Snapshot all files (content or file name when not stable)

CHANGELOG.md

@@ -115,6 +115,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1357](https://github.com/nf-core/rnaseq/pull/1357) - Fix anchor issue in multiqc
 - [PR #1358](https://github.com/nf-core/rnaseq/pull/1358) - Update test profiles to restore a static URI for megatests
 - [PR #1359](https://github.com/nf-core/rnaseq/pull/1359) - Update MultiQC and revert unnecessary workaround
+- [PR #1360](https://github.com/nf-core/rnaseq/pull/1360) - More complete snapshots for pipeline level tests
 - [PR #1361](https://github.com/nf-core/rnaseq/pull/1361) - Animate subway map
 - [PR #1362](https://github.com/nf-core/rnaseq/pull/1362) - Move multiqc module prefix for nf-test to module
 

tests/kallisto.nf.test.snap

@@ -0,0 +1,241 @@
+{
+    "multiqc_data": {
+        "content": [
+            "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1",
+            "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f",
+            "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c",
+            "fastqc-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
+            "fastqc_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
+            "fastqc_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e",
+            "fastqc_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
+            "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
+            "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
+            "fastqc_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
+            "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c",
+            "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
+            "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
+            "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee",
+            "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
+            "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
+            "fastqc_top_overrepresented_sequences_table.txt",
+            "kallisto_alignment.txt",
+            "multiqc_data.json",
+            "multiqc_general_stats.txt",
+            "multiqc_kallisto.txt",
+            "multiqc_software_versions.txt",
+            "multiqc_sources.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:53:37.272547"
+    },
+    "trimgalore": {
+        "content": [
+            "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"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:35:31.545385"
+    },
+    "kallisto": {
+        "content": [
+            "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
+            "abundance.h5",
+            "abundance.tsv",
+            "kallisto_quant.log",
+            "run_info.json",
+            "abundance.h5",
+            "abundance.tsv",
+            "kallisto_quant.log",
+            "run_info.json",
+            "abundance.h5",
+            "abundance.tsv",
+            "kallisto_quant.log",
+            "run_info.json",
+            "abundance.h5",
+            "abundance.tsv",
+            "kallisto_quant.log",
+            "run_info.json",
+            "abundance.h5",
+            "abundance.tsv",
+            "kallisto_quant.log",
+            "run_info.json",
+            "kallisto.merged.gene_counts.SummarizedExperiment.rds",
+            "kallisto.merged.gene_counts.tsv",
+            "kallisto.merged.gene_counts_length_scaled.SummarizedExperiment.rds",
+            "kallisto.merged.gene_counts_length_scaled.tsv",
+            "kallisto.merged.gene_counts_scaled.SummarizedExperiment.rds",
+            "kallisto.merged.gene_counts_scaled.tsv",
+            "kallisto.merged.gene_lengths.tsv",
+            "kallisto.merged.gene_tpm.tsv",
+            "kallisto.merged.transcript_counts.SummarizedExperiment.rds",
+            "kallisto.merged.transcript_counts.tsv",
+            "kallisto.merged.transcript_lengths.tsv",
+            "kallisto.merged.transcript_tpm.tsv"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:53:37.166056"
+    },
+    "references": {
+        "content": [
+            "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
+            "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:25:12.683541"
+    },
+    "versions": {
+        "content": [
+            "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, KALLISTO_QUANT={kallisto=0.48.0}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:35:31.742801"
+    },
+    "fastqc/trim": {
+        "content": [
+            "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"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:25:12.695474"
+    },
+    "multiqc_plots": {
+        "content": [
+            "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2",
+            "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0",
+            "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50",
+            "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787",
+            "fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890",
+            "fastqc_overrepresented_sequences_plot.png:md5,40e450251b80ec0efc9364434234ec7f",
+            "fastqc_per_sequence_gc_content_plot_Counts.png:md5,8a806cec2142f9911502e0a253d83d13",
+            "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,953929d50c8490029880e205e4db7959",
+            "fastqc_per_sequence_quality_scores_plot.png:md5,d2c29cae169f35744500c751b4a7366e",
+            "fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8",
+            "fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0",
+            "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754",
+            "multiqc_report.html",
+            "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",
+            "kallisto_alignment-cnt.pdf",
+            "kallisto_alignment-pct.pdf",
+            "fastqc_per_base_n_content_plot.png",
+            "fastqc_per_base_sequence_quality_plot.png",
+            "fastqc_sequence_length_distribution_plot.png",
+            "fastqc_top_overrepresented_sequences_table.png",
+            "general_stats_table.png",
+            "kallisto_alignment-cnt.png",
+            "kallisto_alignment-pct.png",
+            "cutadapt_filtered_reads_plot-cnt.svg",
+            "cutadapt_filtered_reads_plot-pct.svg",
+            "cutadapt_trimmed_sequences_plot_3_Counts.svg",
+            "cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
+            "fastqc-status-check-heatmap.svg",
+            "fastqc_overrepresented_sequences_plot.svg",
+            "fastqc_per_base_n_content_plot.svg",
+            "fastqc_per_base_sequence_quality_plot.svg",
+            "fastqc_per_sequence_gc_content_plot_Counts.svg",
+            "fastqc_per_sequence_gc_content_plot_Percentages.svg",
+            "fastqc_per_sequence_quality_scores_plot.svg",
+            "fastqc_sequence_counts_plot-cnt.svg",
+            "fastqc_sequence_counts_plot-pct.svg",
+            "fastqc_sequence_duplication_levels_plot.svg",
+            "fastqc_sequence_length_distribution_plot.svg",
+            "fastqc_top_overrepresented_sequences_table.svg",
+            "general_stats_table.svg",
+            "kallisto_alignment-cnt.svg",
+            "kallisto_alignment-pct.svg"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:53:37.413284"
+    },
+    "bbsplit": {
+        "content": [
+            "RAP1_IAA_30M_REP1.stats.txt",
+            "RAP1_UNINDUCED_REP1.stats.txt",
+            "RAP1_UNINDUCED_REP2.stats.txt",
+            "WT_REP1.stats.txt",
+            "WT_REP2.stats.txt"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:25:12.672876"
+    },
+    "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": {
+        "content": [
+            "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}",
+            "genome_transcriptome.fasta",
+            "genome_transcriptome.gtf",
+            "multiqc_report.html",
+            "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"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T15:36:19.174739"
+    }
+}