diff --git a/CHANGELOG.md b/CHANGELOG.md index 1b838f21b..8c2fa9b77 100644 --- 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 deleted file mode 100644 index 6c4f871df..000000000 --- a/modules/local/gtf2bed/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -gtf2bed: - - "modules/local/gtf2bed/**" diff --git a/modules/local/star_align_igenomes/tests/tags.yml b/modules/local/star_align_igenomes/tests/tags.yml deleted file mode 100644 index 23008800b..000000000 --- a/modules/local/star_align_igenomes/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -STAR_ALIGN_IGENOMES: - - modules/local/star_align_igenomes/** diff --git a/modules/local/star_genomegenerate_igenomes/tests/tags.yml b/modules/local/star_genomegenerate_igenomes/tests/tags.yml deleted file mode 100644 index 2ea1d4211..000000000 --- a/modules/local/star_genomegenerate_igenomes/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -STAR_GENOMEGENERATE_IGENOMES: - - modules/local/star_genomegenerate_igenomes/** diff --git a/modules/nf-core/bbmap/bbsplit/tests/tags.yml b/modules/nf-core/bbmap/bbsplit/tests/tags.yml deleted file mode 100644 index f6943f95d..000000000 --- a/modules/nf-core/bbmap/bbsplit/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bbmap/bbsplit: - - "modules/nf-core/bbmap/bbsplit/**" diff --git a/modules/nf-core/bedtools/genomecov/tests/tags.yml b/modules/nf-core/bedtools/genomecov/tests/tags.yml deleted file mode 100644 index 55fce4780..000000000 --- a/modules/nf-core/bedtools/genomecov/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bedtools/genomecov: - - "modules/nf-core/bedtools/genomecov/**" diff --git a/modules/nf-core/cat/fastq/tests/tags.yml b/modules/nf-core/cat/fastq/tests/tags.yml deleted file mode 100644 index 6ac436140..000000000 --- a/modules/nf-core/cat/fastq/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -cat/fastq: - - modules/nf-core/cat/fastq/** diff --git a/modules/nf-core/custom/catadditionalfasta/tests/tags.yml b/modules/nf-core/custom/catadditionalfasta/tests/tags.yml deleted file mode 100644 index 8e73a0121..000000000 --- a/modules/nf-core/custom/catadditionalfasta/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -custom/catadditionalfasta: - - "modules/nf-core/custom/catadditionalfasta/**" diff --git a/modules/nf-core/custom/getchromsizes/tests/tags.yml b/modules/nf-core/custom/getchromsizes/tests/tags.yml deleted file mode 100644 index d89a805fd..000000000 --- a/modules/nf-core/custom/getchromsizes/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -custom/getchromsizes: - - modules/nf-core/custom/getchromsizes/** diff --git a/modules/nf-core/custom/tx2gene/tests/tags.yml b/modules/nf-core/custom/tx2gene/tests/tags.yml deleted file mode 100644 index 493fbc3b1..000000000 --- a/modules/nf-core/custom/tx2gene/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -custom/tx2gene: - - "modules/nf-core/custom/tx2gene/**" diff --git a/modules/nf-core/dupradar/tests/tags.yml b/modules/nf-core/dupradar/tests/tags.yml deleted file mode 100644 index 255dc4ef3..000000000 --- a/modules/nf-core/dupradar/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -dupradar: - - "modules/nf-core/dupradar/**" diff --git a/modules/nf-core/fastp/tests/tags.yml b/modules/nf-core/fastp/tests/tags.yml deleted file mode 100644 index c1afcce75..000000000 --- a/modules/nf-core/fastp/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -fastp: - - modules/nf-core/fastp/** diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml deleted file mode 100644 index 7834294ba..000000000 --- a/modules/nf-core/fastqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -fastqc: - - modules/nf-core/fastqc/** diff --git a/modules/nf-core/fq/subsample/tests/tags.yml b/modules/nf-core/fq/subsample/tests/tags.yml deleted file mode 100644 index 515643178..000000000 --- a/modules/nf-core/fq/subsample/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -fq/subsample: - - modules/nf-core/fq/subsample/** diff --git a/modules/nf-core/gffread/tests/tags.yml b/modules/nf-core/gffread/tests/tags.yml deleted file mode 100644 index 055760656..000000000 --- a/modules/nf-core/gffread/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -gffread: - - modules/nf-core/gffread/** diff --git a/modules/nf-core/gunzip/tests/tags.yml b/modules/nf-core/gunzip/tests/tags.yml deleted file mode 100644 index fd3f69154..000000000 --- a/modules/nf-core/gunzip/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -gunzip: - - modules/nf-core/gunzip/** diff --git a/modules/nf-core/hisat2/align/tests/tags.yml b/modules/nf-core/hisat2/align/tests/tags.yml deleted file mode 100644 index 3a46cc896..000000000 --- a/modules/nf-core/hisat2/align/tests/tags.yml +++ /dev/null @@ -1,4 +0,0 @@ -hisat2/align: - - modules/nf-core/hisat2/align/** - - modules/nf-core/hisat2/build/** - - modules/nf-core/hisat2/extractsplicesites/** diff --git a/modules/nf-core/hisat2/build/tests/tags.yml b/modules/nf-core/hisat2/build/tests/tags.yml deleted file mode 100644 index a7faecb27..000000000 --- a/modules/nf-core/hisat2/build/tests/tags.yml +++ /dev/null @@ -1,3 +0,0 @@ -hisat2/build: - - modules/nf-core/hisat2/build/** - - modules/nf-core/hisat2/extractsplicesites/** diff --git a/modules/nf-core/hisat2/extractsplicesites/tests/tags.yml b/modules/nf-core/hisat2/extractsplicesites/tests/tags.yml deleted file mode 100644 index 4b0ed4010..000000000 --- a/modules/nf-core/hisat2/extractsplicesites/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -hisat2/extractsplicesites: - - modules/nf-core/hisat2/extractsplicesites/** diff --git a/modules/nf-core/kallisto/index/tests/tags.yml b/modules/nf-core/kallisto/index/tests/tags.yml deleted file mode 100644 index 9f47b88a1..000000000 --- a/modules/nf-core/kallisto/index/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -kallisto/index: - - modules/nf-core/kallisto/index/** diff --git a/modules/nf-core/kallisto/quant/tests/tags.yml b/modules/nf-core/kallisto/quant/tests/tags.yml deleted file mode 100644 index 460936583..000000000 --- a/modules/nf-core/kallisto/quant/tests/tags.yml +++ /dev/null @@ -1,3 +0,0 @@ -kallisto/quant: - - modules/nf-core/kallisto/index/** - - modules/nf-core/kallisto/quant/** diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml deleted file mode 100644 index bea6c0d37..000000000 --- a/modules/nf-core/multiqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -multiqc: - - modules/nf-core/multiqc/** diff --git a/modules/nf-core/picard/markduplicates/tests/tags.yml b/modules/nf-core/picard/markduplicates/tests/tags.yml deleted file mode 100644 index 4f213d620..000000000 --- a/modules/nf-core/picard/markduplicates/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -picard/markduplicates: - - modules/nf-core/picard/markduplicates/** diff --git a/modules/nf-core/preseq/lcextrap/tests/tags.yml b/modules/nf-core/preseq/lcextrap/tests/tags.yml deleted file mode 100644 index b9e25ea71..000000000 --- a/modules/nf-core/preseq/lcextrap/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -preseq/lcextrap: - - modules/nf-core/preseq/lcextrap/** diff --git a/modules/nf-core/qualimap/rnaseq/tests/tags.yml b/modules/nf-core/qualimap/rnaseq/tests/tags.yml deleted file mode 100644 index 74269debe..000000000 --- a/modules/nf-core/qualimap/rnaseq/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -qualimap/rnaseq: - - modules/nf-core/qualimap/rnaseq/** diff --git a/modules/nf-core/rsem/calculateexpression/tests/tags.yml b/modules/nf-core/rsem/calculateexpression/tests/tags.yml deleted file mode 100644 index 654756aa5..000000000 --- a/modules/nf-core/rsem/calculateexpression/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -rsem/calculateexpression: - - modules/nf-core/rsem/calculateexpression/** diff --git a/modules/nf-core/rsem/preparereference/tests/tags.yml b/modules/nf-core/rsem/preparereference/tests/tags.yml deleted file mode 100644 index 112904564..000000000 --- a/modules/nf-core/rsem/preparereference/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -rsem/preparereference: - - modules/nf-core/rsem/preparereference/** diff --git a/modules/nf-core/rseqc/bamstat/tests/tags.yml b/modules/nf-core/rseqc/bamstat/tests/tags.yml deleted file mode 100644 index ed9a41fa9..000000000 --- a/modules/nf-core/rseqc/bamstat/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -rseqc/bamstat: - - modules/nf-core/rseqc/bamstat/** diff --git a/modules/nf-core/rseqc/inferexperiment/tests/tags.yml