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@maxulysse
maxulysse committed Sep 18, 2024
1 parent a3e0328 commit 4811e91
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Showing 4 changed files with 67 additions and 77 deletions.
22 changes: 11 additions & 11 deletions tests/hisat2.nf.test.snap
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Expand Up @@ -604,11 +604,6 @@
"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_stats.txt",
Expand Down Expand Up @@ -936,7 +931,7 @@
"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:md5,5c0d00bfee4ff563521f6458a13f9476",
"WT_REP2.hisat2.summary.log:md5,e622496abff3ce68afcd1c21a7a1e0df",
"bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
"bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
"comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
Expand Down Expand Up @@ -1091,6 +1086,11 @@
"multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
"multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
"multiqc_featurecounts_biotype_plot.txt:md5,d35ad008181f0f7be84d5770d17a3a65",
"multiqc_salmon_deseq2_clustering-plot.txt:md5,c39fd219828df33259e48aadcdd1997c",
"multiqc_salmon_deseq2_clustering-plot_1.txt:md5,6ccabfcdd11d36e140a7d6615c73ae85",
"multiqc_salmon_deseq2_clustering-plot_2.txt:md5,792ce8a58aefbbd10c0f182fcbc37c7a",
"multiqc_salmon_deseq2_clustering-plot_3.txt:md5,3080d13dee6e437084f27937296ede8a",
"multiqc_salmon_deseq2_clustering-plot_4.txt:md5,c750d2fa8d6dc8a2370335a71d2fa637",
"multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49",
"picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
Expand All @@ -1102,10 +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,ec0f89f703d3ee1c1d7c59fe712d6467",
"hisat2_pe_plot-pct.pdf:md5,75522edf01667236474caa26c40c4e82",
"hisat2_se_plot-cnt.pdf:md5,15692ca0b4144b4c97094178dcdb39de",
"hisat2_se_plot-pct.pdf:md5,f56040af7a091869364ed1dc8853bc31",
"hisat2_pe_plot-cnt.pdf:md5,597b9758f57712f66956d1065f72f68c",
"hisat2_pe_plot-pct.pdf:md5,6baadc07e1d4b51a872fdf288d3a5dcd",
"hisat2_se_plot-cnt.pdf:md5,ad78c3a76df184a45d0b9f905ed979d0",
"hisat2_se_plot-pct.pdf:md5,60a38be9382dbf103bb0832c2f1bca6c",
"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 Down Expand Up @@ -1175,6 +1175,6 @@
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-18T12:56:26.579349"
"timestamp": "2024-09-18T14:05:59.799519"
}
}
52 changes: 21 additions & 31 deletions tests/lib/UTILS.groovy
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Expand Up @@ -110,11 +110,9 @@ class UTILS {
/general_stats_table\.pdf/,
/general_stats_table\.png/,
/general_stats_table\.svg/,
/hisat2_pe_plot.*\.png/,
/hisat2_pe_plot.*\.svg/,
/hisat2_(pe|se)_plot-(cnt|pct)\.(png|svg)/,
/hisat2_pe_plot\.txt/,
