From 155c6358879c006ded8ecfd19b5bd2a3e8e77a19 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 13 Mar 2024 17:58:26 +0000 Subject: [PATCH 1/3] Delete unecessary tags from nt.test files for modules --- modules/local/gtf2bed/tests/main.nf.test | 4 ---- modules/local/star_align_igenomes/tests/main.nf.test | 2 +- .../star_genomegenerate_igenomes/tests/main.nf.test | 2 -- modules/nf-core/bbmap/bbsplit/tests/main.nf.test | 4 ---- .../nf-core/bedtools/genomecov/tests/main.nf.test | 5 ----- modules/nf-core/cat/fastq/tests/main.nf.test | 4 ---- .../custom/catadditionalfasta/tests/main.nf.test | 5 ----- .../nf-core/custom/getchromsizes/tests/main.nf.test | 5 ----- modules/nf-core/custom/tx2gene/tests/main.nf.test | 7 +------ modules/nf-core/dupradar/tests/main.nf.test | 4 ---- modules/nf-core/fastp/tests/main.nf.test | 3 --- modules/nf-core/fastqc/tests/main.nf.test | 4 ---- modules/nf-core/fq/subsample/tests/main.nf.test | 5 ----- modules/nf-core/gffread/tests/main.nf.test | 4 ---- modules/nf-core/gunzip/tests/main.nf.test | 3 --- modules/nf-core/hisat2/align/tests/main.nf.test | 8 ++------ modules/nf-core/hisat2/build/tests/main.nf.test | 6 +----- .../hisat2/extractsplicesites/tests/main.nf.test | 4 ---- modules/nf-core/kallisto/index/tests/main.nf.test | 4 ---- modules/nf-core/kallisto/quant/tests/main.nf.test | 6 +----- modules/nf-core/multiqc/tests/main.nf.test | 4 ---- .../nf-core/picard/markduplicates/tests/main.nf.test | 4 ---- modules/nf-core/preseq/lcextrap/tests/main.nf.test | 4 ---- modules/nf-core/qualimap/rnaseq/tests/main.nf.test | 4 ---- .../rsem/calculateexpression/tests/main.nf.test | 8 ++------ .../nf-core/rsem/preparereference/tests/main.nf.test | 4 ---- modules/nf-core/rseqc/bamstat/tests/main.nf.test | 5 ----- .../nf-core/rseqc/inferexperiment/tests/main.nf.test | 5 ----- .../nf-core/rseqc/innerdistance/tests/main.nf.test | 5 ----- .../rseqc/junctionannotation/tests/main.nf.test | 5 ----- .../rseqc/junctionsaturation/tests/main.nf.test | 5 ----- .../rseqc/readdistribution/tests/main.nf.test | 4 ---- .../nf-core/rseqc/readduplication/tests/main.nf.test | 4 ---- modules/nf-core/rseqc/tin/tests/main.nf.test | 4 ---- modules/nf-core/salmon/index/tests/main.nf.test | 4 ---- modules/nf-core/salmon/quant/tests/main.nf.test | 6 +----- modules/nf-core/samtools/flagstat/tests/main.nf.test | 4 ---- modules/nf-core/samtools/idxstats/tests/main.nf.test | 4 ---- modules/nf-core/samtools/index/tests/main.nf.test | 4 ---- modules/nf-core/samtools/sort/tests/main.nf.test | 4 ---- modules/nf-core/samtools/stats/tests/main.nf.test | 4 ---- modules/nf-core/sortmerna/tests/main.nf.test | 3 --- modules/nf-core/star/align/tests/main.nf.test | 6 +----- .../nf-core/star/genomegenerate/tests/main.nf.test | 4 ---- .../nf-core/stringtie/stringtie/tests/main.nf.test | 4 ---- .../nf-core/subread/featurecounts/tests/main.nf.test | 4 ---- .../summarizedexperiment/tests/main.nf.test | 12 +++--------- modules/nf-core/trimgalore/tests/main.nf.test | 3 --- modules/nf-core/tximeta/tximport/tests/main.nf.test | 9 ++------- modules/nf-core/ucsc/bedclip/tests/main.nf.test | 4 ---- .../nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test | 4 ---- modules/nf-core/umitools/dedup/tests/main.nf.test | 5 ----- modules/nf-core/umitools/extract/tests/main.nf.test | 4 ---- .../umitools/prepareforrsem/tests/main.nf.test | 5 ----- modules/nf-core/untar/tests/main.nf.test | 4 +--- 55 files changed, 16 insertions(+), 239 deletions(-) diff --git a/modules/local/gtf2bed/tests/main.nf.test b/modules/local/gtf2bed/tests/main.nf.test index cfa9c48b0..698714f8b 100644 --- a/modules/local/gtf2bed/tests/main.nf.test +++ b/modules/local/gtf2bed/tests/main.nf.test @@ -4,10 +4,6 @@ nextflow_process { script "../main.nf" process "GTF2BED" - tag "modules" - tag "modules_local" - tag "gtf2bed" - test("sarscov2 - bam") { when { diff --git a/modules/local/star_align_igenomes/tests/main.nf.test b/modules/local/star_align_igenomes/tests/main.nf.test index 5c7f33d2b..088796410 100644 --- a/modules/local/star_align_igenomes/tests/main.nf.test +++ b/modules/local/star_align_igenomes/tests/main.nf.test @@ -4,7 +4,7 @@ nextflow_process { script "../main.nf" process "STAR_ALIGN_IGENOMES" tag "STAR_ALIGN_IGENOMES" - tag "STAR_GENOMEGENERATE_IGENOMES_IGENOMES" + tag "STAR_GENOMEGENERATE_IGENOMES" setup { run("STAR_GENOMEGENERATE_IGENOMES") { diff --git a/modules/local/star_genomegenerate_igenomes/tests/main.nf.test b/modules/local/star_genomegenerate_igenomes/tests/main.nf.test index e32eedafc..aea6305c4 100644 --- a/modules/local/star_genomegenerate_igenomes/tests/main.nf.test +++ b/modules/local/star_genomegenerate_igenomes/tests/main.nf.test @@ -4,8 +4,6 @@ nextflow_process { script "../main.nf" process "STAR_GENOMEGENERATE_IGENOMES" - tag "STAR_GENOMEGENERATE_IGENOMES" - test("fasta with gtf") { when { diff --git a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test index 8fb130abb..0257fedac 100644 --- a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test +++ b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process BBMAP_BBSPLIT" script "../main.nf" process "BBMAP_BBSPLIT" - tag "modules" - tag "modules_nfcore" - tag "bbmap" - tag "bbmap/bbsplit" test("sarscov2_se_fastq_fasta_chr22_fasta") { diff --git a/modules/nf-core/bedtools/genomecov/tests/main.nf.test b/modules/nf-core/bedtools/genomecov/tests/main.nf.test