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@maxulysse
maxulysse committed Sep 18, 2024
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28 changes: 14 additions & 14 deletions tests/hisat2.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -717,6 +717,10 @@
"fastqc_top_overrepresented_sequences_table-1.png",
"fastqc_top_overrepresented_sequences_table.png",
"general_stats_table.png",
"hisat2_pe_plot-cnt.png",
"hisat2_pe_plot-pct.png",
"hisat2_se_plot-cnt.png",
"hisat2_se_plot-pct.png",
"picard_deduplication-cnt.png",
"picard_deduplication-pct.png",
"qualimap_genomic_origin-cnt.png",
Expand Down Expand Up @@ -775,6 +779,10 @@
"featurecounts_biotype_plot-cnt.svg",
"featurecounts_biotype_plot-pct.svg",
"general_stats_table.svg",
"hisat2_pe_plot-cnt.svg",
"hisat2_pe_plot-pct.svg",
"hisat2_se_plot-cnt.svg",
"hisat2_se_plot-pct.svg",
"picard_deduplication-cnt.svg",
"picard_deduplication-pct.svg",
"qualimap_gene_coverage_profile_Counts.svg",
Expand Down Expand Up @@ -928,7 +936,7 @@
"RAP1_UNINDUCED_REP1.hisat2.summary.log:md5,e322e4f7bce12d889a59db517c2ad678",
"RAP1_UNINDUCED_REP2.hisat2.summary.log:md5,3f41605b1fbd4d40983915617f8a91f9",
"WT_REP1.hisat2.summary.log:md5,50cd2a4fe1f041774c572d09156d4ae8",
"WT_REP2.hisat2.summary.log:md5,e622496abff3ce68afcd1c21a7a1e0df",
"WT_REP2.hisat2.summary.log:md5,5c0d00bfee4ff563521f6458a13f9476",
"bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
"bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
"comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
Expand Down Expand Up @@ -1094,10 +1102,10 @@
"samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
"samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3625f666cc09d0f07990716aeccd869f",
"samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,6c323b383a6506d124506405b9463d93",
"hisat2_pe_plot-cnt.pdf:md5,5ea21b11336a653206216b189619615d",
"hisat2_pe_plot-pct.pdf:md5,97920acd4cd0ef6c347d1e5196378316",
"hisat2_se_plot-cnt.pdf:md5,162ad273b806726ee519dd85a0ee5521",
"hisat2_se_plot-pct.pdf:md5,6fad42a1c9973d5315bfa6895ef0b8a0",
"hisat2_pe_plot-cnt.pdf:md5,ec0f89f703d3ee1c1d7c59fe712d6467",
"hisat2_pe_plot-pct.pdf:md5,75522edf01667236474caa26c40c4e82",
"hisat2_se_plot-cnt.pdf:md5,15692ca0b4144b4c97094178dcdb39de",
"hisat2_se_plot-pct.pdf:md5,f56040af7a091869364ed1dc8853bc31",
"cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50",
"cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787",
"dupradar-section-plot.png:md5,6074ea2315d296094bd10fad3dcc475b",
Expand All @@ -1119,10 +1127,6 @@
"fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780",
"featurecounts_biotype_plot-cnt.png:md5,138e00d2fe0af27f2979cf7bdff83b46",
"featurecounts_biotype_plot-pct.png:md5,3b7550efe9068f3ada2cc64e311f3338",
"hisat2_pe_plot-cnt.png:md5,1e0841cb32f6aaad84772ff2267b70ad",
"hisat2_pe_plot-pct.png:md5,e201931cd7b31e7227a6273ca1587f56",
"hisat2_se_plot-cnt.png:md5,840937eb5952fa98987a1d2aa8267959",
"hisat2_se_plot-pct.png:md5,51bb5f9ba36dab1ba32fc4e273e865a9",
"qualimap_gene_coverage_profile_Counts.png:md5,1aa39028b017760d0b09f1b6f8c1fa3a",
"qualimap_gene_coverage_profile_Normalised.png:md5,1cd382a79b89564a006afe431aa3916d",
"rseqc_infer_experiment_plot.png:md5,73f5b860029912da9c3f6a887238d251",
Expand All @@ -1133,10 +1137,6 @@
"samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,3bb99f72a15a4159860008beea8c802b",
"samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,25015f9be4710c4eccc50f30db3bf521",
"samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,baa90f5ad4d999fc60db30840b72d8c6",
"hisat2_pe_plot-cnt.svg:md5,dae72c87e9e5892ebc1ed5937b737d66",
"hisat2_pe_plot-pct.svg:md5,37d72b7dfc24210dd4f8322f2bb7c801",
"hisat2_se_plot-cnt.svg:md5,785d8da961280cfcd6562bb8b1f8b682",
"hisat2_se_plot-pct.svg:md5,ae694bcf0d5019a534517583507aaaa9",
"ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401",
"expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
"observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
Expand Down Expand Up @@ -1175,6 +1175,6 @@
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-17T18:44:49.645101"
"timestamp": "2024-09-18T12:56:26.579349"
}
}
36 changes: 18 additions & 18 deletions tests/kallisto.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -89,18 +89,28 @@
"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",
"abundance.tsv",
"kallisto_quant.log",
"run_info.json",
"WT_REP1",
"abundance.h5",
"abundance.tsv",
"kallisto_quant.log",
"run_info.json",
"WT_REP2",
"abundance.h5",
"abundance.tsv",
"kallisto_quant.log",
"run_info.json",
"kallisto.merged.gene_counts.SummarizedExperiment.rds",
"kallisto.merged.gene_counts.tsv",
Expand Down Expand Up @@ -143,6 +153,8 @@
"fastqc_sequence_length_distribution_plot.pdf",
"fastqc_top_overrepresented_sequences_table.pdf",
"general_stats_table.pdf",
"kallisto_alignment-cnt.pdf",
"kallisto_alignment-pct.pdf",
"png",
"cutadapt_filtered_reads_plot-cnt.png",
"cutadapt_filtered_reads_plot-pct.png",
Expand All @@ -151,6 +163,8 @@
"fastqc_sequence_length_distribution_plot.png",
"fastqc_top_overrepresented_sequences_table.png",
"general_stats_table.png",
"kallisto_alignment-cnt.png",
"kallisto_alignment-pct.png",
"svg",
"cutadapt_filtered_reads_plot-cnt.svg",
"cutadapt_filtered_reads_plot-pct.svg",
Expand All @@ -169,6 +183,8 @@
"fastqc_sequence_length_distribution_plot.svg",
"fastqc_top_overrepresented_sequences_table.svg",
"general_stats_table.svg",
"kallisto_alignment-cnt.svg",
"kallisto_alignment-pct.svg",
"pipeline_info",
"nf_core_rnaseq_software_mqc_versions.yml",
"trimgalore",
Expand All @@ -184,16 +200,6 @@
[
"genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
"genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28",
"abundance.tsv:md5,b6ae4ef44f718a789f58dc6451b6eebb",
"kallisto_quant.log:md5,88a4a4c71762af549f1c42308fe80605",
"abundance.tsv:md5,a2c6108c384662f4da8c7b7fe8f27e02",
"kallisto_quant.log:md5,b9c4528ce7c00f5f94e7570507d00a51",
"abundance.tsv:md5,6fd77021287360f5005c90807233ab23",
"kallisto_quant.log:md5,8a9605e9d228c9cbec97b0883d909754",
"abundance.tsv:md5,7b62c5df0930e9f5ebc6e90d6aa600f6",
"kallisto_quant.log:md5,5a7f563172800853c627e8e4f5da6bdc",
"abundance.tsv:md5,6fb211dc8e4fd238ca68d21d6cc83cf5",
"kallisto_quant.log:md5,3447f945ddb20a8eca8aef31b088b8d5",
"tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
"cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1",
"cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f",
Expand All @@ -211,8 +217,6 @@
"multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee",
"multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
"multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
"kallisto_alignment-cnt.pdf:md5,a2aa89be43ff1264be51860419219648",
"kallisto_alignment-pct.pdf:md5,41ac1dcf4b41baa598368783eadd92ab",
"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",
Expand All @@ -222,18 +226,14 @@
"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",
"kallisto_alignment-cnt.png:md5,989083624e0905b82cbca32f7001a225",
"kallisto_alignment-pct.png:md5,f4de4c6c0fa3ccc83deca870ea2448d2",
"kallisto_alignment-cnt.svg:md5,fc7978ac83c82a3fcc58bb981471a1ee",
"kallisto_alignment-pct.svg:md5,bba0ff4f756a99d943b5b7fff4ab668e"
"fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-17T18:49:01.323612"
"timestamp": "2024-09-18T13:00:14.319235"
},
"Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": {
"content": [
Expand Down
24 changes: 23 additions & 1 deletion tests/lib/UTILS.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,7 @@ class UTILS {
/cutadapt_trimmed_sequences_.*\.svg/,
/dupradar-section-plot\.pdf/,
/dupradar-section-plot\.svg/,
/fail_mapped_samples_table.*/,
