From 1d35e2a1e00e48fd3e7dfedf5f9bfec93087cd12 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 2 Oct 2024 08:41:08 +0200 Subject: [PATCH] use nft-utils 0.0.2 to get relative path in snapshots --- nf-test.config | 2 +- tests/default.nf.test | 8 +- tests/default.nf.test.snap | 2178 +++++++++--------- tests/featurecounts_group_type.nf.test | 8 +- tests/featurecounts_group_type.nf.test.snap | 2120 +++++++++--------- tests/hisat2.nf.test | 8 +- tests/hisat2.nf.test.snap | 1926 ++++++++-------- tests/kallisto.nf.test | 8 +- tests/kallisto.nf.test.snap | 352 +-- tests/min_mapped_reads.nf.test | 8 +- tests/min_mapped_reads.nf.test.snap | 1844 ++++++++-------- tests/remove_ribo_rna.nf.test | 8 +- tests/remove_ribo_rna.nf.test.snap | 2204 +++++++++---------- tests/salmon.nf.test | 8 +- tests/salmon.nf.test.snap | 456 ++-- tests/skip_qc.nf.test | 8 +- tests/skip_qc.nf.test.snap | 1018 ++++----- tests/skip_trimming.nf.test | 4 +- tests/skip_trimming.nf.test.snap | 1940 ++++++++-------- tests/star_rsem.nf.test | 8 +- tests/star_rsem.nf.test.snap | 2038 ++++++++--------- 21 files changed, 8077 insertions(+), 8077 deletions(-) diff --git a/nf-test.config b/nf-test.config index 2f04d4302..c843dabec 100644 --- a/nf-test.config +++ b/nf-test.config @@ -13,6 +13,6 @@ config { // load the necessary plugins plugins { load "nft-bam@0.3.0" - load "nft-utils@0.0.1" + load "nft-utils@0.0.2" } } diff --git a/tests/default.nf.test b/tests/default.nf.test index 1e5c84d4b..80b19646a 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -23,8 +23,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } @@ -54,8 +54,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index e262b5263..13dccd5f5 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -48,38 +48,38 @@ }, [ "custom", - "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", + "custom/out", + "custom/out/genome_transcriptome.fasta", + "custom/out/genome_transcriptome.gtf", "fastqc", - "raw", - "RAP1_IAA_30M_REP1_raw.html", - "RAP1_IAA_30M_REP1_raw.zip", - "RAP1_UNINDUCED_REP1_raw.html", - "RAP1_UNINDUCED_REP1_raw.zip", - "RAP1_UNINDUCED_REP2_raw.html", - "RAP1_UNINDUCED_REP2_raw.zip", - "WT_REP1_raw.html", - "WT_REP1_raw.zip", - "WT_REP2_raw.html", - "WT_REP2_raw.zip", - "trim", + "fastqc/raw", + "fastqc/raw/RAP1_IAA_30M_REP1_raw.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw.zip", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw.html", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw.html", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip", + "fastqc/raw/WT_REP1_raw.html", + "fastqc/raw/WT_REP1_raw.zip", + "fastqc/raw/WT_REP2_raw.html", + "fastqc/raw/WT_REP2_raw.zip", + "fastqc/trim", "multiqc", - "star_salmon", - "multiqc_data", - "multiqc_plots", - "multiqc_report.html", + "multiqc/star_salmon", + "multiqc/star_salmon/multiqc_data", + "multiqc/star_salmon/multiqc_plots", + "multiqc/star_salmon/multiqc_report.html", "pipeline_info", - "nf_core_rnaseq_software_mqc_versions.yml", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -90,7 +90,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T18:59:55.019534" + "timestamp": "2024-10-02T07:30:25.608093" }, "Params: default": { "content": [ @@ -232,1071 +232,1071 @@ }, [ "bbsplit", - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt", + "bbsplit/RAP1_IAA_30M_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP2.stats.txt", + "bbsplit/WT_REP1.stats.txt", + "bbsplit/WT_REP2.stats.txt", "custom", - "out", - "genome_gfp.fasta", - "genome_gfp.gtf", + "custom/out", + "custom/out/genome_gfp.fasta", + "custom/out/genome_gfp.gtf", "fastqc", - "raw", - "RAP1_IAA_30M_REP1_raw_1_fastqc.html", - "RAP1_IAA_30M_REP1_raw_1_fastqc.zip", - "RAP1_IAA_30M_REP1_raw_2_fastqc.html", - "RAP1_IAA_30M_REP1_raw_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_raw_fastqc.html", - "RAP1_UNINDUCED_REP1_raw_fastqc.zip", - "RAP1_UNINDUCED_REP2_raw_fastqc.html", - "RAP1_UNINDUCED_REP2_raw_fastqc.zip", - "WT_REP1_raw_1_fastqc.html", - "WT_REP1_raw_1_fastqc.zip", - "WT_REP1_raw_2_fastqc.html", - "WT_REP1_raw_2_fastqc.zip", - "WT_REP2_raw_1_fastqc.html", - "WT_REP2_raw_1_fastqc.zip", - "WT_REP2_raw_2_fastqc.html", - "WT_REP2_raw_2_fastqc.zip", - "trim", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", - "WT_REP1_trimmed_1_val_1_fastqc.html", - "WT_REP1_trimmed_1_val_1_fastqc.zip", - "WT_REP1_trimmed_2_val_2_fastqc.html", - "WT_REP1_trimmed_2_val_2_fastqc.zip", - "WT_REP2_trimmed_1_val_1_fastqc.html", - "WT_REP2_trimmed_1_val_1_fastqc.zip", - "WT_REP2_trimmed_2_val_2_fastqc.html", - "WT_REP2_trimmed_2_val_2_fastqc.zip", + "fastqc/raw", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip", + "fastqc/raw/WT_REP1_raw_1_fastqc.html", + "fastqc/raw/WT_REP1_raw_1_fastqc.zip", + "fastqc/raw/WT_REP1_raw_2_fastqc.html", + "fastqc/raw/WT_REP1_raw_2_fastqc.zip", + "fastqc/raw/WT_REP2_raw_1_fastqc.html", + "fastqc/raw/WT_REP2_raw_1_fastqc.zip", + "fastqc/raw/WT_REP2_raw_2_fastqc.html", + "fastqc/raw/WT_REP2_raw_2_fastqc.zip", + "fastqc/trim", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip", "multiqc", - 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"fastqc_sequence_duplication_levels_plot-1.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_sequence_length_distribution_plot.txt", - "fastqc_top_overrepresented_sequences_table-1.txt", - "fastqc_top_overrepresented_sequences_table.txt", - "junction_saturation_known.txt", - "junction_saturation_novel.txt", - "multiqc_citations.txt", - "multiqc_cutadapt.txt", - "multiqc_data.json", - "multiqc_dupradar-section-plot.txt", - "multiqc_fail_strand_check_table.txt", - "multiqc_fastqc_fastqc_raw.txt", - "multiqc_fastqc_fastqc_trimmed.txt", - "multiqc_featurecounts_biotype_plot.txt", - "multiqc_general_stats.txt", - "multiqc_picard_dups.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_salmon_deseq2_clustering-plot.txt", - "multiqc_salmon_deseq2_clustering-plot_1.txt", - "multiqc_salmon_deseq2_clustering-plot_2.txt", - "multiqc_salmon_deseq2_clustering-plot_3.txt", - "multiqc_salmon_deseq2_clustering-plot_4.txt", - "multiqc_salmon_deseq2_pca-plot.txt", - "multiqc_samtools_flagstat.txt", - "multiqc_samtools_idxstats.txt", - "multiqc_samtools_stats.txt", - "multiqc_software_versions.txt", - "multiqc_sources.txt", - "multiqc_star.txt", - "multiqc_star_salmon_deseq2_clustering-plot.txt", - "multiqc_star_salmon_deseq2_clustering-plot_1.txt", - "multiqc_star_salmon_deseq2_clustering-plot_2.txt", - "multiqc_star_salmon_deseq2_clustering-plot_3.txt", - "multiqc_star_salmon_deseq2_clustering-plot_4.txt", - "multiqc_star_salmon_deseq2_pca-plot.txt", - "picard_deduplication.txt", - "picard_histogram.txt", - "picard_histogram_1.txt", - "picard_histogram_2.txt", - "qualimap_gene_coverage_profile_Counts.txt", - "qualimap_gene_coverage_profile_Normalised.txt", - "qualimap_genomic_origin.txt", - "qualimap_rnaseq_cov_hist.txt", - "qualimap_rnaseq_genome_results.txt", - "rseqc_bam_stat.txt", - 