index 8213cff95..fe1567d89 100644 --- a/modules/nf-core/bedtools/genomecov/tests/main.nf.test +++ b/modules/nf-core/bedtools/genomecov/tests/main.nf.test @@ -4,11 +4,6 @@ nextflow_process { process "BEDTOOLS_GENOMECOV" config "./nextflow.config" - tag "modules" - tag "modules_nfcore" - tag "bedtools" - tag "bedtools/genomecov" - test("sarscov2 - no scale") { when { process { diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test index dab2e14c0..ab7cdada9 100644 --- a/modules/nf-core/cat/fastq/tests/main.nf.test +++ b/modules/nf-core/cat/fastq/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process CAT_FASTQ" script "../main.nf" process "CAT_FASTQ" - tag "modules" - tag "modules_nfcore" - tag "cat" - tag "cat/fastq" test("test_cat_fastq_single_end") { diff --git a/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test b/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test index 7905f231d..7cf230bd7 100644 --- a/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test +++ b/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test @@ -4,11 +4,6 @@ nextflow_process { script "../main.nf" process "CUSTOM_CATADDITIONALFASTA" - tag "modules" - tag "modules_nfcore" - tag "custom" - tag "custom/catadditionalfasta" - test("sarscov2 - fastq - gtf") { when { diff --git a/modules/nf-core/custom/getchromsizes/tests/main.nf.test b/modules/nf-core/custom/getchromsizes/tests/main.nf.test index 9f6b5640e..3b18914b1 100644 --- a/modules/nf-core/custom/getchromsizes/tests/main.nf.test +++ b/modules/nf-core/custom/getchromsizes/tests/main.nf.test @@ -4,11 +4,6 @@ nextflow_process { script "../main.nf" process "CUSTOM_GETCHROMSIZES" - tag "modules" - tag "modules_nfcore" - tag "custom" - tag "custom/getchromsizes" - test("test_custom_getchromsizes") { when { diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test b/modules/nf-core/custom/tx2gene/tests/main.nf.test index b15592798..a3f0d0d64 100644 --- a/modules/nf-core/custom/tx2gene/tests/main.nf.test +++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test @@ -3,12 +3,7 @@ nextflow_process { name "Test Process CUSTOM_TX2GENE" script "../main.nf" process "CUSTOM_TX2GENE" - - tag "modules" - tag "modules_nfcore" - tag "custom" - tag "custom/tx2gene" - tag "untar" + tag "UNTAR" setup { diff --git a/modules/nf-core/dupradar/tests/main.nf.test b/modules/nf-core/dupradar/tests/main.nf.test index f7f0933c8..e4bfcb917 100644 --- a/modules/nf-core/dupradar/tests/main.nf.test +++ b/modules/nf-core/dupradar/tests/main.nf.test @@ -4,10 +4,6 @@ nextflow_process { script "../main.nf" process "DUPRADAR" - tag "modules" - tag "modules_nfcore" - tag "dupradar" - test("sarscov2 - bam - single_end") { config './nextflow.config' diff --git a/modules/nf-core/fastp/tests/main.nf.test b/modules/nf-core/fastp/tests/main.nf.test index 9b3f9a38c..e67eacd6f 100644 --- a/modules/nf-core/fastp/tests/main.nf.test +++ b/modules/nf-core/fastp/tests/main.nf.test @@ -3,9 +3,6 @@ nextflow_process { name "Test Process FASTP" script "../main.nf" process "FASTP" - tag "modules" - tag "modules_nfcore" - tag "fastp" test("test_fastp_single_end") { diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 70edae4d9..c69808d8c 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -4,10 +4,6 @@ nextflow_process { script "../main.nf" process "FASTQC" - tag "modules" - tag "modules_nfcore" - tag "fastqc" - test("sarscov2 single-end [fastq]") { when { diff --git a/modules/nf-core/fq/subsample/tests/main.nf.test b/modules/nf-core/fq/subsample/tests/main.nf.test index 285f30c77..c2817748c 100644 --- a/modules/nf-core/fq/subsample/tests/main.nf.test +++ b/modules/nf-core/fq/subsample/tests/main.nf.test @@ -4,11 +4,6 @@ nextflow_process { script "../main.nf" process "FQ_SUBSAMPLE" - tag "modules" - tag "modules_nfcore" - tag "fq" - tag "fq/subsample" - test("test_fq_subsample_no_args") { config "./nextflow_no_args.config" when { diff --git a/modules/nf-core/gffread/tests/main.nf.test b/modules/nf-core/gffread/tests/main.nf.test index 452aba1ba..82bb66925 100644 --- a/modules/nf-core/gffread/tests/main.nf.test +++ b/modules/nf-core/gffread/tests/main.nf.test @@ -4,10 +4,6 @@ nextflow_process { script "../main.nf" process "GFFREAD" - tag "gffread" - tag "modules_nfcore" - tag "modules" - test("sarscov2-gff3-gtf") { config "./nextflow.config" diff --git a/modules/nf-core/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test index 6406008ef..5ebf7ca24 100644 --- a/modules/nf-core/gunzip/tests/main.nf.test +++ b/modules/nf-core/gunzip/tests/main.nf.test @@ -3,9 +3,6 @@ nextflow_process { name "Test Process GUNZIP" script "../main.nf" process "GUNZIP" - tag "gunzip" - tag "modules_nfcore" - tag "modules" test("Should run without failures") { diff --git a/modules/nf-core/hisat2/align/tests/main.nf.test b/modules/nf-core/hisat2/align/tests/main.nf.test index 3a520e9a0..660647edb 100644 --- a/modules/nf-core/hisat2/align/tests/main.nf.test +++ b/modules/nf-core/hisat2/align/tests/main.nf.test @@ -3,12 +3,8 @@ nextflow_process { name "Test Process HISAT2_ALIGN" script "../main.nf" process "HISAT2_ALIGN" - tag "modules" - tag "modules_nfcore" - tag "hisat2" - tag "hisat2/align" - tag "hisat2/build" - tag "hisat2/extractsplicesites" + 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 5b31debc4..05b71f08c 100644 --- a/modules/nf-core/hisat2/build/tests/main.nf.test +++ b/modules/nf-core/hisat2/build/tests/main.nf.test @@ -3,11 +3,7 @@ nextflow_process { name "Test Process HISAT2_BUILD" script "../main.nf" process "HISAT2_BUILD" - tag "modules" - tag "modules_nfcore" - tag "hisat2" - tag "hisat2/build" - tag "hisat2/extractsplicesites" + tag "HISAT2_EXTRACTSPLICESITES" test("Should run without failures") { diff --git a/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test b/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test index 72eb6d53b..10b8cf8e8 100644 --- a/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test +++ b/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process HISAT2_EXTRACTSPLICESITES" script "../main.nf" process "HISAT2_EXTRACTSPLICESITES" - tag "modules" - tag "modules_nfcore" - tag "hisat2" - tag "hisat2/extractsplicesites" test("Should run without failures") { diff --git a/modules/nf-core/kallisto/index/tests/main.nf.test b/modules/nf-core/kallisto/index/tests/main.nf.test index 63469c5d5..7999daf41 100644 --- a/modules/nf-core/kallisto/index/tests/main.nf.test +++ b/modules/nf-core/kallisto/index/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process KALLISTO_INDEX" script "../main.nf" process "KALLISTO_INDEX" - tag "modules" - tag "modules_nfcore" - tag "kallisto" - tag "kallisto/index" test("sarscov2 transcriptome.fasta") { diff --git a/modules/nf-core/kallisto/quant/tests/main.nf.test b/modules/nf-core/kallisto/quant/tests/main.nf.test index ad7391270..dec8b8d4b 100644 --- a/modules/nf-core/kallisto/quant/tests/main.nf.test +++ b/modules/nf-core/kallisto/quant/tests/main.nf.test @@ -3,11 +3,7 @@ nextflow_process { name "Test Process KALLISTO_QUANT" script "../main.nf" process "KALLISTO_QUANT" - tag "modules" - tag "modules_nfcore" - tag "kallisto" - tag "kallisto/quant" - tag "kallisto/index" + tag "KALLISTO_INDEX" setup { run("KALLISTO_INDEX") { diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index f1c4242ef..813b438eb 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -4,10 +4,6 @@ nextflow_process { script "../main.nf" process "MULTIQC" - tag "modules" - tag "modules_nfcore" - tag "multiqc" - test("sarscov2 single-end [fastqc]") { when { diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test b/modules/nf-core/picard/markduplicates/tests/main.nf.test index c5a29b4bd..f0caf0fa3 100644 --- a/modules/nf-core/picard/markduplicates/tests/main.nf.test +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test @@ -4,10 +4,6 @@ nextflow_process { script "../main.nf" process "PICARD_MARKDUPLICATES" config "./nextflow.config" - tag "modules" - tag "modules_nfcore" - tag "picard" - tag "picard/markduplicates" test("sarscov2 [unsorted bam]") { diff --git a/modules/nf-core/preseq/lcextrap/tests/main.nf.test b/modules/nf-core/preseq/lcextrap/tests/main.nf.test index aa12bc1ab..92750c9ed 100644 --- a/modules/nf-core/preseq/lcextrap/tests/main.nf.test +++ b/modules/nf-core/preseq/lcextrap/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process PRESEQ_LCEXTRAP" script "../main.nf" process "PRESEQ_LCEXTRAP" - tag "modules" - tag "modules_nfcore" - tag "preseq" - tag "preseq/lcextrap" test("sarscov2 - single_end") { when { diff --git a/modules/nf-core/qualimap/rnaseq/tests/main.nf.test b/modules/nf-core/qualimap/rnaseq/tests/main.nf.test index 4f02b8fba..42403c502 100644 --- a/modules/nf-core/qualimap/rnaseq/tests/main.nf.test +++ b/modules/nf-core/qualimap/rnaseq/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process QUALIMAP_RNASEQ" script "../main.nf" process "QUALIMAP_RNASEQ" - tag "modules" - tag "modules_nfcore" - tag "qualimap" - tag "qualimap/rnaseq" test("homo_sapiens [bam]") { diff --git a/modules/nf-core/rsem/calculateexpression/tests/main.nf.test b/modules/nf-core/rsem/calculateexpression/tests/main.nf.test index 63e1ebc0b..445e58d85 100644 --- a/modules/nf-core/rsem/calculateexpression/tests/main.nf.test +++ b/modules/nf-core/rsem/calculateexpression/tests/main.nf.test @@ -3,13 +3,9 @@ nextflow_process { name "Test Process RSEM_CALCULATEEXPRESSION" script "../main.nf" process "RSEM_CALCULATEEXPRESSION" + tag "RSEM_PREPAREREFERENCE" config "./nextflow.config" - tag "modules" - tag "modules_nfcore" - tag "rsem" - tag "rsem/calculateexpression" - tag "rsem/preparereference" - + test("homo_sapiens") { setup { diff --git a/modules/nf-core/rsem/preparereference/tests/main.nf.test b/modules/nf-core/rsem/preparereference/tests/main.nf.test index b4493d1ab..4353d4d9b 100644 --- a/modules/nf-core/rsem/preparereference/tests/main.nf.test +++ b/modules/nf-core/rsem/preparereference/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process RSEM_PREPAREREFERENCE" script "../main.nf" process "RSEM_PREPAREREFERENCE" - tag "modules" - tag "modules_nfcore" - tag "rsem" - tag "rsem/preparereference" test("homo_sapiens") { diff --git a/modules/nf-core/rseqc/bamstat/tests/main.nf.test b/modules/nf-core/rseqc/bamstat/tests/main.nf.test index 2f209b0a7..6a64b602b 100644 --- a/modules/nf-core/rseqc/bamstat/tests/main.nf.test +++ b/modules/nf-core/rseqc/bamstat/tests/main.nf.test @@ -4,11 +4,6 @@ nextflow_process { script "../main.nf" process "RSEQC_BAMSTAT" - tag "modules" - tag "modules_nfcore" - tag "rseqc" - tag "rseqc/bamstat" - config "./nextflow.config" test("sarscov2 - [meta] - bam") { diff --git a/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test