Merge pull request #1250 from adamrtalbot/remove_tags.yml

Remove all tags.yml files
nf-core · Mar 12, 2024 · 31037e1 · 31037e1
2 parents e6d6efe + c5dbbf7
commit 31037e1
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,15 +12,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1186](https://github.com/nf-core/rnaseq/pull/1186) - Properly update qualimap/rnaseq module (ie not patch)
 - [PR #1201](https://github.com/nf-core/rnaseq/pull/1201) - Template update for nf-core/tools v2.12
 - [PR #1206](https://github.com/nf-core/rnaseq/pull/1206) - Remove `lib/` directory and `modules.config`
-- [PR #1212](https://github.com/nf-core/rnaseq/pull/1212) - Update all modules and subworkflows to latest versions
 - [PR #1210](https://github.com/nf-core/rnaseq/pull/1210) - Use pseudoalignment subworkflow components from nf-core/modules
-- [PR #1214](https://github.com/nf-core/rnaseq/pull/1214) - Bump umitools + delocalise prepareforrsem ([#831](https://github.com/nf-core/rnaseq/issues/831))
+- [PR #1212](https://github.com/nf-core/rnaseq/pull/1212) - Update all modules and subworkflows to latest versions
 - [PR #1213](https://github.com/nf-core/rnaseq/pull/1213) - Pass transcriptome fasta through to samtools stats
+- [PR #1214](https://github.com/nf-core/rnaseq/pull/1214) - Bump umitools + delocalise prepareforrsem ([#831](https://github.com/nf-core/rnaseq/issues/831))
 - [PR #1216](https://github.com/nf-core/rnaseq/pull/1216) - Delocalise catadditionalfasta ([#1162](https://github.com/nf-core/rnaseq/issues/1162))
 - [PR #1218](https://github.com/nf-core/rnaseq/pull/1218) - Template update for nf-core/tools v2.13
 - [PR #1220](https://github.com/nf-core/rnaseq/pull/1220) - Initialise nf-test and add pipeline level test
 - [PR #1221](https://github.com/nf-core/rnaseq/pull/1221) - Use nf-test test for all nf-core components
 - [PR #1226](https://github.com/nf-core/rnaseq/pull/1226) - Reuse bbsplit index and don't keep overwriting ([#1225](https://github.com/nf-core/rnaseq/issues/1225))
+- [PR #1228](https://github.com/nf-core/rnaseq/pull/1228) - Make README usage consistent with docs/usage.md
 - [PR #1229](https://github.com/nf-core/rnaseq/pull/1229) - Template update for nf-core/tools v2.13.1
 - [PR #1231](https://github.com/nf-core/rnaseq/pull/1231) - Add sortmerna index possibilities
 - [PR #1232](https://github.com/nf-core/rnaseq/pull/1232) - Add nf-test tests to star_genomegenerate_igenomes
@@ -35,7 +36,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1241](https://github.com/nf-core/rnaseq/pull/1241) - Add nf-test tests to deseq2_qc
 - [PR #1242](https://github.com/nf-core/rnaseq/pull/1242) - Use dupradar from nf-core/modules
 - [PR #1244](https://github.com/nf-core/rnaseq/pull/1244) - Add gtf2bed tests
-- [PR #1228](https://github.com/nf-core/rnaseq/pull/1228) - Change CI/CD testing logic to pass if no nf-tests have been ran
+- [PR #1250](https://github.com/nf-core/rnaseq/pull/1250) - Remove all tags.yml files because the testing system has changed
 
 ### Parameters
 

diff --git a/modules/local/gtf2bed/tests/tags.yml b/modules/local/gtf2bed/tests/tags.yml
diff --git a/modules/local/star_align_igenomes/tests/tags.yml b/modules/local/star_align_igenomes/tests/tags.yml
diff --git a/modules/local/star_genomegenerate_igenomes/tests/tags.yml b/modules/local/star_genomegenerate_igenomes/tests/tags.yml
diff --git a/modules/nf-core/bbmap/bbsplit/tests/tags.yml b/modules/nf-core/bbmap/bbsplit/tests/tags.yml