/hisat2_se_plot.*\.png/,
/hisat2_se_plot.*\.svg/,
/hisat2_se_plot.*\.(png|svg)/,
/junction_saturation_known\.txt/,
/junction_saturation_novel\.txt/,
/kallisto_alignment.*.pdf/,
Expand All @@ -135,17 +133,17 @@ class UTILS {
/multiqc_rseqc_junction_annotation\.txt/,
/multiqc_rseqc_read_distribution\.txt/,
/multiqc_salmon\.txt/,
/multiqc_salmon_deseq2_clustering-plot\.txt/,
/multiqc_salmon_deseq2_clustering-plot_.*\.txt/,
/(star_rsem|multiqc_salmon)_deseq2_clustering-plot-\.txt/,
/(star_rsem|multiqc_salmon)_deseq2_clustering_-lot_-.*\.txt/,
/multiqc_salmon_deseq2_pca-plot\.txt/,
/multiqc_samtools_flagstat\.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_.*\.txt/,
/(star_rsem|multiqc_star_salmon)_deseq2_clustering-plot-\.txt/,
/(star_rsem|multiqc_star_salmon)_deseq2_clustering_-lot_-.*\.txt/,
/multiqc_star_salmon_deseq2_pca-plot\.txt/,
/picard_deduplication-cnt\.pdf/,
/picard_deduplication-cnt\.png/,
Expand All @@ -167,9 +165,8 @@ 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/,
/rsem_assignment_plot-(cnt|pct)\.(pdf|svg)/,
/rsem_multimapping_rates\.(pdf|svg|txt)/,
/rseqc_bam_stat\.pdf/,
/rseqc_bam_stat\.png/,
/rseqc_bam_stat\.svg/,
Expand Down Expand Up @@ -223,12 +220,12 @@ class UTILS {
/rseqc_read_dups_plot\.pdf/,
/rseqc_read_dups_plot\.svg/,
/rseqc_read_dups_plot\.txt/,
/salmon_deseq2_clustering-plot\.pdf/,
/salmon_deseq2_clustering-plot\.png/,
/salmon_deseq2_clustering-plot\.svg/,
/salmon_deseq2_pca-plot\.pdf/,
/salmon_deseq2_pca-plot\.png/,
/salmon_deseq2_pca-plot\.svg/,
/(salmon|star_rsem)_deseq2_(clustering|pca)-plot\.pdf/,
/(salmon|star_rsem)_deseq2_(clustering|pca)-plot\.png/,
/(salmon|star_rsem)_deseq2_(clustering|pca)-plot\.svg/,
/(salmon|star_rsem)_deseq2_(pca|pca)-plot\.pdf/,
/(salmon|star_rsem)_deseq2_(pca|pca)-plot\.png/,
/(salmon|star_rsem)_deseq2_(pca|pca)-plot\.svg/,
/salmon_plot\.pdf/,
/salmon_plot\.png/,
/salmon_plot\.svg/,
Expand Down Expand Up @@ -264,17 +261,15 @@ class UTILS {
/samtools_alignment_plot-pct\.png/,
/samtools_alignment_plot-pct\.svg/,
/samtools_alignment_plot\.txt/,
/sortmerna-detailed-plot\.*/,
/sortmerna-detailed-plot-(cnt|pct)\.(pdf|svg)/,
/star_alignment_plot-cnt\.pdf/,
/star_alignment_plot-cnt\.png/,
/star_alignment_plot-cnt\.svg/,
/star_alignment_plot-pct\.pdf/,
/star_alignment_plot-pct\.png/,
/star_alignment_plot-pct\.svg/,
/star_alignment_plot\.txt/,
/star_salmon_deseq2_clustering-plot\.pdf/,
/star_salmon_deseq2_clustering-plot\.png/,
/star_salmon_deseq2_clustering-plot\.svg/,
/(star_rsem|star_salmon)_deseq2_(clustering|pca)-plot-\.(pdf|png|svg)/,
/star_salmon_deseq2_pca-plot\.pdf/,
/star_salmon_deseq2_pca-plot\.png/,
/star_salmon_deseq2_pca-plot\.svg/,
Expand Down Expand Up @@ -379,12 +374,10 @@ class UTILS {
/.*\.bam_stat\.txt/,