b/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test index 4234829a7..6218de6d8 100644 --- a/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test +++ b/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test @@ -5,11 +5,6 @@ nextflow_process { process "RSEQC_INFEREXPERIMENT" config "./nextflow.config" - tag "modules" - tag "modules_nfcore" - tag "rseqc" - tag "rseqc/inferexperiment" - test("sarscov2 - [[meta] - bam] - bed") { when { diff --git a/modules/nf-core/rseqc/innerdistance/tests/main.nf.test b/modules/nf-core/rseqc/innerdistance/tests/main.nf.test index 0f07e3a87..2d4cc4fd6 100644 --- a/modules/nf-core/rseqc/innerdistance/tests/main.nf.test +++ b/modules/nf-core/rseqc/innerdistance/tests/main.nf.test @@ -5,11 +5,6 @@ nextflow_process { process "RSEQC_INNERDISTANCE" config "./nextflow.config" - tag "modules" - tag "modules_nfcore" - tag "rseqc" - tag "rseqc/innerdistance" - test("sarscov2 - [[meta] - bam] - bed") { when { diff --git a/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test b/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test index fd8cab96c..885d9a7b7 100644 --- a/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test +++ b/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test @@ -4,11 +4,6 @@ nextflow_process { script "../main.nf" process "RSEQC_JUNCTIONANNOTATION" - tag "modules" - tag "modules_nfcore" - tag "rseqc" - tag "rseqc/junctionannotation" - test("sarscov2 - paired end [bam]") { when { diff --git a/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test b/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test index af801dd64..b8b4381b4 100644 --- a/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test +++ b/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test @@ -4,11 +4,6 @@ nextflow_process { script "../main.nf" process "RSEQC_JUNCTIONSATURATION" - tag "modules" - tag "modules_nfcore" - tag "rseqc" - tag "rseqc/junctionsaturation" - test("sarscov2 paired-end [bam]") { when { diff --git a/modules/nf-core/rseqc/readdistribution/tests/main.nf.test b/modules/nf-core/rseqc/readdistribution/tests/main.nf.test index 8e630062f..d479d9f12 100644 --- a/modules/nf-core/rseqc/readdistribution/tests/main.nf.test +++ b/modules/nf-core/rseqc/readdistribution/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process RSEQC_READDISTRIBUTION" script "../main.nf" process "RSEQC_READDISTRIBUTION" - tag "modules" - tag "modules_nfcore" - tag "rseqc" - tag "rseqc/readdistribution" test("sarscov2 paired-end [bam]") { diff --git a/modules/nf-core/rseqc/readduplication/tests/main.nf.test b/modules/nf-core/rseqc/readduplication/tests/main.nf.test index d48e23b17..9c5675874 100644 --- a/modules/nf-core/rseqc/readduplication/tests/main.nf.test +++ b/modules/nf-core/rseqc/readduplication/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process RSEQC_READDUPLICATION" script "../main.nf" process "RSEQC_READDUPLICATION" - tag "modules" - tag "modules_nfcore" - tag "rseqc" - tag "rseqc/readduplication" test("sarscov2 paired-end [bam]") { diff --git a/modules/nf-core/rseqc/tin/tests/main.nf.test b/modules/nf-core/rseqc/tin/tests/main.nf.test index 95c04d93c..063d45674 100644 --- a/modules/nf-core/rseqc/tin/tests/main.nf.test +++ b/modules/nf-core/rseqc/tin/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process RSEQC_TIN" script "../main.nf" process "RSEQC_TIN" - tag "modules" - tag "modules_nfcore" - tag "rseqc" - tag "rseqc/tin" test("sarscov2 paired-end [bam]") { diff --git a/modules/nf-core/salmon/index/tests/main.nf.test b/modules/nf-core/salmon/index/tests/main.nf.test index 538b231b4..aaf2dbdb7 100644 --- a/modules/nf-core/salmon/index/tests/main.nf.test +++ b/modules/nf-core/salmon/index/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process SALMON_INDEX" script "../main.nf" process "SALMON_INDEX" - tag "modules" - tag "modules_nfcore" - tag "salmon" - tag "salmon/index" test("sarscov2") { diff --git a/modules/nf-core/salmon/quant/tests/main.nf.test b/modules/nf-core/salmon/quant/tests/main.nf.test index 04e61e2b3..fdc07db76 100644 --- a/modules/nf-core/salmon/quant/tests/main.nf.test +++ b/modules/nf-core/salmon/quant/tests/main.nf.test @@ -3,12 +3,8 @@ nextflow_process { name "Test Process SALMON_QUANT" script "../main.nf" process "SALMON_QUANT" + tag "SALMON_INDEX" config "./nextflow.config" - tag "modules" - tag "modules_nfcore" - tag "salmon" - tag "salmon/quant" - tag "salmon/index" setup { run("SALMON_INDEX") { diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test b/modules/nf-core/samtools/flagstat/tests/main.nf.test index 24c3c04b0..4d3742361 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process SAMTOOLS_FLAGSTAT" script "../main.nf" process "SAMTOOLS_FLAGSTAT" - tag "modules" - tag "modules_nfcore" - tag "samtools" - tag "samtools/flagstat" test("BAM") { diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test b/modules/nf-core/samtools/idxstats/tests/main.nf.test index a2dcb27c7..e6c427053 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process SAMTOOLS_IDXSTATS" script "../main.nf" process "SAMTOOLS_IDXSTATS" - tag "modules" - tag "modules_nfcore" - tag "samtools" - tag "samtools/idxstats" test("bam") { diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test index bb7756d1c..e3f918965 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process SAMTOOLS_INDEX" script "../main.nf" process "SAMTOOLS_INDEX" - tag "modules" - tag "modules_nfcore" - tag "samtools" - tag "samtools/index" test("bai") { diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index 8360e2b1f..728201ded 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process SAMTOOLS_SORT" script "../main.nf" process "SAMTOOLS_SORT" - tag "modules" - tag "modules_nfcore" - tag "samtools" - tag "samtools/sort" test("bam") { diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test index e3d5cb14c..a28964666 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test +++ b/modules/nf-core/samtools/stats/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process SAMTOOLS_STATS" script "../main.nf" process "SAMTOOLS_STATS" - tag "modules" - tag "modules_nfcore" - tag "samtools" - tag "samtools/stats" test("bam") { diff --git a/modules/nf-core/sortmerna/tests/main.nf.test b/modules/nf-core/sortmerna/tests/main.nf.test index 73bc11950..4388cda0c 100644 --- a/modules/nf-core/sortmerna/tests/main.nf.test +++ b/modules/nf-core/sortmerna/tests/main.nf.test @@ -3,9 +3,6 @@ nextflow_process { name "Test Process SORTMERNA" script "../main.nf" process "SORTMERNA" - tag "modules" - tag "modules_nfcore" - tag "sortmerna" test("sarscov2 indexing only") { diff --git a/modules/nf-core/star/align/tests/main.nf.test b/modules/nf-core/star/align/tests/main.nf.test index 6ecd77863..8b34ae793 100644 --- a/modules/nf-core/star/align/tests/main.nf.test +++ b/modules/nf-core/star/align/tests/main.nf.test @@ -3,11 +3,7 @@ nextflow_process { name "Test Process STAR_ALIGN" script "../main.nf" process "STAR_ALIGN" - tag "modules" - tag "modules_nfcore" - tag "star" - tag "star/align" - tag "star/genomegenerate" + tag "STAR_GENOMEGENERATE" setup { run("STAR_GENOMEGENERATE") { diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test b/modules/nf-core/star/genomegenerate/tests/main.nf.test index c17c8ba45..3467a3567 100644 --- a/modules/nf-core/star/genomegenerate/tests/main.nf.test +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process STAR_GENOMEGENERATE" script "../main.nf" process "STAR_GENOMEGENERATE" - tag "modules" - tag "modules_nfcore" - tag "star" - tag "star/genomegenerate" test("fasta_gtf") { diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test b/modules/nf-core/stringtie/stringtie/tests/main.nf.test index 00efe8f1a..68baaf289 100644 --- a/modules/nf-core/stringtie/stringtie/tests/main.nf.test +++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process STRINGTIE_STRINGTIE" script "../main.nf" process "STRINGTIE_STRINGTIE" - tag "modules" - tag "modules_nfcore" - tag "stringtie" - tag "stringtie/stringtie" test("sarscov2 [bam] - forward strandedness") { diff --git a/modules/nf-core/subread/featurecounts/tests/main.nf.test b/modules/nf-core/subread/featurecounts/tests/main.nf.test index 00d157d97..e8e0fa70e 100644 --- a/modules/nf-core/subread/featurecounts/tests/main.nf.test +++ b/modules/nf-core/subread/featurecounts/tests/main.nf.test @@ -4,10 +4,6 @@ nextflow_process { script "../main.nf" process "SUBREAD_FEATURECOUNTS" config "./nextflow.config" - tag "modules" - tag "modules_nfcore" - tag "subread" - tag "subread/featurecounts" test("sarscov2 [bam] - forward") { diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test index b51a76cda..4dda21181 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test @@ -3,15 +3,9 @@ nextflow_process { name "Test Process SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT" script "../main.nf" process "SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT" - - tag "modules" - tag "modules_nfcore" - tag "custom/tx2gene" - tag "tximeta" - tag "tximeta/tximport" - tag "summarizedexperiment" - tag "summarizedexperiment/summarizedexperiment" - tag "untar" + tag "UNTAR" + tag "CUSTOM_TX2GENE" + tag "TXIMETA_TXIMPORT" setup { diff --git a/modules/nf-core/trimgalore/tests/main.nf.test b/modules/nf-core/trimgalore/tests/main.nf.test index 43904ac32..93e30325a 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test +++ b/modules/nf-core/trimgalore/tests/main.nf.test @@ -3,9 +3,6 @@ nextflow_process { name "Test Process TRIMGALORE" script "../main.nf" process "TRIMGALORE" - tag "modules" - tag "modules_nfcore" - tag "trimgalore" test("test_trimgalore_single_end") { diff --git a/modules/nf-core/tximeta/tximport/tests/main.nf.test b/modules/nf-core/tximeta/tximport/tests/main.nf.test index 5cf6af83e..8f27bc928 100644 --- a/modules/nf-core/tximeta/tximport/tests/main.nf.test +++ b/modules/nf-core/tximeta/tximport/tests/main.nf.test @@ -3,13 +3,8 @@ nextflow_process { name "Test Process TXIMETA_TXIMPORT" script "../main.nf" process "TXIMETA_TXIMPORT" - - tag "modules" - tag "modules_nfcore" - tag "custom/tx2gene" - tag "tximeta" - tag "tximeta/tximport" - tag "untar" + tag "UNTAR" + tag "CUSTOM_TX2GENE" test("saccharomyces_cerevisiae - kallisto - gtf") { diff --git a/modules/nf-core/ucsc/bedclip/tests/main.nf.test b/modules/nf-core/ucsc/bedclip/tests/main.nf.test index f26764529..f4fa61b5e 100644 --- a/modules/nf-core/ucsc/bedclip/tests/main.nf.test +++ b/modules/nf-core/ucsc/bedclip/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process UCSC_BEDCLIP" script "../main.nf" process "UCSC_BEDCLIP" - tag "modules" - tag "modules_nfcore" - tag "ucsc" - tag "ucsc/bedclip" test("sarscov2") { config "./nextflow.config" diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test