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"star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed", + "star_salmon/rseqc/junction_annotation/log", + "star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log", + "star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log", + "star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log", + "star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log", + "star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log", + "star_salmon/rseqc/junction_annotation/pdf", + "star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf", + "star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf", + "star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf", + "star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf", + "star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf", + "star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf", + "star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf", + "star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf", + "star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf", + "star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf", + "star_salmon/rseqc/junction_annotation/rscript", + "star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r", + "star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r", + "star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r", + "star_salmon/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r", + "star_salmon/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r", + "star_salmon/rseqc/junction_annotation/xls", + "star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls", + "star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls", + "star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls", + "star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls", + "star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls", + "star_salmon/rseqc/junction_saturation", + "star_salmon/rseqc/junction_saturation/pdf", + "star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf", + "star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf", + "star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf", + "star_salmon/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf", + "star_salmon/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf", + "star_salmon/rseqc/junction_saturation/rscript", + "star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r", + "star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r", + "star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r", + "star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r", + "star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r", + "star_salmon/rseqc/read_distribution", + "star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt", + "star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt", + "star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt", + "star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt", + "star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt", + "star_salmon/rseqc/read_duplication", + "star_salmon/rseqc/read_duplication/pdf", + "star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/rscript", + "star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls", + "star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds", + "star_salmon/salmon.merged.gene_counts.tsv", + "star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds", + "star_salmon/salmon.merged.gene_counts_length_scaled.tsv", + "star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds", + "star_salmon/salmon.merged.gene_counts_scaled.tsv", + "star_salmon/salmon.merged.gene_lengths.tsv", + "star_salmon/salmon.merged.gene_tpm.tsv", + "star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds", + "star_salmon/salmon.merged.transcript_counts.tsv", + "star_salmon/salmon.merged.transcript_lengths.tsv", + "star_salmon/salmon.merged.transcript_tpm.tsv", + "star_salmon/samtools_stats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.stats", + "star_salmon/stringtie", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf", + "star_salmon/stringtie/WT_REP1.ballgown", + "star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/WT_REP1.coverage.gtf", + "star_salmon/stringtie/WT_REP1.gene.abundance.txt", + "star_salmon/stringtie/WT_REP1.transcripts.gtf", + "star_salmon/stringtie/WT_REP2.ballgown", + "star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab", + "star_salmon/stringtie/WT_REP2.coverage.gtf", + "star_salmon/stringtie/WT_REP2.gene.abundance.txt", + "star_salmon/stringtie/WT_REP2.transcripts.gtf", + "star_salmon/tx2gene.tsv", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -1591,8 +1591,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.08.0" }, - "timestamp": "2024-09-19T18:59:10.651567" + "timestamp": "2024-10-02T08:39:09.000328" } } \ No newline at end of file diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index a05949f84..fcd11c1da 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } @@ -56,8 +56,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 6b66ed182..a74557fc7 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -48,38 +48,38 @@ }, [ "custom", - "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", + "custom/out", + "custom/out/genome_transcriptome.fasta", + "custom/out/genome_transcriptome.gtf", "fastqc", - "raw", - "RAP1_IAA_30M_REP1_raw.html", - "RAP1_IAA_30M_REP1_raw.zip", - "RAP1_UNINDUCED_REP1_raw.html", - "RAP1_UNINDUCED_REP1_raw.zip", - "RAP1_UNINDUCED_REP2_raw.html", - "RAP1_UNINDUCED_REP2_raw.zip", - "WT_REP1_raw.html", - "WT_REP1_raw.zip", - "WT_REP2_raw.html", - "WT_REP2_raw.zip", - "trim", + "fastqc/raw", + "fastqc/raw/RAP1_IAA_30M_REP1_raw.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw.zip", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw.html", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw.html", + 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"WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -90,7 +90,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:07:58.904122" + "timestamp": "2024-10-02T07:38:08.811967" }, "Params: --featurecounts_group_type false": { "content": [ @@ -226,1043 +226,1043 @@ }, [ "bbsplit", - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - 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"star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.stats", + "star_salmon/stringtie", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf", + "star_salmon/stringtie/WT_REP1.ballgown", + "star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/WT_REP1.coverage.gtf", + "star_salmon/stringtie/WT_REP1.gene.abundance.txt", + "star_salmon/stringtie/WT_REP1.transcripts.gtf", + "star_salmon/stringtie/WT_REP2.ballgown", + "star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab", + "star_salmon/stringtie/WT_REP2.coverage.gtf", + "star_salmon/stringtie/WT_REP2.gene.abundance.txt", + "star_salmon/stringtie/WT_REP2.transcripts.gtf", + "star_salmon/tx2gene.tsv", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -1541,6 +1541,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:07:14.922532" + "timestamp": "2024-10-02T07:37:24.538529" } } \ No newline at end of file diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index ff9e4d99d..e743a37d4 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } @@ -56,8 +56,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index e22c96e5c..99ddfa937 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -49,38 +49,38 @@ }, [ "custom", - "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", + "custom/out", + "custom/out/genome_transcriptome.fasta", + "custom/out/genome_transcriptome.gtf", "fastqc", - "raw", - "RAP1_IAA_30M_REP1_raw.html", - "RAP1_IAA_30M_REP1_raw.zip", - "RAP1_UNINDUCED_REP1_raw.html", - "RAP1_UNINDUCED_REP1_raw.zip", - "RAP1_UNINDUCED_REP2_raw.html", - "RAP1_UNINDUCED_REP2_raw.zip", - "WT_REP1_raw.html", - "WT_REP1_raw.zip", - "WT_REP2_raw.html", - "WT_REP2_raw.zip", - "trim", + "fastqc/raw", + "fastqc/raw/RAP1_IAA_30M_REP1_raw.