// To exclude from samtools stats
/.*\.markdup\.sorted\.bam\.flagstat/,
/.*\.markdup\.sorted\.bam\.idxstats/,
/.*\.markdup\.sorted\.bam\.stats/,
/.*\.sorted\.bam\.flagstat/,
/.*\.sorted\.bam\.idxstats/,
/.*\.sorted\.bam\.stats/,
/.*\.sorted\.bam\.(flagstat|idxstats|stats)/,

// To exclude from hisat2
/.*hisat2\.summary/,

// To exclude from stringtie
/t_data\.ctab/,
Expand All @@ -407,10 +400,7 @@ class UTILS {
/.*\.markdup\.sorted\.bam\.bai/,

// To exclude trimgalore
/.*\.fastq\.gz_trimming_report\.txt/,

// To exclude params files with timestamps
/params_\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}\.json/
/.*\.fastq\.gz_trimming_report\.txt/
]

}
38 changes: 19 additions & 19 deletions tests/remove_ribo_rna.nf.test.snap
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Expand Up @@ -205,23 +205,13 @@
"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_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",
"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",
"qualimap_genomic_origin.txt",
Expand Down Expand Up @@ -315,9 +305,10 @@
"samtools-stats-dp.pdf",
"samtools_alignment_plot-cnt.pdf",
"samtools_alignment_plot-pct.pdf",
"sortmerna-detailed-plot-cnt.pdf",
"sortmerna-detailed-plot-pct.pdf",
"star_alignment_plot-cnt.pdf",
"star_alignment_plot-pct.pdf",
"star_salmon_deseq2_clustering-plot.pdf",
"star_salmon_deseq2_pca-plot.pdf",
"star_summary_table.pdf",
"png",
Expand Down Expand Up @@ -359,7 +350,6 @@
"samtools_alignment_plot-pct.png",
"star_alignment_plot-cnt.png",
"star_alignment_plot-pct.png",
"star_salmon_deseq2_clustering-plot.png",
"star_salmon_deseq2_pca-plot.png",
"star_summary_table.png",
"svg",
Expand Down Expand Up @@ -430,9 +420,10 @@
"samtools-stats-dp.svg",
"samtools_alignment_plot-cnt.svg",
"samtools_alignment_plot-pct.svg",
"sortmerna-detailed-plot-cnt.svg",
"sortmerna-detailed-plot-pct.svg",
"star_alignment_plot-cnt.svg",
"star_alignment_plot-pct.svg",
"star_salmon_deseq2_clustering-plot.svg",
"star_salmon_deseq2_pca-plot.svg",
"star_summary_table.svg",
"pipeline_info",
Expand Down Expand Up @@ -963,7 +954,17 @@
"multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
"multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
"multiqc_featurecounts_biotype_plot.txt:md5,54f0eef4ab0ecf6a03505b18752b43cd",
"multiqc_salmon_deseq2_clustering-plot.txt:md5,b84f4797086941a5014d88dc46115832",
"multiqc_salmon_deseq2_clustering-plot_1.txt:md5,7494c2892cc5b058da9e2296f7be5a8c",
"multiqc_salmon_deseq2_clustering-plot_2.txt:md5,4b6e40f595eb28ceaadf43ffe187b752",
"multiqc_salmon_deseq2_clustering-plot_3.txt:md5,d0d2a9e2bf3d4e81fef9b2450e5e29b8",
"multiqc_salmon_deseq2_clustering-plot_4.txt:md5,0ab6a0bc900cb8bae5aa280e2d13397a",
"multiqc_samtools_idxstats.txt:md5,413ba06f3d8e4ab0dbde8ef8952c4b32",
"multiqc_star_salmon_deseq2_clustering-plot.txt:md5,99d097781c6761b6894e6bcc7999e1ba",
"multiqc_star_salmon_deseq2_clustering-plot_1.txt:md5,88bcc02233b2df2876678d186df8d32a",
"multiqc_star_salmon_deseq2_clustering-plot_2.txt:md5,8673d08e63e16dc7993f99f15c8377e1",
"multiqc_star_salmon_deseq2_clustering-plot_3.txt:md5,b65a05ab4904d2992d3bf664ad0e82f1",
"multiqc_star_salmon_deseq2_clustering-plot_4.txt:md5,5c77c5fefc953051de1fc1e6d8377cf2",
"picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
Expand All @@ -974,9 +975,8 @@
"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.txt:md5,245e3f5575f2886943c833a4d26e5b8c",
"sortmerna-detailed-plot-cnt.pdf:md5,c99ee88cfbaa772aabd2c13e0d41d774",
"sortmerna-detailed-plot-pct.pdf:md5,956d8f55067b3e1bfa5b86797d701e6e",
"sortmerna-detailed-plot.txt:md5,b93dadb4ca77c6af68ef2c00a8626f17",
"star_salmon_deseq2_clustering-plot.pdf:md5,1a1cfea5266d1857da02f0e7c9e062bb",
"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 @@ -1010,8 +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:md5,46aca790cbf000df1d77df814dc9f0a1",
"sortmerna-detailed-plot-pct.svg:md5,3be76f5e789415280b17689f90869fac",
"star_salmon_deseq2_clustering-plot.png:md5,86ae8d342372b9fe5c8ad3108890606a",
"star_salmon_deseq2_clustering-plot.svg:md5,d414f141d8af259802fb059c8a376ac5",
"ambig_info.tsv:md5,25ced9693254994a7878241225baabb6",
"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": "2024-09-18T13:21:54.460278"
"timestamp": "2024-09-18T14:19:29.058683"
},
"Params: --remove_ribo_rna - stub": {
"content": [
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