diff --git a/modules/nf-core/bedtools/genomecov/tests/tags.yml b/modules/nf-core/bedtools/genomecov/tests/tags.yml
diff --git a/modules/nf-core/cat/fastq/tests/tags.yml b/modules/nf-core/cat/fastq/tests/tags.yml
diff --git a/modules/nf-core/custom/catadditionalfasta/tests/tags.yml b/modules/nf-core/custom/catadditionalfasta/tests/tags.yml
diff --git a/modules/nf-core/custom/getchromsizes/tests/tags.yml b/modules/nf-core/custom/getchromsizes/tests/tags.yml
diff --git a/modules/nf-core/custom/tx2gene/tests/tags.yml b/modules/nf-core/custom/tx2gene/tests/tags.yml
diff --git a/modules/nf-core/dupradar/tests/tags.yml b/modules/nf-core/dupradar/tests/tags.yml
diff --git a/modules/nf-core/fastp/tests/tags.yml b/modules/nf-core/fastp/tests/tags.yml
diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml
diff --git a/modules/nf-core/fq/subsample/tests/tags.yml b/modules/nf-core/fq/subsample/tests/tags.yml
diff --git a/modules/nf-core/gffread/tests/tags.yml b/modules/nf-core/gffread/tests/tags.yml
diff --git a/modules/nf-core/gunzip/tests/tags.yml b/modules/nf-core/gunzip/tests/tags.yml
diff --git a/modules/nf-core/hisat2/align/tests/tags.yml b/modules/nf-core/hisat2/align/tests/tags.yml
diff --git a/modules/nf-core/hisat2/build/tests/tags.yml b/modules/nf-core/hisat2/build/tests/tags.yml
diff --git a/modules/nf-core/hisat2/extractsplicesites/tests/tags.yml b/modules/nf-core/hisat2/extractsplicesites/tests/tags.yml
diff --git a/modules/nf-core/kallisto/index/tests/tags.yml b/modules/nf-core/kallisto/index/tests/tags.yml
diff --git a/modules/nf-core/kallisto/quant/tests/tags.yml b/modules/nf-core/kallisto/quant/tests/tags.yml
diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml
diff --git a/modules/nf-core/picard/markduplicates/tests/tags.yml b/modules/nf-core/picard/markduplicates/tests/tags.yml
diff --git a/modules/nf-core/preseq/lcextrap/tests/tags.yml b/modules/nf-core/preseq/lcextrap/tests/tags.yml
diff --git a/modules/nf-core/qualimap/rnaseq/tests/tags.yml b/modules/nf-core/qualimap/rnaseq/tests/tags.yml
diff --git a/modules/nf-core/rsem/calculateexpression/tests/tags.yml b/modules/nf-core/rsem/calculateexpression/tests/tags.yml
diff --git a/modules/nf-core/rsem/preparereference/tests/tags.yml b/modules/nf-core/rsem/preparereference/tests/tags.yml
diff --git a/modules/nf-core/rseqc/bamstat/tests/tags.yml b/modules/nf-core/rseqc/bamstat/tests/tags.yml
diff --git a/modules/nf-core/rseqc/inferexperiment/tests/tags.yml b/modules/nf-core/rseqc/inferexperiment/tests/tags.yml
diff --git a/modules/nf-core/rseqc/innerdistance/tests/tags.yml b/modules/nf-core/rseqc/innerdistance/tests/tags.yml
diff --git a/modules/nf-core/rseqc/junctionannotation/tests/tags.yml b/modules/nf-core/rseqc/junctionannotation/tests/tags.yml
diff --git a/modules/nf-core/rseqc/junctionsaturation/tests/tags.yml b/modules/nf-core/rseqc/junctionsaturation/tests/tags.yml
diff --git a/modules/nf-core/rseqc/readdistribution/tests/tags.yml b/modules/nf-core/rseqc/readdistribution/tests/tags.yml
diff --git a/modules/nf-core/rseqc/readduplication/tests/tags.yml b/modules/nf-core/rseqc/readduplication/tests/tags.yml
diff --git a/modules/nf-core/rseqc/tin/tests/tags.yml b/modules/nf-core/rseqc/tin/tests/tags.yml
diff --git a/modules/nf-core/salmon/index/tests/tags.yml b/modules/nf-core/salmon/index/tests/tags.yml
diff --git a/modules/nf-core/salmon/quant/tests/tags.yml b/modules/nf-core/salmon/quant/tests/tags.yml