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw.zip", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw.html", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw.html", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip", + "fastqc/raw/WT_REP1_raw.html", + "fastqc/raw/WT_REP1_raw.zip", + "fastqc/raw/WT_REP2_raw.html", + "fastqc/raw/WT_REP2_raw.zip", + "fastqc/trim", "multiqc", - "hisat2", - "multiqc_data", - "multiqc_plots", - "multiqc_report.html", + "multiqc/hisat2", + "multiqc/hisat2/multiqc_data", + "multiqc/hisat2/multiqc_plots", + "multiqc/hisat2/multiqc_report.html", "pipeline_info", - "nf_core_rnaseq_software_mqc_versions.yml", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -91,7 +91,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:13:54.347768" + "timestamp": "2024-10-02T07:43:50.371605" }, "Params: --aligner hisat2": { "content": [ @@ -229,946 +229,946 @@ }, [ "bbsplit", - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt", + "bbsplit/RAP1_IAA_30M_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP2.stats.txt", + "bbsplit/WT_REP1.stats.txt", + "bbsplit/WT_REP2.stats.txt", "custom", - "out", - "genome_gfp.fasta", - "genome_gfp.gtf", + "custom/out", + "custom/out/genome_gfp.fasta", + "custom/out/genome_gfp.gtf", "fastqc", - "raw", - "RAP1_IAA_30M_REP1_raw_1_fastqc.html", - "RAP1_IAA_30M_REP1_raw_1_fastqc.zip", - "RAP1_IAA_30M_REP1_raw_2_fastqc.html", - "RAP1_IAA_30M_REP1_raw_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_raw_fastqc.html", - "RAP1_UNINDUCED_REP1_raw_fastqc.zip", - "RAP1_UNINDUCED_REP2_raw_fastqc.html", - "RAP1_UNINDUCED_REP2_raw_fastqc.zip", - "WT_REP1_raw_1_fastqc.html", - "WT_REP1_raw_1_fastqc.zip", - "WT_REP1_raw_2_fastqc.html", - "WT_REP1_raw_2_fastqc.zip", - "WT_REP2_raw_1_fastqc.html", - "WT_REP2_raw_1_fastqc.zip", - "WT_REP2_raw_2_fastqc.html", - "WT_REP2_raw_2_fastqc.zip", - "trim", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", - "WT_REP1_trimmed_1_val_1_fastqc.html", - "WT_REP1_trimmed_1_val_1_fastqc.zip", - "WT_REP1_trimmed_2_val_2_fastqc.html", - "WT_REP1_trimmed_2_val_2_fastqc.zip", - "WT_REP2_trimmed_1_val_1_fastqc.html", - "WT_REP2_trimmed_1_val_1_fastqc.zip", - "WT_REP2_trimmed_2_val_2_fastqc.html", - "WT_REP2_trimmed_2_val_2_fastqc.zip", + "fastqc/raw", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip", + "fastqc/raw/WT_REP1_raw_1_fastqc.html", + "fastqc/raw/WT_REP1_raw_1_fastqc.zip", + "fastqc/raw/WT_REP1_raw_2_fastqc.html", + "fastqc/raw/WT_REP1_raw_2_fastqc.zip", + "fastqc/raw/WT_REP2_raw_1_fastqc.html", + "fastqc/raw/WT_REP2_raw_1_fastqc.zip", + "fastqc/raw/WT_REP2_raw_2_fastqc.html", + "fastqc/raw/WT_REP2_raw_2_fastqc.zip", + "fastqc/trim", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip", "hisat2", - "RAP1_IAA_30M_REP1.markdup.sorted.bam", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", - "WT_REP1.markdup.sorted.bam", - "WT_REP1.markdup.sorted.bam.bai", - "WT_REP2.markdup.sorted.bam", - "WT_REP2.markdup.sorted.bam.bai", - "bigwig", - "RAP1_IAA_30M_REP1.forward.bigWig", - "RAP1_IAA_30M_REP1.reverse.bigWig", - "RAP1_UNINDUCED_REP1.forward.bigWig", - 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"salmon/RAP1_IAA_30M_REP1/aux_info", + "salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv", + "salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz", + "salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz", + "salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json", + "salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz", + "salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz", + "salmon/RAP1_IAA_30M_REP1/cmd_info.json", + "salmon/RAP1_IAA_30M_REP1/libParams", + "salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt", + "salmon/RAP1_IAA_30M_REP1/lib_format_counts.json", + "salmon/RAP1_IAA_30M_REP1/logs", + "salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log", + "salmon/RAP1_IAA_30M_REP1/quant.genes.sf", + "salmon/RAP1_IAA_30M_REP1/quant.sf", + "salmon/RAP1_UNINDUCED_REP1", + "salmon/RAP1_UNINDUCED_REP1/aux_info", + "salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv", + "salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz", + "salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz", + "salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json", + "salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz", + "salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz", + "salmon/RAP1_UNINDUCED_REP1/cmd_info.json", + "salmon/RAP1_UNINDUCED_REP1/libParams", + "salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt", + "salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json", + "salmon/RAP1_UNINDUCED_REP1/logs", + "salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log", + "salmon/RAP1_UNINDUCED_REP1/quant.genes.sf", + "salmon/RAP1_UNINDUCED_REP1/quant.sf", + "salmon/RAP1_UNINDUCED_REP2", + "salmon/RAP1_UNINDUCED_REP2/aux_info", + "salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv", + "salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz", + "salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz", + "salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json", + "salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz", + "salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz", + "salmon/RAP1_UNINDUCED_REP2/cmd_info.json", + "salmon/RAP1_UNINDUCED_REP2/libParams", + "salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt", + "salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json", + "salmon/RAP1_UNINDUCED_REP2/logs", + "salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log", + "salmon/RAP1_UNINDUCED_REP2/quant.genes.sf", + "salmon/RAP1_UNINDUCED_REP2/quant.sf", + "salmon/WT_REP1", + "salmon/WT_REP1/aux_info", + "salmon/WT_REP1/aux_info/ambig_info.tsv", + "salmon/WT_REP1/aux_info/expected_bias.gz", + "salmon/WT_REP1/aux_info/fld.gz", + "salmon/WT_REP1/aux_info/meta_info.json", + "salmon/WT_REP1/aux_info/observed_bias.gz", + "salmon/WT_REP1/aux_info/observed_bias_3p.gz", + "salmon/WT_REP1/cmd_info.json", + "salmon/WT_REP1/libParams", + "salmon/WT_REP1/libParams/flenDist.txt", + "salmon/WT_REP1/lib_format_counts.json", + "salmon/WT_REP1/logs", + "salmon/WT_REP1/logs/salmon_quant.log", + "salmon/WT_REP1/quant.genes.sf", + "salmon/WT_REP1/quant.sf", + "salmon/WT_REP2", + "salmon/WT_REP2/aux_info", + "salmon/WT_REP2/aux_info/ambig_info.tsv", + "salmon/WT_REP2/aux_info/expected_bias.gz", + "salmon/WT_REP2/aux_info/fld.gz", + "salmon/WT_REP2/aux_info/meta_info.json", + "salmon/WT_REP2/aux_info/observed_bias.gz", + "salmon/WT_REP2/aux_info/observed_bias_3p.gz", + "salmon/WT_REP2/cmd_info.json", + "salmon/WT_REP2/libParams", + "salmon/WT_REP2/libParams/flenDist.txt", + "salmon/WT_REP2/lib_format_counts.json", + "salmon/WT_REP2/logs", + "salmon/WT_REP2/logs/salmon_quant.log", + "salmon/WT_REP2/quant.genes.sf", + "salmon/WT_REP2/quant.sf", + "salmon/deseq2_qc", + "salmon/deseq2_qc/R_sessionInfo.log", + "salmon/deseq2_qc/deseq2.dds.RData", + "salmon/deseq2_qc/deseq2.pca.vals.txt", + "salmon/deseq2_qc/deseq2.plots.pdf", + "salmon/deseq2_qc/deseq2.sample.dists.txt", + "salmon/deseq2_qc/size_factors", + "salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt", + "salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt", + "salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt", + "salmon/deseq2_qc/size_factors/WT_REP1.txt", + "salmon/deseq2_qc/size_factors/WT_REP2.txt", + "salmon/deseq2_qc/size_factors/deseq2.size_factors.RData", + "salmon/salmon.merged.gene_counts.SummarizedExperiment.rds", + "salmon/salmon.merged.gene_counts.tsv", + "salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds", + "salmon/salmon.merged.gene_counts_length_scaled.tsv", + "salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds", + "salmon/salmon.merged.gene_counts_scaled.tsv", + "salmon/salmon.merged.gene_lengths.tsv", + "salmon/salmon.merged.gene_tpm.tsv", + "salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds", + "salmon/salmon.merged.transcript_counts.tsv", + "salmon/salmon.merged.transcript_lengths.tsv", + "salmon/salmon.merged.transcript_tpm.tsv", + "salmon/tx2gene.tsv", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -1439,6 +1439,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:13:07.804677" + "timestamp": "2024-10-02T07:43:07.13584" } } \ No newline at end of file diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index fed4532f8..0c6816a59 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -26,8 +26,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } @@ -60,8 +60,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 1cf20c754..d69ef977c 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -61,170 +61,170 @@ }, [ "bbsplit", - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt", + "bbsplit/RAP1_IAA_30M_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP2.stats.txt", + "bbsplit/WT_REP1.stats.txt", + "bbsplit/WT_REP2.stats.txt", "custom", - "out", - "genome_gfp.fasta", - "genome_gfp.gtf", + "custom/out", + "custom/out/genome_gfp.fasta", + 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"fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip", "kallisto", - "RAP1_IAA_30M_REP1", - "abundance.h5", - "abundance.tsv", - "kallisto_quant.log", - "run_info.json", - "RAP1_UNINDUCED_REP1", - "abundance.h5", - "abundance.tsv", - "kallisto_quant.log", - "run_info.json", - "RAP1_UNINDUCED_REP2", - "abundance.h5", 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"kallisto/RAP1_IAA_30M_REP1/kallisto_quant.log", + "kallisto/RAP1_IAA_30M_REP1/run_info.json", + "kallisto/RAP1_UNINDUCED_REP1", + "kallisto/RAP1_UNINDUCED_REP1/abundance.h5", + "kallisto/RAP1_UNINDUCED_REP1/abundance.tsv", + "kallisto/RAP1_UNINDUCED_REP1/kallisto_quant.log", + "kallisto/RAP1_UNINDUCED_REP1/run_info.json", + "kallisto/RAP1_UNINDUCED_REP2", + "kallisto/RAP1_UNINDUCED_REP2/abundance.h5", + "kallisto/RAP1_UNINDUCED_REP2/abundance.tsv", + "kallisto/RAP1_UNINDUCED_REP2/kallisto_quant.log", + "kallisto/RAP1_UNINDUCED_REP2/run_info.json", + "kallisto/WT_REP1", + "kallisto/WT_REP1/abundance.h5", + "kallisto/WT_REP1/abundance.tsv", + "kallisto/WT_REP1/kallisto_quant.log", + "kallisto/WT_REP1/run_info.json", + "kallisto/WT_REP2", + "kallisto/WT_REP2/abundance.h5", + "kallisto/WT_REP2/abundance.tsv", + "kallisto/WT_REP2/kallisto_quant.log", + "kallisto/WT_REP2/run_info.json", + "kallisto/kallisto.merged.gene_counts.SummarizedExperiment.rds", + 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"multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", + "multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg", + "multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg", + "multiqc/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg", + "multiqc/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/multiqc_report_plots/svg/general_stats_table.svg", + "multiqc/multiqc_report_plots/svg/kallisto_alignment-cnt.svg", + "multiqc/multiqc_report_plots/svg/kallisto_alignment-pct.svg", "pipeline_info", - "nf_core_rnaseq_software_mqc_versions.yml", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -264,7 +264,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:17:00.197522" + "timestamp": "2024-10-02T07:46:44.393695" }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ @@ -310,26 +310,26 @@ }, [ "custom", - "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", + "custom/out", + "custom/out/genome_transcriptome.fasta", + "custom/out/genome_transcriptome.gtf", "fastqc", - "trim", + "fastqc/trim", "multiqc", - "multiqc_data", - "multiqc_plots", - "multiqc_report.html", + "multiqc/multiqc_data", + "multiqc/multiqc_plots", + "multiqc/multiqc_report.html", "pipeline_info", - "nf_core_rnaseq_software_mqc_versions.yml", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -340,6 +340,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:17:38.870034" + "timestamp": "2024-10-02T07:47:31.044439" } } \ No newline at end of file diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index 04a65c99a..7ffef71de 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } @@ -56,8 +56,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 1323e1090..69637a301 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -139,905 +139,905 @@ }, [ "bbsplit", - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt", + "bbsplit/RAP1_IAA_30M_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP2.stats.txt", + "bbsplit/WT_REP1.stats.txt", + "bbsplit/WT_REP2.stats.txt", "custom", - "out", - "genome_gfp.fasta", - "genome_gfp.gtf", + "custom/out", + "custom/out/genome_gfp.fasta", + 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"star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf", + "star_salmon/tx2gene.tsv", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -1275,7 +1275,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:24:21.094029" + "timestamp": "2024-10-02T07:54:27.006271" }, "Params: --min_mapped_reads 90 - stub": { "content": [ @@ -1326,38 +1326,38 @@ }, [ "custom", - "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", + "custom/out", + "custom/out/genome_transcriptome.fasta", + "custom/out/genome_transcriptome.gtf", "fastqc", - "raw", - "RAP1_IAA_30M_REP1_raw.html", - "RAP1_IAA_30M_REP1_raw.zip", - "RAP1_UNINDUCED_REP1_raw.html", - "RAP1_UNINDUCED_REP1_raw.zip", - "RAP1_UNINDUCED_REP2_raw.html", - "RAP1_UNINDUCED_REP2_raw.zip", - "WT_REP1_raw.html", - "WT_REP1_raw.zip", - "WT_REP2_raw.html", - "WT_REP2_raw.zip", - "trim", + "fastqc/raw", + "fastqc/raw/RAP1_IAA_30M_REP1_raw.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw.zip", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw.html", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw.html", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip", + "fastqc/raw/WT_REP1_raw.html", + "fastqc/raw/WT_REP1_raw.zip", + "fastqc/raw/WT_REP2_raw.html", + "fastqc/raw/WT_REP2_raw.zip", + "fastqc/trim", "multiqc", - "star_salmon", - "multiqc_data", - "multiqc_plots", - "multiqc_report.html", + "multiqc/star_salmon", + "multiqc/star_salmon/multiqc_data", + "multiqc/star_salmon/multiqc_plots", + "multiqc/star_salmon/multiqc_report.html", "pipeline_info", - "nf_core_rnaseq_software_mqc_versions.yml", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1368,6 +1368,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:25:05.823677" + "timestamp": "2024-10-02T07:55:19.233936" } } \ No newline at end of file diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index 7d269c5bf..66084a8c9 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } @@ -56,8 +56,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 6e506b035..528163582 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -145,1085 +145,1085 @@ }, [ "bbsplit", - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt", + "bbsplit/RAP1_IAA_30M_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP2.stats.txt", + "bbsplit/WT_REP1.stats.txt", + "bbsplit/WT_REP2.stats.txt", "custom", - "out", - "genome_gfp.fasta", - "genome_gfp.gtf", + "custom/out", + "custom/out/genome_gfp.fasta", + "custom/out/genome_gfp.gtf", "fastqc", - "raw", - "RAP1_IAA_30M_REP1_raw_1_fastqc.html", - "RAP1_IAA_30M_REP1_raw_1_fastqc.zip", - "RAP1_IAA_30M_REP1_raw_2_fastqc.html", - "RAP1_IAA_30M_REP1_raw_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_raw_fastqc.html", - "RAP1_UNINDUCED_REP1_raw_fastqc.zip", - "RAP1_UNINDUCED_REP2_raw_fastqc.html", - "RAP1_UNINDUCED_REP2_raw_fastqc.zip", - "WT_REP1_raw_1_fastqc.html", - "WT_REP1_raw_1_fastqc.zip", - "WT_REP1_raw_2_fastqc.html", - "WT_REP1_raw_2_fastqc.zip", - "WT_REP2_raw_1_fastqc.html", - "WT_REP2_raw_1_fastqc.zip", - "WT_REP2_raw_2_fastqc.html", - "WT_REP2_raw_2_fastqc.zip", - "trim", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", - "WT_REP1_trimmed_1_val_1_fastqc.html", - "WT_REP1_trimmed_1_val_1_fastqc.zip", - "WT_REP1_trimmed_2_val_2_fastqc.html", - "WT_REP1_trimmed_2_val_2_fastqc.zip", - "WT_REP2_trimmed_1_val_1_fastqc.html", - "WT_REP2_trimmed_1_val_1_fastqc.zip", - "WT_REP2_trimmed_2_val_2_fastqc.html", - "WT_REP2_trimmed_2_val_2_fastqc.zip", + "fastqc/raw", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip", + "fastqc/raw/WT_REP1_raw_1_fastqc.html", + "fastqc/raw/WT_REP1_raw_1_fastqc.zip", + "fastqc/raw/WT_REP1_raw_2_fastqc.html", + "fastqc/raw/WT_REP1_raw_2_fastqc.zip", + "fastqc/raw/WT_REP2_raw_1_fastqc.html", + "fastqc/raw/WT_REP2_raw_1_fastqc.zip", + "fastqc/raw/WT_REP2_raw_2_fastqc.html", + "fastqc/raw/WT_REP2_raw_2_fastqc.zip", + "fastqc/trim", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip", "multiqc", - "star_salmon", - "multiqc_report.html", - "multiqc_report_data", - "cutadapt_filtered_reads_plot.txt", - "cutadapt_trimmed_sequences_plot_3_Counts.txt", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "fastqc-status-check-heatmap-1.txt", - "fastqc-status-check-heatmap.txt", - "fastqc_adapter_content_plot.txt", - "fastqc_overrepresented_sequences_plot-1.