b/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test index a40ee2a32..61beea6b5 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test +++ b/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test @@ -3,10 +3,6 @@ nextflow_process { name "Test Process UCSC_BEDGRAPHTOBIGWIG" script "../main.nf" process "UCSC_BEDGRAPHTOBIGWIG" - tag "modules" - tag "modules_nfcore" - tag "ucsc" - tag "ucsc/bedgraphtobigwig" test("Should run without failures") { diff --git a/modules/nf-core/umitools/dedup/tests/main.nf.test b/modules/nf-core/umitools/dedup/tests/main.nf.test index 84698be42..018bd293d 100644 --- a/modules/nf-core/umitools/dedup/tests/main.nf.test +++ b/modules/nf-core/umitools/dedup/tests/main.nf.test @@ -4,11 +4,6 @@ nextflow_process { script "../main.nf" process "UMITOOLS_DEDUP" - tag "modules" - tag "modules_nfcore" - tag "umitools" - tag "umitools/dedup" - test("se - no stats") { config "./nextflow.config" diff --git a/modules/nf-core/umitools/extract/tests/main.nf.test b/modules/nf-core/umitools/extract/tests/main.nf.test index 2a8eba150..4d9a01567 100644 --- a/modules/nf-core/umitools/extract/tests/main.nf.test +++ b/modules/nf-core/umitools/extract/tests/main.nf.test @@ -4,10 +4,6 @@ nextflow_process { script "../main.nf" process "UMITOOLS_EXTRACT" config "./nextflow.config" - tag "modules_nfcore" - tag "modules" - tag "umitools" - tag "umitools/extract" test("Should run without failures") { diff --git a/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test b/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test index aa31d6593..105093505 100644 --- a/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test +++ b/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test @@ -4,11 +4,6 @@ nextflow_process { script "../main.nf" process "UMITOOLS_PREPAREFORRSEM" - tag "modules" - tag "modules_nfcore" - tag "umitools" - tag "umitools/prepareforrsem" - test("sarscov2 - bam") { when { diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test index 2a7c97bf8..2740dfbcf 100644 --- a/modules/nf-core/untar/tests/main.nf.test +++ b/modules/nf-core/untar/tests/main.nf.test @@ -3,9 +3,7 @@ nextflow_process { name "Test Process UNTAR" script "../main.nf" process "UNTAR" - tag "modules" - tag "modules_nfcore" - tag "untar" + test("test_untar") { when { From 67603dbb88cb9609d9d48c30b9838ad893432704 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 13 Mar 2024 19:07:27 +0000 Subject: [PATCH 2/3] Delete unecessary tags from nt.test files for subworkflows --- .../local/align_star/tests/main.nf.test | 10 +-- .../local/prepare_genome/tests/main.nf.test | 3 - .../tests/main.nf.test | 12 ++-- .../local/quantify_rsem/tests/main.nf.test | 7 +- .../tests/main.function.nf.test | 1 + .../main.pipeline_completion.workflow.nf.test | 1 + .../tests/main.nf.test | 17 ++--- .../tests/main.nf.test | 16 +---- .../nf-core/bam_rseqc/tests/main.nf.test | 22 +++--- .../tests/main.nf.test | 16 ++--- .../bam_stats_samtools/tests/main.nf.test | 12 ++-- .../tests/main.nf.test | 10 +-- .../fastq_align_hisat2/tests/main.nf.test | 70 ++++++++----------- .../tests/main.nf.test | 10 +-- .../tests/main.nf.test | 7 -- .../tests/main.nf.test | 11 ++- .../tests/main.function.nf.test | 6 +- .../tests/main.workflow.nf.test | 3 - .../tests/main.function.nf.test | 7 +- .../tests/main.workflow.nf.test | 4 -- .../tests/main.nf.test | 6 -- 21 files changed, 84 insertions(+), 167 deletions(-) diff --git a/subworkflows/local/align_star/tests/main.nf.test b/subworkflows/local/align_star/tests/main.nf.test index f42f90932..9ad089fe0 100644 --- a/subworkflows/local/align_star/tests/main.nf.test +++ b/subworkflows/local/align_star/tests/main.nf.test @@ -5,14 +5,10 @@ nextflow_workflow { workflow "ALIGN_STAR" config "./nextflow.config" - tag "ALIGN_STAR" - - tag "star/align" - tag "star/genomegenerate" - - tag "STAR_ALIGN_IGENOMES" + 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 129b66127..506ea4663 100644 --- a/subworkflows/local/prepare_genome/tests/main.nf.test +++ b/subworkflows/local/prepare_genome/tests/main.nf.test @@ -5,8 +5,6 @@ nextflow_workflow { workflow "PREPARE_GENOME" config "./nextflow.config" - tag "PREPARE_GENOME" - tag "BBMAP_BBSPLIT" tag "CUSTOM_CATADDITIONALFASTA" tag "CUSTOM_GETCHROMSIZES" @@ -19,7 +17,6 @@ nextflow_workflow { tag "KALLISTO_INDEX" tag "PREPROCESS_TRANSCRIPTS_FASTA_GENCODE" tag "RSEM_PREPAREREFERENCE" - tag "RSEM_PREPAREREFERENCE" tag "SALMON_INDEX" tag "SORTMERNA" tag "STAR_GENOMEGENERATE" diff --git a/subworkflows/local/quantify_pseudo_alignment/tests/main.nf.test b/subworkflows/local/quantify_pseudo_alignment/tests/main.nf.test index 9309200d7..cdeeb0206 100644 --- a/subworkflows/local/quantify_pseudo_alignment/tests/main.nf.test +++ b/subworkflows/local/quantify_pseudo_alignment/tests/main.nf.test @@ -4,11 +4,13 @@ nextflow_workflow { script "../main.nf" workflow "QUANTIFY_PSEUDO_ALIGNMENT" - tag 'SALMON_QUANT' - tag 'KALLISTO_QUANT' - tag 'CUSTOM_TX2GENE' - tag 'TXIMETA_TXIMPORT' - tag 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' + tag "SALMON_INDEX" + tag "SALMON_QUANT" + tag "KALLISTO_INDEX" + tag "KALLISTO_QUANT" + tag "CUSTOM_TX2GENE" + tag "TXIMETA_TXIMPORT" + tag "SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT" test("salmon") { diff --git a/subworkflows/local/quantify_rsem/tests/main.nf.test