Merge branch 'dev' into prepare_3.15.2

CHANGELOG.md

@@ -58,6 +58,7 @@ Special thanks to the following for their contributions to the release:
 ### Enhancements & fixes
 
 - [PR #1374](https://github.com/nf-core/rnaseq/pull/1374) - Bump pipeline version to 3.16.0dev
+- [PR #1379](https://github.com/nf-core/rnaseq/pull/1379) - Enhance pipeline level test snapshots
 - [PR #1380](https://github.com/nf-core/rnaseq/pull/1380) - Fix issues with R modules changing sample names
 - [PR #1381](https://github.com/nf-core/rnaseq/pull/1381) - Update all modules following massive conda usage update in nf-core modules
 - [PR #1382](https://github.com/nf-core/rnaseq/pull/1381) - Slight fixes for rnaseq preprocessing

nf-test.config

@@ -13,5 +13,6 @@ config {
     // load the necessary plugins
     plugins {
         load "[email protected]"
+        load "[email protected]"
     }
 }

tests/.nftignore

@@ -0,0 +1,125 @@
+**/*DupRate_plot.{pdf,r}
+**/*Log.out
+**/*Log.{final,progress}.out
+**/*_fastqc.{html,zip}
+**/*_raw.{html,zip}
+**/*_{duprateExpBoxplot,duprateExpDens,expressionHist}.{pdf,png,svg}
+**/*bam_stat.txt
+**/*coverage.gtf
+**/*fastq.gz_trimming_report.txt
+**/*featureCounts.txt.summary
+**/*gene.abundance.txt
+**/*hisat2.summary
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+**/*read_distribution.txt
+**/*sorted.bam.{flagstat,idxstats,stats}
+**/*sortmerna.log
+**/*splice_{events,junction}.{pdf,png,svg}
+**/*transcripts.gtf
+**/*{cnt,model,theta}
+**/*{css,gif,js}
+**/*{forward,reverse}.bigWig
+**/*{genes,isoforms}.results
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+**/Junction*.png
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+**/multiqc_general_stats.txt
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+**/multiqc_report.html
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+**/multiqc_rseqc_bam_stat.txt
+**/multiqc_rseqc_infer_experiment.txt
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+**/multiqc_rseqc_read_distribution.txt
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+**/multiqc_samtools_flagstat.txt
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+**/multiqc_software_versions.txt
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+**/picard_deduplication.txt
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+**/qualimap_gene_coverage_profile_Normalised.{pdf,svg}
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+**/qualimap_genomic_origin.txt
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+**/quant.sf
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+**/rsem_assignment_plot.txt
+**/rsem_multimapping_rates.{pdf,svg,txt}
+**/rseqc_bam_stat.{pdf,png,svg,txt}
+**/rseqc_infer_experiment_plot.{pdf,svg}
+**/rseqc_inner_*
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+**/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.{pdf,svg}
+**/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-{cnt,pct}.{pdf,svg}
+**/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.{pdf,svg}
+**/samtools-idxstats-mapped-reads-plot_Raw_Counts-{cnt,pct}.{pdf,svg}
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+**/sortmerna-detailed-plot-{cnt,pct}.{pdf,svg}
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+**/star_summary_table.{pdf,png,svg,txt}
+**/t_data.ctab
+**/{kallisto,salmon}.merged*
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+**/{salmon,star_rsem}_deseq2_{pca,pca}-plot.{pdf,png,svg}
+**/{samtools,star}_alignment_plot*
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