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot-1.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot-1.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot-1.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot-1.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot-1.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_sequence_length_distribution_plot.txt", - "fastqc_top_overrepresented_sequences_table-1.txt", - "fastqc_top_overrepresented_sequences_table.txt", - "junction_saturation_known.txt", - "junction_saturation_novel.txt", - "multiqc_citations.txt", - "multiqc_cutadapt.txt", - "multiqc_data.json", - "multiqc_dupradar-section-plot.txt", - "multiqc_fail_strand_check_table.txt", - "multiqc_fastqc_fastqc_raw.txt", - "multiqc_fastqc_fastqc_trimmed.txt", - "multiqc_featurecounts_biotype_plot.txt", - "multiqc_general_stats.txt", - "multiqc_picard_dups.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_salmon_deseq2_clustering-plot.txt", - "multiqc_salmon_deseq2_clustering-plot_1.txt", - "multiqc_salmon_deseq2_clustering-plot_2.txt", - "multiqc_salmon_deseq2_clustering-plot_3.txt", - "multiqc_salmon_deseq2_clustering-plot_4.txt", - "multiqc_salmon_deseq2_pca-plot.txt", - "multiqc_samtools_flagstat.txt", - "multiqc_samtools_idxstats.txt", - "multiqc_samtools_stats.txt", - "multiqc_software_versions.txt", - "multiqc_sortmerna.txt", - "multiqc_sources.txt", - "multiqc_star.txt", - "multiqc_star_salmon_deseq2_clustering-plot.txt", - "multiqc_star_salmon_deseq2_clustering-plot_1.txt", - 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"RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -1522,7 +1522,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:36:38.346296" + "timestamp": 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"fastqc/raw/WT_REP2_raw.zip", + "fastqc/trim", "multiqc", - "star_salmon", - "multiqc_data", - "multiqc_plots", - "multiqc_report.html", + "multiqc/star_salmon", + "multiqc/star_salmon/multiqc_data", + "multiqc/star_salmon/multiqc_plots", + "multiqc/star_salmon/multiqc_report.html", "pipeline_info", - "nf_core_rnaseq_software_mqc_versions.yml", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1618,6 +1618,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:37:24.981917" + "timestamp": "2024-10-02T08:08:00.752563" } -} +} \ No newline at end of file diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index 01d7a27fe..c0a386da0 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -26,8 +26,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } @@ -60,8 +60,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 6ec67755a..a66fb0068 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -55,222 +55,222 @@ }, [ "bbsplit", - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt", + "bbsplit/RAP1_IAA_30M_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP2.stats.txt", + "bbsplit/WT_REP1.stats.txt", + "bbsplit/WT_REP2.stats.txt", "custom", - "out", - "genome_gfp.fasta", - "genome_gfp.gtf", + "custom/out", + "custom/out/genome_gfp.fasta", + "custom/out/genome_gfp.gtf", "fastqc", - "trim", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", - "WT_REP1_trimmed_1_val_1_fastqc.html", - "WT_REP1_trimmed_1_val_1_fastqc.zip", - "WT_REP1_trimmed_2_val_2_fastqc.html", - "WT_REP1_trimmed_2_val_2_fastqc.zip", - "WT_REP2_trimmed_1_val_1_fastqc.html", - "WT_REP2_trimmed_1_val_1_fastqc.zip", - "WT_REP2_trimmed_2_val_2_fastqc.html", - "WT_REP2_trimmed_2_val_2_fastqc.zip", + "fastqc/trim", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip", "multiqc", - "multiqc_report.html", - "multiqc_report_data", - "cutadapt_filtered_reads_plot.txt", - "cutadapt_trimmed_sequences_plot_3_Counts.txt", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "fastqc-status-check-heatmap.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_sequence_length_distribution_plot.txt", - "fastqc_top_overrepresented_sequences_table.txt", - "multiqc_citations.txt", - "multiqc_cutadapt.txt", - "multiqc_data.json", - "multiqc_fastqc_fastqc_trimmed.txt", - "multiqc_general_stats.txt", - "multiqc_salmon.txt", - "multiqc_software_versions.txt", - "multiqc_sources.txt", - "salmon_plot.txt", - "multiqc_report_plots", - "pdf", - "cutadapt_filtered_reads_plot-cnt.pdf", - "cutadapt_filtered_reads_plot-pct.pdf", - "cutadapt_trimmed_sequences_plot_3_Counts.pdf", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "fastqc-status-check-heatmap.pdf", - "fastqc_overrepresented_sequences_plot.pdf", - "fastqc_per_base_n_content_plot.pdf", - "fastqc_per_base_sequence_quality_plot.pdf", - "fastqc_per_sequence_gc_content_plot_Counts.pdf", - "fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "fastqc_per_sequence_quality_scores_plot.pdf", - "fastqc_sequence_counts_plot-cnt.pdf", - "fastqc_sequence_counts_plot-pct.pdf", - "fastqc_sequence_duplication_levels_plot.pdf", - "fastqc_sequence_length_distribution_plot.pdf", - "fastqc_top_overrepresented_sequences_table.pdf", - "general_stats_table.pdf", - "salmon_plot.pdf", - "png", - "cutadapt_filtered_reads_plot-cnt.png", - "cutadapt_filtered_reads_plot-pct.png", - "cutadapt_trimmed_sequences_plot_3_Counts.png", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "fastqc-status-check-heatmap.png", - "fastqc_overrepresented_sequences_plot.png", - "fastqc_per_base_n_content_plot.png", - "fastqc_per_base_sequence_quality_plot.png", - "fastqc_per_sequence_gc_content_plot_Counts.png", - "fastqc_per_sequence_gc_content_plot_Percentages.png", - "fastqc_per_sequence_quality_scores_plot.png", - "fastqc_sequence_counts_plot-cnt.png", - "fastqc_sequence_counts_plot-pct.png", - "fastqc_sequence_duplication_levels_plot.png", - "fastqc_sequence_length_distribution_plot.png", - "fastqc_top_overrepresented_sequences_table.png", - "general_stats_table.png", - 