b/subworkflows/local/quantify_rsem/tests/main.nf.test index ae8fcff3a..1a0dc38bc 100644 --- a/subworkflows/local/quantify_rsem/tests/main.nf.test +++ b/subworkflows/local/quantify_rsem/tests/main.nf.test @@ -5,9 +5,10 @@ nextflow_workflow { workflow "QUANTIFY_RSEM" config "./nextflow.config" - tag 'RSEM_CALCULATEEXPRESSION' - tag 'RSEM_MERGE_COUNTS' - tag 'BAM_SORT_STATS_SAMTOOLS' + 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 3bc86b908..37d5e6bbe 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 @@ -2,6 +2,7 @@ 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 85de53a69..fb7e7a145 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 @@ -3,6 +3,7 @@ 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 476e7320e..ae36541fe 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 @@ -3,19 +3,10 @@ nextflow_workflow { name "Test Workflow BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS" script "../main.nf" workflow "BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "subworkflows/bam_dedup_stats_samtools_umitools" - tag "subworkflows/bam_stats_samtools" - tag "bam_dedup_stats_samtools_umitools" - tag "bam_stats_samtools" - tag "samtools" - tag "samtools/index" - tag "samtools/stats" - tag "samtools/idxstats" - tag "samtools/flagstat" - tag "umitools" - tag "umitools/dedup" + + 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 d8d242908..bb3ef8f4d 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test @@ -4,19 +4,9 @@ nextflow_workflow { script "../main.nf" workflow "BAM_MARKDUPLICATES_PICARD" - tag "picard" - tag "picard/markduplicates" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "bam_markduplicates_picard" - tag "subworkflows/bam_markduplicates_picard" - tag "subworkflows/bam_stats_samtools" - tag "bam_stats_samtools" - tag "samtools" - tag "samtools/flagstat" - tag "samtools/idxstats" - tag "samtools/index" - tag "samtools/stats" + 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 cc1cea4ec..784f5dfbc 100644 --- a/subworkflows/nf-core/bam_rseqc/tests/main.nf.test +++ b/subworkflows/nf-core/bam_rseqc/tests/main.nf.test @@ -3,19 +3,15 @@ nextflow_workflow { name "Test Workflow BAM_RSEQC" script "../main.nf" workflow "BAM_RSEQC" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "subworkflows/bam_rseqc" - tag "bam_rseqc" - tag "rseqc" - tag "rseqc/bamstat" - tag "rseqc/inferexperiment" - tag "rseqc/innerdistance" - tag "rseqc/junctionannotation" - tag "rseqc/junctionsaturation" - tag "rseqc/readdistribution" - tag "rseqc/readduplication" - tag "rseqc/tin" + + 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 75b5b9345..18a971352 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 @@ -3,18 +3,10 @@ nextflow_workflow { name "Test Workflow BAM_SORT_STATS_SAMTOOLS" script "../main.nf" workflow "BAM_SORT_STATS_SAMTOOLS" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "subworkflows/bam_sort_stats_samtools" - tag "bam_sort_stats_samtools" - tag "subworkflows/bam_stats_samtools" - tag "bam_stats_samtools" - tag "samtools" - tag "samtools/index" - tag "samtools/sort" - tag "samtools/stats" - tag "samtools/idxstats" - tag "samtools/flagstat" + + 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 c8b21f280..0a6bff66a 100644 --- a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test +++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test @@ -3,14 +3,10 @@ nextflow_workflow { name "Test Workflow BAM_STATS_SAMTOOLS" script "../main.nf" workflow "BAM_STATS_SAMTOOLS" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "bam_stats_samtools" - tag "subworkflows/bam_stats_samtools" - tag "samtools" - tag "samtools/flagstat" - tag "samtools/idxstats" - tag "samtools/stats" + + 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 620bc8ba0..992ded0d1 100644 --- a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test +++ b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test @@ -4,14 +4,10 @@ nextflow_workflow { script "../main.nf" workflow "BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG" config "./nextflow.config" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "subworkflows/bedgraph_bedclip_bedgraphtobigwig" - tag "bedgraph_bedclip_bedgraphtobigwig" - tag "ucsc" - tag "ucsc/bedclip" - tag "ucsc/bedgraphtobigwig" + tag "UCSC_BEDCLIP" + tag "UCSC_BEDGRAPHTOBIGWIG" + test("sarscov2 [bedgraph] [genome_sizes]") { when { 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 b0c0ca512..51f7e20d5 100644 --- a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test @@ -5,50 +5,40 @@ nextflow_workflow { workflow "FASTQ_ALIGN_HISAT2" config "./nextflow.config" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "subworkflows/fastq_align_hisat2" + tag "HISAT2_EXTRACTSPLICESITES" + tag "HISAT2_BUILD" + tag "HISAT2_ALIGN" + tag "BAM_SORT_STATS_SAMTOOLS" - tag "hisat2/align" - tag "hisat2/build" - tag "hisat2/extractsplicesites" - - tag "samtools/flagstat" - tag "samtools/idxstats" - tag "samtools/index" - tag "samtools/sort" - tag "samtools/stats" - tag "subworkflows/bam_sort_stats_samtools" - - setup { - run("HISAT2_EXTRACTSPLICESITES") { - script "../../../../modules/nf-core/hisat2/extractsplicesites/main.nf" - process { - """ - input[0] = Channel.of([ - [id: 'test'], - file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true) - ]) - """ - } + setup { + run("HISAT2_EXTRACTSPLICESITES") { + script "../../../../modules/nf-core/hisat2/extractsplicesites/main.nf" + process { + """ + input[0] = Channel.of([ + [id: 'test'], + file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true) + ]) + """ } - run("HISAT2_BUILD") { - script "../../../../modules/nf-core/hisat2/build/main.nf" - process { - """ - input[0] = Channel.of([ - [id: 'test'], - file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) - ]) - input[1] = Channel.of([ - [id: 'test'], - file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true) - ]) - input[2] = HISAT2_EXTRACTSPLICESITES.out.txt - """ - } + } + run("HISAT2_BUILD") { + script "../../../../modules/nf-core/hisat2/build/main.nf" + process { + """ + input[0] = Channel.of([ + [id: 'test'], + file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) + ]) + input[1] = Channel.of([ + [id: 'test'], + file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true) + ]) + input[2] = HISAT2_EXTRACTSPLICESITES.out.txt + """ } } + } test("sarscov2 - bam - single_end") { 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 8f1d82d39..7dc05d923 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 @@ -3,14 +3,10 @@ nextflow_workflow { name "Test Workflow FASTQ_FASTQC_UMITOOLS_FASTP" script "../main.nf" workflow "FASTQ_FASTQC_UMITOOLS_FASTP" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "subworkflows/fastq_fastqc_umitools_fastp" - tag "fastq_fastqc_umitools_fastp" - tag "fastqc" - tag "umitools/extract" - tag "fastp" + 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 79f71d2d4..10681e8a2 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 @@ -5,13 +5,6 @@ nextflow_workflow { workflow "FASTQ_FASTQC_UMITOOLS_TRIMGALORE" config './nextflow.config' - tag "subworkflows" - tag "subworkflows_nfcore" - tag "subworkflows/fastq_fastqc_umitools_trimgalore" - tag "fastqc" - tag "umitools/extract" - tag "trimgalore" - tag "FASTQC" tag "UMITOOLS_EXTRACT" tag "TRIMGALORE" 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 6342449a1..949e6861b 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 @@ -4,13 +4,10 @@ nextflow_workflow { script "../main.nf" workflow "FASTQ_SUBSAMPLE_FQ_SALMON" config "./nextflow.config" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "subworkflows/fastq_subsample_fq_salmon" - tag "fastq_subsample_fq_salmon" - tag "salmon/index" - tag "fq/subsample" - tag "salmon/quant" + + tag "SALMON_INDEX" + tag "FQ_SUBSAMPLE" + tag "SALMON_QUANT" test("homo_sapiens paired-end [fastq]") { 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 68718e4f5..8b838192f 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 @@ -4,10 +4,8 @@ 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 'subworkflows' - tag 'utils_nextflow_pipeline' - tag 'subworkflows/utils_nextflow_pipeline' - + tag "UTILS_NEXTFLOW_PIPELINE" + test("Test Function getWorkflowVersion") { function "getWorkflowVersion" 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 ca964ce8e..13782037c 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 @@ -4,9 +4,6 @@ nextflow_workflow { script "../main.nf" config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" workflow "UTILS_NEXTFLOW_PIPELINE" - tag 'subworkflows' - tag 'utils_nextflow_pipeline' - tag 'subworkflows/utils_nextflow_pipeline' test("Should run no inputs") { 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 1dc317f8f..41b8d19e2 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 @@ -3,11 +3,8 @@ nextflow_function { name "Test Functions" script "../main.nf" - config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "utils_nfcore_pipeline" - tag "subworkflows/utils_nfcore_pipeline" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + tag "UTILS_NFCORE_PIPELINE" test("Test Function checkConfigProvided") { 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 8940d32d1..ff1ae72a9 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 @@ -4,10 +4,6 @@ nextflow_workflow { script "../main.nf" config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" workflow "UTILS_NFCORE_PIPELINE" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "utils_nfcore_pipeline" - tag "subworkflows/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 5784a33f2..5649654e6 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test @@ -3,12 +3,6 @@ nextflow_workflow { name "Test Workflow UTILS_NFVALIDATION_PLUGIN" script "../main.nf" workflow "UTILS_NFVALIDATION_PLUGIN" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "plugin/nf-validation" - tag "'plugin/nf-validation'" - tag "utils_nfvalidation_plugin" - tag "subworkflows/utils_nfvalidation_plugin" test("Should run nothing") { From 7b6397352deaa4bfb56a83c3e12a6eb0969f3404 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 13 Mar 2024 19:16:04 +0000 Subject: [PATCH 3/3] Update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3bd574684..a8ad30d25 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -60,6 +60,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1250](https://github.com/nf-core/rnaseq/pull/1250) - Remove all tags.yml files because the testing system has changed - [PR #1251](https://github.com/nf-core/rnaseq/pull/1251) - Replace deseq2_qc paths - [PR #1265](https://github.com/nf-core/rnaseq/pull/1265) - Small updates noticed during code review +- [PR #1266](https://github.com/nf-core/rnaseq/pull/1266) - Delete unecessary tags from nf.test files for modules and subworkflows ### Parameters