b/modules/nf-core/rseqc/inferexperiment/tests/tags.yml deleted file mode 100644 index f9ba7e26a..000000000 --- a/modules/nf-core/rseqc/inferexperiment/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -rseqc/inferexperiment: - - modules/nf-core/rseqc/inferexperiment/** diff --git a/modules/nf-core/rseqc/innerdistance/tests/tags.yml b/modules/nf-core/rseqc/innerdistance/tests/tags.yml deleted file mode 100644 index 4a9d0acf9..000000000 --- a/modules/nf-core/rseqc/innerdistance/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -rseqc/innerdistance: - - modules/nf-core/rseqc/innerdistance/** diff --git a/modules/nf-core/rseqc/junctionannotation/tests/tags.yml b/modules/nf-core/rseqc/junctionannotation/tests/tags.yml deleted file mode 100644 index 5f719fb8d..000000000 --- a/modules/nf-core/rseqc/junctionannotation/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -rseqc/junctionannotation: - - modules/nf-core/rseqc/junctionannotation/** diff --git a/modules/nf-core/rseqc/junctionsaturation/tests/tags.yml b/modules/nf-core/rseqc/junctionsaturation/tests/tags.yml deleted file mode 100644 index 7022b59ad..000000000 --- a/modules/nf-core/rseqc/junctionsaturation/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -rseqc/junctionsaturation: - - modules/nf-core/rseqc/junctionsaturation/** diff --git a/modules/nf-core/rseqc/readdistribution/tests/tags.yml b/modules/nf-core/rseqc/readdistribution/tests/tags.yml deleted file mode 100644 index c0c477b6d..000000000 --- a/modules/nf-core/rseqc/readdistribution/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -rseqc/readdistribution: - - modules/nf-core/rseqc/readdistribution/** diff --git a/modules/nf-core/rseqc/readduplication/tests/tags.yml b/modules/nf-core/rseqc/readduplication/tests/tags.yml deleted file mode 100644 index fce3d35d4..000000000 --- a/modules/nf-core/rseqc/readduplication/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -rseqc/readduplication: - - modules/nf-core/rseqc/readduplication/** diff --git a/modules/nf-core/rseqc/tin/tests/tags.yml b/modules/nf-core/rseqc/tin/tests/tags.yml deleted file mode 100644 index 741bbd0c0..000000000 --- a/modules/nf-core/rseqc/tin/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -rseqc/tin: - - modules/nf-core/rseqc/tin/** diff --git a/modules/nf-core/salmon/index/tests/tags.yml b/modules/nf-core/salmon/index/tests/tags.yml deleted file mode 100644 index 02997890f..000000000 --- a/modules/nf-core/salmon/index/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -salmon/index: - - modules/nf-core/salmon/index/** diff --git a/modules/nf-core/salmon/quant/tests/tags.yml b/modules/nf-core/salmon/quant/tests/tags.yml deleted file mode 100644 index 048d81642..000000000 --- a/modules/nf-core/salmon/quant/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -salmon/quant: - - modules/nf-core/salmon/quant/** diff --git a/modules/nf-core/samtools/flagstat/tests/tags.yml b/modules/nf-core/samtools/flagstat/tests/tags.yml deleted file mode 100644 index 2d2b7255e..000000000 --- a/modules/nf-core/samtools/flagstat/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -samtools/flagstat: - - modules/nf-core/samtools/flagstat/** diff --git a/modules/nf-core/samtools/idxstats/tests/tags.yml b/modules/nf-core/samtools/idxstats/tests/tags.yml deleted file mode 100644 index d3057c61f..000000000 --- a/modules/nf-core/samtools/idxstats/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -samtools/idxstats: - - modules/nf-core/samtools/idxstats/** diff --git a/modules/nf-core/samtools/index/tests/tags.yml b/modules/nf-core/samtools/index/tests/tags.yml deleted file mode 100644 index e0f58a7a3..000000000 --- a/modules/nf-core/samtools/index/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -samtools/index: - - modules/nf-core/samtools/index/** diff --git a/modules/nf-core/samtools/sort/tests/tags.yml b/modules/nf-core/samtools/sort/tests/tags.yml deleted file mode 100644 index cd63ea208..000000000 --- a/modules/nf-core/samtools/sort/tests/tags.yml +++ /dev/null @@ -1,3 +0,0 @@ -samtools/sort: - - modules/nf-core/samtools/sort/** - - tests/modules/nf-core/samtools/sort/** diff --git a/modules/nf-core/samtools/stats/tests/tags.yml b/modules/nf-core/samtools/stats/tests/tags.yml deleted