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"flenDist.txt", - "lib_format_counts.json", - "logs", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "WT_REP1", - "aux_info", - "ambig_info.tsv", - "expected_bias.gz", - "fld.gz", - "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", - "libParams", - "flenDist.txt", - "lib_format_counts.json", - "logs", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "WT_REP2", - "aux_info", - "ambig_info.tsv", - "expected_bias.gz", - "fld.gz", - "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", - "libParams", - "flenDist.txt", - "lib_format_counts.json", - "logs", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "salmon.merged.gene_counts.SummarizedExperiment.rds", - "salmon.merged.gene_counts.tsv", - "salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds", - "salmon.merged.gene_counts_length_scaled.tsv", - "salmon.merged.gene_counts_scaled.SummarizedExperiment.rds", - "salmon.merged.gene_counts_scaled.tsv", - "salmon.merged.gene_lengths.tsv", - "salmon.merged.gene_tpm.tsv", - "salmon.merged.transcript_counts.SummarizedExperiment.rds", - "salmon.merged.transcript_counts.tsv", - "salmon.merged.transcript_lengths.tsv", - "salmon.merged.transcript_tpm.tsv", - "tx2gene.tsv", + "salmon/RAP1_IAA_30M_REP1", + "salmon/RAP1_IAA_30M_REP1/aux_info", + "salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv", + "salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz", + "salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz", + "salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json", + "salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz", + "salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz", + "salmon/RAP1_IAA_30M_REP1/cmd_info.json", + "salmon/RAP1_IAA_30M_REP1/libParams", + "salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt", + "salmon/RAP1_IAA_30M_REP1/lib_format_counts.json", + "salmon/RAP1_IAA_30M_REP1/logs", + "salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log", + "salmon/RAP1_IAA_30M_REP1/quant.genes.sf", + "salmon/RAP1_IAA_30M_REP1/quant.sf", + "salmon/RAP1_UNINDUCED_REP1", + "salmon/RAP1_UNINDUCED_REP1/aux_info", + "salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv", + "salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz", + "salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz", + "salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json", + "salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz", + "salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz", + "salmon/RAP1_UNINDUCED_REP1/cmd_info.json", + "salmon/RAP1_UNINDUCED_REP1/libParams", + "salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt", + "salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json", + "salmon/RAP1_UNINDUCED_REP1/logs", + "salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log", + "salmon/RAP1_UNINDUCED_REP1/quant.genes.sf", + "salmon/RAP1_UNINDUCED_REP1/quant.sf", + "salmon/RAP1_UNINDUCED_REP2", + "salmon/RAP1_UNINDUCED_REP2/aux_info", + "salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv", + "salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz", + "salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz", + "salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json", + "salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz", + "salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz", + "salmon/RAP1_UNINDUCED_REP2/cmd_info.json", + "salmon/RAP1_UNINDUCED_REP2/libParams", + "salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt", + "salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json", + "salmon/RAP1_UNINDUCED_REP2/logs", + "salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log", + "salmon/RAP1_UNINDUCED_REP2/quant.genes.sf", + "salmon/RAP1_UNINDUCED_REP2/quant.sf", + "salmon/WT_REP1", + "salmon/WT_REP1/aux_info", + "salmon/WT_REP1/aux_info/ambig_info.tsv", + "salmon/WT_REP1/aux_info/expected_bias.gz", + "salmon/WT_REP1/aux_info/fld.gz", + "salmon/WT_REP1/aux_info/meta_info.json", + "salmon/WT_REP1/aux_info/observed_bias.gz", + "salmon/WT_REP1/aux_info/observed_bias_3p.gz", + "salmon/WT_REP1/cmd_info.json", + "salmon/WT_REP1/libParams", + "salmon/WT_REP1/libParams/flenDist.txt", + "salmon/WT_REP1/lib_format_counts.json", + "salmon/WT_REP1/logs", + "salmon/WT_REP1/logs/salmon_quant.log", + "salmon/WT_REP1/quant.genes.sf", + "salmon/WT_REP1/quant.sf", + "salmon/WT_REP2", + "salmon/WT_REP2/aux_info", + "salmon/WT_REP2/aux_info/ambig_info.tsv", + "salmon/WT_REP2/aux_info/expected_bias.gz", + "salmon/WT_REP2/aux_info/fld.gz", + "salmon/WT_REP2/aux_info/meta_info.json", + "salmon/WT_REP2/aux_info/observed_bias.gz", + "salmon/WT_REP2/aux_info/observed_bias_3p.gz", + "salmon/WT_REP2/cmd_info.json", + "salmon/WT_REP2/libParams", + "salmon/WT_REP2/libParams/flenDist.txt", + "salmon/WT_REP2/lib_format_counts.json", + "salmon/WT_REP2/logs", + "salmon/WT_REP2/logs/salmon_quant.log", + "salmon/WT_REP2/quant.genes.sf", + "salmon/WT_REP2/quant.sf", + "salmon/salmon.merged.gene_counts.SummarizedExperiment.rds", + "salmon/salmon.merged.gene_counts.tsv", + "salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds", + "salmon/salmon.merged.gene_counts_length_scaled.tsv", + "salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds", + "salmon/salmon.merged.gene_counts_scaled.tsv", + "salmon/salmon.merged.gene_lengths.tsv", + "salmon/salmon.merged.gene_tpm.tsv", + "salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds", + "salmon/salmon.merged.transcript_counts.tsv", + "salmon/salmon.merged.transcript_lengths.tsv", + "salmon/salmon.merged.transcript_tpm.tsv", + "salmon/tx2gene.tsv", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -340,7 +340,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:40:28.607731" + "timestamp": "2024-10-02T08:10:56.056197" }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ @@ -383,26 +383,26 @@ }, [ "custom", - "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", + "custom/out", + "custom/out/genome_transcriptome.fasta", + "custom/out/genome_transcriptome.gtf", "fastqc", - "trim", + "fastqc/trim", "multiqc", - "multiqc_data", - "multiqc_plots", - "multiqc_report.html", + "multiqc/multiqc_data", + "multiqc/multiqc_plots", + "multiqc/multiqc_report.html", "pipeline_info", - "nf_core_rnaseq_software_mqc_versions.yml", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -413,6 +413,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:41:05.28637" + "timestamp": "2024-10-02T08:11:32.236118" } } \ No newline at end of file diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test index 74e09f92d..3c03631cc 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } @@ -56,8 +56,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 316818792..ff25d5c62 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -45,27 +45,27 @@ }, [ "custom", - "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", + "custom/out", + "custom/out/genome_transcriptome.fasta", + "custom/out/genome_transcriptome.gtf", "fastqc", - "trim", + "fastqc/trim", "multiqc", - "star_salmon", - "multiqc_data", - "multiqc_plots", - "multiqc_report.html", + "multiqc/star_salmon", + "multiqc/star_salmon/multiqc_data", + "multiqc/star_salmon/multiqc_plots", + "multiqc/star_salmon/multiqc_report.html", "pipeline_info", - "nf_core_rnaseq_software_mqc_versions.yml", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -76,7 +76,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:47:43.501368" + "timestamp": "2024-10-02T08:17:45.954114" }, "Params: --skip_qc": { "content": [ @@ -174,503 +174,503 @@ }, [ "bbsplit", - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt", + "bbsplit/RAP1_IAA_30M_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP2.stats.txt", + "bbsplit/WT_REP1.stats.txt", + "bbsplit/WT_REP2.stats.txt", "custom", - "out", - "genome_gfp.fasta", - "genome_gfp.gtf", + "custom/out", + "custom/out/genome_gfp.fasta", + "custom/out/genome_gfp.gtf", "fastqc", - "trim", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", - "WT_REP1_trimmed_1_val_1_fastqc.html", - "WT_REP1_trimmed_1_val_1_fastqc.zip", - "WT_REP1_trimmed_2_val_2_fastqc.html", - "WT_REP1_trimmed_2_val_2_fastqc.zip", - "WT_REP2_trimmed_1_val_1_fastqc.html", - "WT_REP2_trimmed_1_val_1_fastqc.zip", - "WT_REP2_trimmed_2_val_2_fastqc.html", - "WT_REP2_trimmed_2_val_2_fastqc.zip", + "fastqc/trim", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip", "multiqc", - "star_salmon", - "multiqc_report.html", - "multiqc_report_data", - "cutadapt_filtered_reads_plot.txt", - "cutadapt_trimmed_sequences_plot_3_Counts.txt", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "fastqc-status-check-heatmap.