pipeline by skipping trimming options"
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script "../main.nf"
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tag "RNASEQ"
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tag "PIPELINE"
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test("Params: --skip_trimming") {
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