/fail_strand_check_table.*/,
/fastqc-status-check-.*\.pdf/,
/fastqc-status-check-.*\.svg/,
Expand Down Expand Up @@ -109,9 +110,16 @@ class UTILS {
/general_stats_table\.pdf/,
/general_stats_table\.png/,
/general_stats_table\.svg/,
/hisat2_pe_plot.*\.png/,
/hisat2_pe_plot.*\.svg/,
/hisat2_pe_plot\.txt/,
/hisat2_se_plot.*\.png/,
/hisat2_se_plot.*\.svg/,
/junction_saturation_known\.txt/,
/junction_saturation_novel\.txt/,
/kallisto_alignment.*.pdf/,
/kallisto_alignment.*.png/,
/kallisto_alignment.*.svg/,
/kallisto_alignment\.txt/,
/multiqc_data\.json/,
/multiqc_dupradar-section-plot\.txt/,
Expand Down Expand Up @@ -159,6 +167,8 @@ class UTILS {
/qualimap_genomic_origin\.txt/,
/qualimap_rnaseq_genome_results\.txt/,
/rsem_assignment_plot\.txt/,
/rsem_assignment_plot-.*\.pdf/,
/rsem_assignment_plot-.*\.svgf/,
/rsem_multimapping_rates\.txt/,
/rseqc_bam_stat\.pdf/,
/rseqc_bam_stat\.png/,
Expand Down Expand Up @@ -254,7 +264,7 @@ class UTILS {
/samtools_alignment_plot-pct\.png/,
/samtools_alignment_plot-pct\.svg/,
/samtools_alignment_plot\.txt/,
/sortmerna-detailed-plot\.txt/,
/sortmerna-detailed-plot\.*/,
/star_alignment_plot-cnt\.pdf/,
/star_alignment_plot-cnt\.png/,
/star_alignment_plot-cnt\.svg/,
Expand Down Expand Up @@ -286,6 +296,8 @@ class UTILS {
/deseq2\.size_factors\.RData/,

// To exclude from kallisto
/abundance\.tsv/,
/kallisto_quant\.log/,
/kallisto\.merged\.gene_counts\.tsv/,
/kallisto\.merged\.gene_counts_length_scaled\.tsv/,
/kallisto\.merged\.gene_counts_scaled\.tsv/,
Expand Down Expand Up @@ -380,6 +392,16 @@ class UTILS {
/.*\.gene\.abundance\.txt/,
/.*\.transcripts\.gtf/,

// To exclude from sortmerna
/.*\.sortmerna\.log/,

// To exclude log from star rsem
/RAP1_IAA_30M_REP1\.log/,
/RAP1_UNINDUCED_REP1\.log/,
/RAP1_UNINDUCED_REP2\.log/,
/WT_REP1\.log/,
/WT_REP2\.log/,

// To exclude markdup
/.*\.markdup\.sorted\.bam/,
/.*\.markdup\.sorted\.bam\.bai/,
Expand Down
8 changes: 4 additions & 4 deletions tests/min_mapped_reads.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -246,6 +246,7 @@
"cutadapt_trimmed_sequences_plot_3_Counts.pdf",
"cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
"dupradar-section-plot.pdf",
"fail_mapped_samples_table.pdf",
"fail_strand_check_table.pdf",
"fastqc-status-check-heatmap-1.pdf",
"fastqc-status-check-heatmap.pdf",
Expand Down Expand Up @@ -316,6 +317,7 @@
"png",
"cutadapt_filtered_reads_plot-cnt.png",
"cutadapt_filtered_reads_plot-pct.png",
"fail_mapped_samples_table.png",
"fail_strand_check_table.png",
"fastqc_adapter_content_plot.png",
"fastqc_per_base_n_content_plot-1.png",
Expand Down Expand Up @@ -361,6 +363,7 @@
"cutadapt_trimmed_sequences_plot_3_Counts.svg",
"cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
"dupradar-section-plot.svg",
"fail_mapped_samples_table.svg",
"fail_strand_check_table.svg",
"fastqc-status-check-heatmap-1.svg",
"fastqc-status-check-heatmap.svg",
Expand Down Expand Up @@ -852,11 +855,9 @@
"samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
"samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070",
"samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6",
"fail_mapped_samples_table.pdf:md5,0d7f9889a09b43eb633b643fd2607442",
"cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50",
"cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787",
"dupradar-section-plot.png:md5,eacbc664cc29a7a59a6aa366b4618582",
"fail_mapped_samples_table.png:md5,e0702273ab75b55895e566cb2945d893",
"fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890",
"fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84",
"fastqc_overrepresented_sequences_plot-1.png:md5,40e450251b80ec0efc9364434234ec7f",
Expand Down Expand Up @@ -885,7 +886,6 @@
"samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d",
"samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,a6849cd92ae738441212b681a411614d",
"samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,4c06988372df63a1fb5f8be93f73ae8f",
"fail_mapped_samples_table.svg:md5,e98423866a8f26e67866e81342862256",
"ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401",
"expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
"observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
Expand Down Expand Up @@ -1046,7 +1046,7 @@
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-17T18:56:30.086204"
"timestamp": "2024-09-18T13:07:21.624648"
},
"Params: --min_mapped_reads 90 - stub": {
"content": [
Expand Down
22 changes: 11 additions & 11 deletions tests/remove_ribo_rna.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -244,7 +244,6 @@
"samtools-flagstat-dp_Read_counts.txt",
"samtools-stats-dp.txt",
"samtools_alignment_plot.txt",
"sortmerna-detailed-plot.txt",
"star_alignment_plot.txt",
"star_summary_table.txt",
"multiqc_report_plots",
Expand Down Expand Up @@ -514,6 +513,11 @@
"salmon.merged.transcript_lengths.tsv",
"salmon.merged.transcript_tpm.tsv",
"sortmerna",
"RAP1_IAA_30M_REP1.sortmerna.log",
"RAP1_UNINDUCED_REP1.sortmerna.log",
"RAP1_UNINDUCED_REP2.sortmerna.log",
"WT_REP1.sortmerna.log",
"WT_REP2.sortmerna.log",
"star_salmon",
"RAP1_IAA_30M_REP1",
"RAP1_IAA_30M_REP1.markdup.sorted.bam",
Expand Down Expand Up @@ -970,8 +974,9 @@
"samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
"samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,53addd7b78d8ae224920ec9b97489d72",
"samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,97fc7bde65a7efc5ab3af48ef0400c20",
"sortmerna-detailed-plot-cnt.pdf:md5,45068e9eb0457fa236aa842eb20e6579",
"sortmerna-detailed-plot-pct.pdf:md5,141dbadd12bdfe5e424089f547ae9241",
"sortmerna-detailed-plot.txt:md5,245e3f5575f2886943c833a4d26e5b8c",
"sortmerna-detailed-plot-cnt.pdf:md5,c99ee88cfbaa772aabd2c13e0d41d774",
"sortmerna-detailed-plot-pct.pdf:md5,956d8f55067b3e1bfa5b86797d701e6e",
"cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50",
"cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787",
"dupradar-section-plot.png:md5,62ee84d3b32bdbfb9766fa970680f92c",
Expand Down Expand Up @@ -1005,8 +1010,8 @@
"samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,1a029e5d23f82d537470363a065b644a",
"sortmerna-detailed-plot-cnt.png:md5,3875997f21c98e8906cd182d959e0020",
"sortmerna-detailed-plot-pct.png:md5,971398875e5cbd50313b6fee7eeb302c",
"sortmerna-detailed-plot-cnt.svg:md5,4cf8f33f9c4b5fa32ca5fa0f1da34521",
"sortmerna-detailed-plot-pct.svg:md5,9e3e7732d400e8fed44bd9b5442f7f9e",
"sortmerna-detailed-plot-cnt.svg:md5,46aca790cbf000df1d77df814dc9f0a1",
"sortmerna-detailed-plot-pct.svg:md5,3be76f5e789415280b17689f90869fac",
"ambig_info.tsv:md5,25ced9693254994a7878241225baabb6",
"expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
"observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
Expand Down Expand Up @@ -1039,11 +1044,6 @@
"lib_format_counts.json:md5,e6e3d7746e9abee6a0e097ae0ee1781a",
"R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
"tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
"RAP1_IAA_30M_REP1.sortmerna.log:md5,b178353fbd4dbc526ddeb8cd62692898",
"RAP1_UNINDUCED_REP1.sortmerna.log:md5,9fc2dc3709b7b316a7c1c4b60d02b192",
"RAP1_UNINDUCED_REP2.sortmerna.log:md5,3ed13bf8ec109ab8e8da6224d0dd29c0",
"WT_REP1.sortmerna.log:md5,5b4548062572db0b14ab05c66e2914bb",
"WT_REP2.sortmerna.log:md5,976d7a76f560c3107c670396b93b9fbb",
"ambig_info.tsv:md5,6cd02367152bb2dd59a6f1f70df2d7f8",
"expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
"observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
Expand Down Expand Up @@ -1232,7 +1232,7 @@
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-17T19:09:08.723809"
"timestamp": "2024-09-18T13:21:54.460278"
},
"Params: --remove_ribo_rna - stub": {
"content": [
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