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_sequence_length_distribution_plot.txt", - "fastqc_top_overrepresented_sequences_table.txt", - "multiqc_citations.txt", - "multiqc_cutadapt.txt", - "multiqc_data.json", - "multiqc_fastqc_fastqc_trimmed.txt", - "multiqc_general_stats.txt", - "multiqc_picard_dups.txt", - "multiqc_salmon.txt", - "multiqc_samtools_flagstat.txt", - "multiqc_samtools_idxstats.txt", - "multiqc_samtools_stats.txt", - "multiqc_software_versions.txt", - "multiqc_sources.txt", - "multiqc_star.txt", - "picard_deduplication.txt", - "picard_histogram.txt", - "picard_histogram_1.txt", - "picard_histogram_2.txt", - "salmon_plot.txt", - "samtools-flagstat-dp_Percentage_of_total.txt", - "samtools-flagstat-dp_Read_counts.txt", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", - "samtools-stats-dp.txt", - "samtools_alignment_plot.txt", - "star_alignment_plot.txt", - "star_summary_table.txt", - "multiqc_report_plots", - "pdf", - "cutadapt_filtered_reads_plot-cnt.pdf", - "cutadapt_filtered_reads_plot-pct.pdf", - "cutadapt_trimmed_sequences_plot_3_Counts.pdf", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "fastqc-status-check-heatmap.pdf", - "fastqc_overrepresented_sequences_plot.pdf", - "fastqc_per_base_n_content_plot.pdf", - "fastqc_per_base_sequence_quality_plot.pdf", - "fastqc_per_sequence_gc_content_plot_Counts.pdf", - "fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "fastqc_per_sequence_quality_scores_plot.pdf", - "fastqc_sequence_counts_plot-cnt.pdf", - "fastqc_sequence_counts_plot-pct.pdf", - "fastqc_sequence_duplication_levels_plot.pdf", - "fastqc_sequence_length_distribution_plot.pdf", - "fastqc_top_overrepresented_sequences_table.pdf", - "general_stats_table.pdf", - "picard_deduplication-cnt.pdf", - "picard_deduplication-pct.pdf", - "salmon_plot.pdf", - "samtools-flagstat-dp_Percentage_of_total.pdf", - "samtools-flagstat-dp_Read_counts.pdf", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf", - 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+ "star_salmon/WT_REP1/aux_info", + "star_salmon/WT_REP1/aux_info/ambig_info.tsv", + "star_salmon/WT_REP1/aux_info/expected_bias.gz", + "star_salmon/WT_REP1/aux_info/fld.gz", + "star_salmon/WT_REP1/aux_info/meta_info.json", + "star_salmon/WT_REP1/aux_info/observed_bias.gz", + "star_salmon/WT_REP1/aux_info/observed_bias_3p.gz", + "star_salmon/WT_REP1/cmd_info.json", + "star_salmon/WT_REP1/libParams", + "star_salmon/WT_REP1/libParams/flenDist.txt", + "star_salmon/WT_REP1/logs", + "star_salmon/WT_REP1/logs/salmon_quant.log", + "star_salmon/WT_REP1/quant.genes.sf", + "star_salmon/WT_REP1/quant.sf", + "star_salmon/WT_REP2", + "star_salmon/WT_REP2.markdup.sorted.bam", + "star_salmon/WT_REP2.markdup.sorted.bam.bai", + "star_salmon/WT_REP2/aux_info", + "star_salmon/WT_REP2/aux_info/ambig_info.tsv", + "star_salmon/WT_REP2/aux_info/expected_bias.gz", + "star_salmon/WT_REP2/aux_info/fld.gz", + "star_salmon/WT_REP2/aux_info/meta_info.json", + "star_salmon/WT_REP2/aux_info/observed_bias.gz", + "star_salmon/WT_REP2/aux_info/observed_bias_3p.gz", + "star_salmon/WT_REP2/cmd_info.json", + "star_salmon/WT_REP2/libParams", + "star_salmon/WT_REP2/libParams/flenDist.txt", + "star_salmon/WT_REP2/logs", + "star_salmon/WT_REP2/logs/salmon_quant.log", + "star_salmon/WT_REP2/quant.genes.sf", + "star_salmon/WT_REP2/quant.sf", + "star_salmon/bigwig", + "star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig", + "star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig", + "star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig", + "star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig", + "star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig", + "star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig", + "star_salmon/bigwig/WT_REP1.forward.bigWig", + "star_salmon/bigwig/WT_REP1.reverse.bigWig", + "star_salmon/bigwig/WT_REP2.forward.bigWig", + "star_salmon/bigwig/WT_REP2.reverse.bigWig", + "star_salmon/log", + "star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out", + "star_salmon/log/RAP1_IAA_30M_REP1.Log.out", + "star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out", + "star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab", + "star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out", + "star_salmon/log/RAP1_UNINDUCED_REP1.Log.out", + "star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out", + "star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab", + "star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out", + "star_salmon/log/RAP1_UNINDUCED_REP2.Log.out", + "star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out", + "star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab", + "star_salmon/log/WT_REP1.Log.final.out", + "star_salmon/log/WT_REP1.Log.out", + "star_salmon/log/WT_REP1.Log.progress.out", + "star_salmon/log/WT_REP1.SJ.out.tab", + "star_salmon/log/WT_REP2.Log.final.out", + "star_salmon/log/WT_REP2.Log.out", + "star_salmon/log/WT_REP2.Log.progress.out", + "star_salmon/log/WT_REP2.SJ.out.tab", + "star_salmon/picard_metrics", + "star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", + "star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", + "star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt", + "star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt", + "star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt", + "star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds", + "star_salmon/salmon.merged.gene_counts.tsv", + "star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds", + "star_salmon/salmon.merged.gene_counts_length_scaled.tsv", + "star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds", + "star_salmon/salmon.merged.gene_counts_scaled.tsv", + "star_salmon/salmon.merged.gene_lengths.tsv", + "star_salmon/salmon.merged.gene_tpm.tsv", + "star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds", + "star_salmon/salmon.merged.transcript_counts.tsv", + "star_salmon/salmon.merged.transcript_lengths.tsv", + "star_salmon/salmon.merged.transcript_tpm.tsv", + "star_salmon/samtools_stats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.stats", + "star_salmon/stringtie", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf", + "star_salmon/stringtie/WT_REP1.ballgown", + "star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/WT_REP1.coverage.gtf", + "star_salmon/stringtie/WT_REP1.gene.abundance.txt", + "star_salmon/stringtie/WT_REP1.transcripts.gtf", + "star_salmon/stringtie/WT_REP2.ballgown", + "star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab", + "star_salmon/stringtie/WT_REP2.coverage.gtf", + "star_salmon/stringtie/WT_REP2.gene.abundance.txt", + "star_salmon/stringtie/WT_REP2.transcripts.gtf", + "star_salmon/tx2gene.tsv", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -804,6 +804,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:46:49.794228" + "timestamp": "2024-10-02T08:17:03.577873" } } \ No newline at end of file diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index b7600628f..5053e103f 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 8591548f9..bbdcc5a51 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -135,981 +135,981 @@ }, [ "bbsplit", - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt", + "bbsplit/RAP1_IAA_30M_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP2.stats.txt", + "bbsplit/WT_REP1.stats.txt", + "bbsplit/WT_REP2.stats.txt", "custom", - "out", - "genome_gfp.fasta", - "genome_gfp.gtf", + "custom/out", + "custom/out/genome_gfp.fasta", + "custom/out/genome_gfp.gtf", "fastqc", - "raw", - "RAP1_IAA_30M_REP1_raw_1_fastqc.html", - "RAP1_IAA_30M_REP1_raw_1_fastqc.zip", - "RAP1_IAA_30M_REP1_raw_2_fastqc.html", - "RAP1_IAA_30M_REP1_raw_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_raw_fastqc.html", - "RAP1_UNINDUCED_REP1_raw_fastqc.zip", - "RAP1_UNINDUCED_REP2_raw_fastqc.html", - "RAP1_UNINDUCED_REP2_raw_fastqc.zip", - "WT_REP1_raw_1_fastqc.html", - "WT_REP1_raw_1_fastqc.zip", - "WT_REP1_raw_2_fastqc.html", - "WT_REP1_raw_2_fastqc.zip", - "WT_REP2_raw_1_fastqc.html", - "WT_REP2_raw_1_fastqc.zip", - "WT_REP2_raw_2_fastqc.html", - "WT_REP2_raw_2_fastqc.zip", + "fastqc/raw", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip", + "fastqc/raw/WT_REP1_raw_1_fastqc.html", + "fastqc/raw/WT_REP1_raw_1_fastqc.zip", + "fastqc/raw/WT_REP1_raw_2_fastqc.html", + "fastqc/raw/WT_REP1_raw_2_fastqc.zip", + "fastqc/raw/WT_REP2_raw_1_fastqc.html", + "fastqc/raw/WT_REP2_raw_1_fastqc.zip", + "fastqc/raw/WT_REP2_raw_2_fastqc.html", + "fastqc/raw/WT_REP2_raw_2_fastqc.zip", "multiqc", - "star_salmon", - "multiqc_report.html", - "multiqc_report_data", - "fastqc-status-check-heatmap.txt", - "fastqc_adapter_content_plot.