file mode 100644 index 7c28e30f3..000000000 --- a/modules/nf-core/samtools/stats/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -samtools/stats: - - modules/nf-core/samtools/stats/** diff --git a/modules/nf-core/sortmerna/tests/tags.yml b/modules/nf-core/sortmerna/tests/tags.yml deleted file mode 100644 index e088480c7..000000000 --- a/modules/nf-core/sortmerna/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -sortmerna: - - modules/nf-core/sortmerna/** diff --git a/modules/nf-core/star/align/tests/tags.yml b/modules/nf-core/star/align/tests/tags.yml deleted file mode 100644 index 8beace16e..000000000 --- a/modules/nf-core/star/align/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -star/align: - - modules/nf-core/star/align/** diff --git a/modules/nf-core/star/genomegenerate/tests/tags.yml b/modules/nf-core/star/genomegenerate/tests/tags.yml deleted file mode 100644 index 79f619bfe..000000000 --- a/modules/nf-core/star/genomegenerate/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -star/genomegenerate: - - modules/nf-core/star/genomegenerate/** diff --git a/modules/nf-core/stringtie/stringtie/tests/tags.yml b/modules/nf-core/stringtie/stringtie/tests/tags.yml deleted file mode 100644 index da9b051c3..000000000 --- a/modules/nf-core/stringtie/stringtie/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -stringtie/stringtie: - - modules/nf-core/stringtie/stringtie/** diff --git a/modules/nf-core/subread/featurecounts/tests/tags.yml b/modules/nf-core/subread/featurecounts/tests/tags.yml deleted file mode 100644 index 6d2534bf4..000000000 --- a/modules/nf-core/subread/featurecounts/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subread/featurecounts: - - modules/nf-core/subread/featurecounts/** diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/tags.yml b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/tags.yml deleted file mode 100644 index 9856e958c..000000000 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -summarizedexperiment/summarizedexperiment: - - "modules/nf-core/summarizedexperiment/summarizedexperiment/**" diff --git a/modules/nf-core/trimgalore/tests/tags.yml b/modules/nf-core/trimgalore/tests/tags.yml deleted file mode 100644 index e9937691a..000000000 --- a/modules/nf-core/trimgalore/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -trimgalore: - - modules/nf-core/trimgalore/** diff --git a/modules/nf-core/tximeta/tximport/tests/tags.yml b/modules/nf-core/tximeta/tximport/tests/tags.yml deleted file mode 100644 index fc96a89e0..000000000 --- a/modules/nf-core/tximeta/tximport/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -tximeta/tximport: - - "modules/nf-core/tximeta/tximport/**" diff --git a/modules/nf-core/ucsc/bedclip/tests/tags.yml b/modules/nf-core/ucsc/bedclip/tests/tags.yml deleted file mode 100644 index 0fcc90e32..000000000 --- a/modules/nf-core/ucsc/bedclip/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -ucsc/bedclip: - - modules/nf-core/ucsc/bedclip/** diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/tests/tags.yml b/modules/nf-core/ucsc/bedgraphtobigwig/tests/tags.yml deleted file mode 100644 index 481e8b8bf..000000000 --- a/modules/nf-core/ucsc/bedgraphtobigwig/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -ucsc/bedgraphtobigwig: - - modules/nf-core/ucsc/bedgraphtobigwig/** diff --git a/modules/nf-core/umitools/dedup/tests/tags.yml b/modules/nf-core/umitools/dedup/tests/tags.yml deleted file mode 100644 index 5934c5cb7..000000000 --- a/modules/nf-core/umitools/dedup/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -umitools/dedup: - - "modules/nf-core/umitools/dedup/**" diff --git a/modules/nf-core/umitools/extract/tests/tags.yml b/modules/nf-core/umitools/extract/tests/tags.yml deleted file mode 100644 index c3fb23de4..000000000 --- a/modules/nf-core/umitools/extract/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -umitools/extract: - - modules/nf-core/umitools/extract/** diff --git a/modules/nf-core/umitools/prepareforrsem/tests/tags.yml b/modules/nf-core/umitools/prepareforrsem/tests/tags.yml deleted file mode 100644 index 804c113dd..000000000 --- a/modules/nf-core/umitools/prepareforrsem/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -umitools/prepareforrsem: - - "modules/nf-core/umitools/prepareforrsem/**" diff --git a/modules/nf-core/untar/tests/tags.yml b/modules/nf-core/untar/tests/tags.yml deleted file mode 100644 index feb6f15c0..000000000 --- a/modules/nf-core/untar/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -untar: - - modules/nf-core/untar/** 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 deleted file mode 100644 index bfd5e023e..000000000 --- a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/bam_dedup_stats_samtools_umitools: - - subworkflows/nf-core/bam_dedup_stats_samtools_umitools/** diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/tags.yml b/subworkflows/nf-core/bam_markduplicates_picard/tests/tags.yml deleted file mode 100644 index 10b852706..000000000 --- a/subworkflows/nf-core/bam_markduplicates_picard/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/bam_markduplicates_picard: - - subworkflows/nf-core/bam_markduplicates_picard/** diff --git a/subworkflows/nf-core/bam_rseqc/tests/tags.yml b/subworkflows/nf-core/bam_rseqc/tests/tags.yml deleted file mode 100644 index c8dfce3a9..000000000 --- a/subworkflows/nf-core/bam_rseqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/bam_rseqc: - - subworkflows/nf-core/bam_rseqc/** diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/tags.yml b/subworkflows/nf-core/bam_sort_stats_samtools/tests/tags.yml deleted file mode 100644 index 30b69d6a4..000000000 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/bam_sort_stats_samtools: - - subworkflows/nf-core/bam_sort_stats_samtools/** diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml b/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml deleted file mode 100644 index ec2f2d68f..000000000 --- a/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/bam_stats_samtools: - - subworkflows/nf-core/bam_stats_samtools/** diff --git a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/tags.yml b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/tags.yml deleted file mode 100644 index 83a103035..000000000 --- a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/bedgraph_bedclip_bedgraphtobigwig: - - subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/** diff --git a/subworkflows/nf-core/fastq_align_hisat2/tests/tags.yml b/subworkflows/nf-core/fastq_align_hisat2/tests/tags.yml deleted file mode 100644 index 8993cde0c..000000000 --- a/subworkflows/nf-core/fastq_align_hisat2/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/fastq_align_hisat2: - - subworkflows/nf-core/fastq_align_hisat2/** diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/tags.yml b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/tags.yml deleted file mode 100644 index 84a4b5676..000000000 --- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/fastq_fastqc_umitools_fastp: - - subworkflows/nf-core/fastq_fastqc_umitools_fastp/** diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/tags.yml b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/tags.yml deleted file mode 100644 index 5bf59db41..000000000 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/fastq_fastqc_umitools_trimgalore: - - subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/** diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/tags.yml b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/tags.yml deleted file mode 100644 index cc809c524..000000000 --- a/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/fastq_subsample_fq_salmon: - - subworkflows/nf-core/fastq_subsample_fq_salmon/** diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml deleted file mode 100644 index f84761125..000000000 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nextflow_pipeline: - - subworkflows/nf-core/utils_nextflow_pipeline/** diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml deleted file mode 100644 index ac8523c9a..000000000 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfcore_pipeline: - - subworkflows/nf-core/utils_nfcore_pipeline/** diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml deleted file mode 100644 index 60b1cfff4..000000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfvalidation_plugin: - - subworkflows/nf-core/utils_nfvalidation_plugin/**