Merge pull request #1379 from maxulysse/better_snapshots

Improve pipeline level snapshots

Author: maxulysse

CHANGELOG.md

@@ -45,6 +45,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### 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 "nft-bam@0.3.0"
+        load "nft-utils@0.0.2"
     }
 }

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
+**/*inner_distance*
+**/*junction*
+**/*markdup.sorted.MarkDuplicates.metrics.txt
+**/*markdup.sorted.{bam,bam.bai}
+**/*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
+**/*{pos,seq}.DupRate.xls
+**/*{salmon,star_salmon,star_rsem}_deseq2_clustering-plot*{pdf,png,txt}
+**/Junction*.png
+**/Reads*.png
+**/abundance.{h5,tsv}
+**/cutadapt_filtered_reads_plot-{cnt,pct}.{pdf,svg}
+**/cutadapt_trimmed_sequences_*{pdf,svg}
+**/deseq2*
+**/dupradar-section-plot.{pdf,svg}
+**/fail_mapped_samples_table*
+**/fail_strand_check_table*
+**/fastqc-status-check-*{pdf,svg}
+**/fastqc_adapter_content_plot.{pdf,png,svg}
+**/fastqc_overrepresented_sequences_plot*{pdf,svg}
+**/fastqc_per_base_*_plot*{pdf,png,svg}
+**/fastqc_per_sequence_*{pdf,svg}
+**/fastqc_sequence_length_distribution_plot.{pdf,png,svg}
+**/fastqc_sequence_{counts,duplication_levels}_plot*{pdf,svg}
+**/fastqc_top_overrepresented_sequences_table*{pdf,png,svg,txt}
+**/featurecounts_biotype_plot-{cnt,pct}.{pdf,svg}
+**/fld.gz
+**/flenDist.txt
+**/general_stats_table.{pdf,png,svg}
+**/hisat2_pe_plot.txt
+**/hisat2_se_plot*{png,svg}
+**/hisat2_{pe,se}_plot-{cnt,pct}.{pdf,png,svg}
+**/junction_saturation_known.txt
+**/junction_saturation_novel.txt
+**/kallisto_alignment*{pdf,png,svg}
+**/kallisto_alignment.txt
+**/kallisto_quant.log
+**/meta_info.json
+**/multiqc_data.json
+**/multiqc_dupradar-section-plot.txt
+**/multiqc_fail_strand_check_table.txt
+**/multiqc_general_stats.txt
+**/multiqc_hisat2.txt
+**/multiqc_kallisto.txt
+**/multiqc_picard_dups.txt
+**/multiqc_plots
+**/multiqc_report.html
+**/multiqc_rsem.txt
+**/multiqc_rseqc_bam_stat.txt
+**/multiqc_rseqc_infer_experiment.txt
+**/multiqc_rseqc_junction_annotation.txt
+**/multiqc_rseqc_read_distribution.txt
+**/multiqc_salmon.txt
+**/multiqc_samtools_flagstat.txt
+**/multiqc_samtools_stats.txt
+**/multiqc_software_versions.txt
+**/multiqc_sortmerna.txt
+**/multiqc_sources.txt
+**/multiqc_star.txt
+**/multiqc_{salmon,star_salmon}_deseq2_pca-plot*txt
+**/picard_deduplication-{cnt,pct}.{pdf,png,svg}
+**/picard_deduplication.txt
+**/qualimapReport.html
+**/qualimap_gene_coverage_profile_Counts.{pdf,svg}
+**/qualimap_gene_coverage_profile_Normalised.{pdf,svg}
+**/qualimap_genomic_origin-{cnt,pct}.{pdf,png,svg}
+**/qualimap_genomic_origin.txt
+**/qualimap_rnaseq_genome_results.txt
+**/quant.genes.sf
+**/quant.sf
+**/rnaseq_qc_results.txt
+**/rsem_assignment_plot-{cnt,pct}.{pdf,png,svg}
+**/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_*
+**/rseqc_junction_*
+**/rseqc_read_distribution_*
+**/rseqc_read_dups.txt
+**/rseqc_read_dups_plot.txt
+**/rseqc_read_dups_plot.{pdf,svg}
+**/run_info.json
+**/salmon_plot.{pdf,png,svg,txt}
+**/salmon_quant.log
+**/samtools-flagstat*
+**/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.{pdf,svg}
+**/samtools-idxstats-mapped-reads-plot_Normalised_Counts-{cnt,pct}.{pdf,svg}
+**/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}
+**/samtools-stats-dp.{pdf,png,svg,txt}
+**/sortmerna-detailed-plot-{cnt,pct}.{pdf,svg}
+**/sortmerna-detailed-plot.txt
+**/star_summary_table.{pdf,png,svg,txt}
+**/t_data.ctab
+**/{kallisto,salmon}.merged*
+**/{salmon,star_rsem}_deseq2_{clustering,pca}-plot.{pdf,png,svg}
+**/{salmon,star_rsem}_deseq2_{pca,pca}-plot.{pdf,png,svg}
+**/{samtools,star}_alignment_plot*
+**/{star_rsem,star_salmon}_deseq2_{clustering,pca}-plot*{pdf,png,svg}
+bbsplit/*.stats.txt
+pipeline_info/*.{html,json,txt,yml}
+**/deseq2_qc/size_factors/*.txt
+star_rsem/log/*.log