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_top_overrepresented_sequences_table.txt", - "junction_saturation_known.txt", - "junction_saturation_novel.txt", - "multiqc_citations.txt", - "multiqc_data.json", - "multiqc_dupradar-section-plot.txt", - "multiqc_fail_strand_check_table.txt", - "multiqc_fastqc_fastqc_raw.txt", - "multiqc_featurecounts_biotype_plot.txt", - "multiqc_general_stats.txt", - "multiqc_picard_dups.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_salmon_deseq2_clustering-plot.txt", - "multiqc_salmon_deseq2_clustering-plot_1.txt", - "multiqc_salmon_deseq2_clustering-plot_2.txt", - "multiqc_salmon_deseq2_clustering-plot_3.txt", - "multiqc_salmon_deseq2_clustering-plot_4.txt", - "multiqc_salmon_deseq2_pca-plot.txt", - "multiqc_samtools_flagstat.txt", - "multiqc_samtools_idxstats.txt", - "multiqc_samtools_stats.txt", - "multiqc_software_versions.txt", - "multiqc_sources.txt", - "multiqc_star.txt", - "multiqc_star_salmon_deseq2_clustering-plot.txt", - "multiqc_star_salmon_deseq2_clustering-plot_1.txt", - "multiqc_star_salmon_deseq2_clustering-plot_2.txt", - "multiqc_star_salmon_deseq2_clustering-plot_3.txt", - "multiqc_star_salmon_deseq2_clustering-plot_4.txt", - "multiqc_star_salmon_deseq2_pca-plot.txt", - "picard_deduplication.txt", - "picard_histogram.txt", - "picard_histogram_1.txt", - "picard_histogram_2.txt", - "qualimap_gene_coverage_profile_Counts.txt", - "qualimap_gene_coverage_profile_Normalised.txt", - "qualimap_genomic_origin.txt", - "qualimap_rnaseq_cov_hist.txt", - "qualimap_rnaseq_genome_results.txt", - "rseqc_bam_stat.txt", - "rseqc_infer_experiment_plot.txt", - "rseqc_inner_distance.txt", - "rseqc_inner_distance_plot_Counts.txt", - "rseqc_inner_distance_plot_Percentages.txt", - "rseqc_junction_annotation_junctions_plot_Events.txt", - "rseqc_junction_annotation_junctions_plot_Junctions.txt", - "rseqc_junction_saturation_all.txt", - "rseqc_junction_saturation_plot_All_Junctions.txt", - "rseqc_junction_saturation_plot_Known_Junctions.txt", - "rseqc_junction_saturation_plot_Novel_Junctions.txt", - 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"star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt", + "star_salmon/rseqc/read_duplication", + "star_salmon/rseqc/read_duplication/pdf", + "star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/rscript", + "star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls", + "star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds", + "star_salmon/salmon.merged.gene_counts.tsv", + "star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds", + "star_salmon/salmon.merged.gene_counts_length_scaled.tsv", + "star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds", + "star_salmon/salmon.merged.gene_counts_scaled.tsv", + "star_salmon/salmon.merged.gene_lengths.tsv", + "star_salmon/salmon.merged.gene_tpm.tsv", + "star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds", + "star_salmon/salmon.merged.transcript_counts.tsv", + "star_salmon/salmon.merged.transcript_lengths.tsv", + "star_salmon/salmon.merged.transcript_tpm.tsv", + "star_salmon/samtools_stats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.stats", + "star_salmon/stringtie", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf", + "star_salmon/stringtie/WT_REP1.ballgown", + "star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/WT_REP1.coverage.gtf", + "star_salmon/stringtie/WT_REP1.gene.abundance.txt", + "star_salmon/stringtie/WT_REP1.transcripts.gtf", + "star_salmon/stringtie/WT_REP2.ballgown", + "star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab", + "star_salmon/stringtie/WT_REP2.coverage.gtf", + "star_salmon/stringtie/WT_REP2.gene.abundance.txt", + "star_salmon/stringtie/WT_REP2.transcripts.gtf", + "star_salmon/tx2gene.tsv" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -1379,6 +1379,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:54:39.111945" + "timestamp": "2024-10-02T08:24:30.328195" } } \ No newline at end of file diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index 6e5e60425..268a1fabb 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } @@ -56,8 +56,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index c9881f337..b4e4f981b 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -139,1002 +139,1002 @@ }, [ "bbsplit", - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt", + "bbsplit/RAP1_IAA_30M_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP2.stats.txt", + "bbsplit/WT_REP1.stats.txt", + "bbsplit/WT_REP2.stats.txt", "custom", - "out", - "genome_gfp.fasta", - "genome_gfp.gtf", + "custom/out", + "custom/out/genome_gfp.fasta", + "custom/out/genome_gfp.gtf", "fastqc", - "raw", - "RAP1_IAA_30M_REP1_raw_1_fastqc.html", - "RAP1_IAA_30M_REP1_raw_1_fastqc.zip", - "RAP1_IAA_30M_REP1_raw_2_fastqc.html", - "RAP1_IAA_30M_REP1_raw_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_raw_fastqc.html", - "RAP1_UNINDUCED_REP1_raw_fastqc.zip", - "RAP1_UNINDUCED_REP2_raw_fastqc.html", - "RAP1_UNINDUCED_REP2_raw_fastqc.zip", - "WT_REP1_raw_1_fastqc.html", - "WT_REP1_raw_1_fastqc.zip", - "WT_REP1_raw_2_fastqc.html", - "WT_REP1_raw_2_fastqc.zip", - "WT_REP2_raw_1_fastqc.html", - "WT_REP2_raw_1_fastqc.zip", - "WT_REP2_raw_2_fastqc.html", - "WT_REP2_raw_2_fastqc.zip", - "trim", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", - "WT_REP1_trimmed_1_val_1_fastqc.html", - "WT_REP1_trimmed_1_val_1_fastqc.zip", - "WT_REP1_trimmed_2_val_2_fastqc.html", - "WT_REP1_trimmed_2_val_2_fastqc.zip", - "WT_REP2_trimmed_1_val_1_fastqc.html", - "WT_REP2_trimmed_1_val_1_fastqc.zip", - "WT_REP2_trimmed_2_val_2_fastqc.html", - "WT_REP2_trimmed_2_val_2_fastqc.zip", + "fastqc/raw", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip", + "fastqc/raw/WT_REP1_raw_1_fastqc.html", + "fastqc/raw/WT_REP1_raw_1_fastqc.zip", + "fastqc/raw/WT_REP1_raw_2_fastqc.html", + "fastqc/raw/WT_REP1_raw_2_fastqc.zip", + "fastqc/raw/WT_REP2_raw_1_fastqc.html", + "fastqc/raw/WT_REP2_raw_1_fastqc.zip", + "fastqc/raw/WT_REP2_raw_2_fastqc.html", + "fastqc/raw/WT_REP2_raw_2_fastqc.zip", + "fastqc/trim", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip", "multiqc", - "star_rsem", - "multiqc_report.html", - "multiqc_report_data", - "cutadapt_filtered_reads_plot.txt", - "cutadapt_trimmed_sequences_plot_3_Counts.txt", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "fastqc-status-check-heatmap-1.txt", - "fastqc-status-check-heatmap.txt", - "fastqc_adapter_content_plot.txt", - "fastqc_overrepresented_sequences_plot-1.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot-1.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot-1.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot-1.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot-1.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot-1.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_sequence_length_distribution_plot.txt", - "fastqc_top_overrepresented_sequences_table-1.txt", - "fastqc_top_overrepresented_sequences_table.txt", 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