diff --git a/modules/nf-core/samtools/flagstat/tests/tags.yml b/modules/nf-core/samtools/flagstat/tests/tags.yml
diff --git a/modules/nf-core/samtools/idxstats/tests/tags.yml b/modules/nf-core/samtools/idxstats/tests/tags.yml
diff --git a/modules/nf-core/samtools/index/tests/tags.yml b/modules/nf-core/samtools/index/tests/tags.yml
diff --git a/modules/nf-core/samtools/sort/tests/tags.yml b/modules/nf-core/samtools/sort/tests/tags.yml
diff --git a/modules/nf-core/samtools/stats/tests/tags.yml b/modules/nf-core/samtools/stats/tests/tags.yml
diff --git a/modules/nf-core/sortmerna/tests/tags.yml b/modules/nf-core/sortmerna/tests/tags.yml
diff --git a/modules/nf-core/star/align/tests/tags.yml b/modules/nf-core/star/align/tests/tags.yml
diff --git a/modules/nf-core/star/genomegenerate/tests/tags.yml b/modules/nf-core/star/genomegenerate/tests/tags.yml
diff --git a/modules/nf-core/stringtie/stringtie/tests/tags.yml b/modules/nf-core/stringtie/stringtie/tests/tags.yml
diff --git a/modules/nf-core/subread/featurecounts/tests/tags.yml b/modules/nf-core/subread/featurecounts/tests/tags.yml
diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/tags.yml b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/tags.yml
diff --git a/modules/nf-core/trimgalore/tests/tags.yml b/modules/nf-core/trimgalore/tests/tags.yml
diff --git a/modules/nf-core/tximeta/tximport/tests/tags.yml b/modules/nf-core/tximeta/tximport/tests/tags.yml
diff --git a/modules/nf-core/ucsc/bedclip/tests/tags.yml b/modules/nf-core/ucsc/bedclip/tests/tags.yml
diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/tests/tags.yml b/modules/nf-core/ucsc/bedgraphtobigwig/tests/tags.yml
diff --git a/modules/nf-core/umitools/dedup/tests/tags.yml b/modules/nf-core/umitools/dedup/tests/tags.yml
diff --git a/modules/nf-core/umitools/extract/tests/tags.yml b/modules/nf-core/umitools/extract/tests/tags.yml
diff --git a/modules/nf-core/umitools/prepareforrsem/tests/tags.yml b/modules/nf-core/umitools/prepareforrsem/tests/tags.yml
diff --git a/modules/nf-core/untar/tests/tags.yml b/modules/nf-core/untar/tests/tags.yml
diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/tags.yml b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/tags.yml
diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/tags.yml b/subworkflows/nf-core/bam_markduplicates_picard/tests/tags.yml
diff --git a/subworkflows/nf-core/bam_rseqc/tests/tags.yml b/subworkflows/nf-core/bam_rseqc/tests/tags.yml
diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/tags.yml b/subworkflows/nf-core/bam_sort_stats_samtools/tests/tags.yml
diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml b/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml
diff --git a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/tags.yml b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/tags.yml
diff --git a/subworkflows/nf-core/fastq_align_hisat2/tests/tags.yml b/subworkflows/nf-core/fastq_align_hisat2/tests/tags.yml
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/tags.yml b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/tags.yml
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/tags.yml b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/tags.yml
diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/tags.yml b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/tags.yml
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml