rescue some snaps

nf-core · Sep 19, 2024 · 742bfa1 · 742bfa1
1 parent d979788
commit 742bfa1
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Showing 10 changed files with 33 additions and 59 deletions.
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
@@ -405,8 +405,6 @@
                 "star_salmon_deseq2_pca-plot.pdf",
                 "star_summary_table.pdf",
                 "png",
-                "cutadapt_filtered_reads_plot-cnt.png",
-                "cutadapt_filtered_reads_plot-pct.png",
                 "fail_strand_check_table.png",
                 "fastqc_adapter_content_plot.png",
                 "fastqc_per_base_n_content_plot-1.png",
@@ -1052,6 +1050,8 @@
                 "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",
+                "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",
                 "dupradar-section-plot.png:md5,3ae5e5cb161b7abd878d718bc71b41f6",
@@ -1303,6 +1303,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-17T18:29:56.535818"
+        "timestamp": "2024-09-19T10:12:58.76862"
     }
 }
diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap
@@ -397,8 +397,6 @@
                 "star_salmon_deseq2_pca-plot.pdf",
                 "star_summary_table.pdf",
                 "png",
-                "cutadapt_filtered_reads_plot-cnt.png",
-                "cutadapt_filtered_reads_plot-pct.png",
                 "fail_strand_check_table.png",
                 "fastqc_adapter_content_plot.png",
                 "fastqc_per_base_n_content_plot-1.png",
@@ -1035,6 +1033,8 @@
                 "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",
+                "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",
                 "dupradar-section-plot.png:md5,3ae5e5cb161b7abd878d718bc71b41f6",
@@ -1269,6 +1269,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-18T11:13:20.643284"
+        "timestamp": "2024-09-19T10:21:06.207795"
     }
 }
diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap
@@ -709,8 +709,6 @@
                 "samtools_alignment_plot-cnt.pdf",
                 "samtools_alignment_plot-pct.pdf",
                 "png",
-                "cutadapt_filtered_reads_plot-cnt.png",
-                "cutadapt_filtered_reads_plot-pct.png",
                 "fail_strand_check_table.png",
                 "fastqc_adapter_content_plot.png",
                 "fastqc_per_base_n_content_plot-1.png",
@@ -1106,6 +1104,8 @@
                 "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",
+                "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",
                 "dupradar-section-plot.png:md5,6074ea2315d296094bd10fad3dcc475b",
@@ -1175,6 +1175,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-18T15:04:27.247526"
+        "timestamp": "2024-09-19T10:28:23.826076"
     }
 }
diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap
@@ -156,8 +156,6 @@
                 "kallisto_alignment-cnt.pdf",
                 "kallisto_alignment-pct.pdf",
                 "png",
-                "cutadapt_filtered_reads_plot-cnt.png",
-                "cutadapt_filtered_reads_plot-pct.png",
                 "fastqc_per_base_n_content_plot.png",
                 "fastqc_per_base_sequence_quality_plot.png",
                 "fastqc_sequence_length_distribution_plot.png",
@@ -217,6 +215,8 @@
                 "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee",
                 "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
                 "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
+                "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",
@@ -233,7 +233,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-18T13:00:14.319235"
+        "timestamp": "2024-09-19T10:32:38.720378"
     },
     "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": {
         "content": [

diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy
@@ -40,9 +40,8 @@ class UTILS {
         /.*_fastqc\.html/,
 
         // To exclude from the MultiQC reports
-        /cutadapt_filtered_reads_plot-.*/,
-        /cutadapt_trimmed_sequences_.*\.pdf/,
-        /cutadapt_trimmed_sequences_.*\.svg/,
+        /cutadapt_filtered_reads_plot-(cnt|pct)\.(pdf|svg)/,
+        /cutadapt_trimmed_sequences_.*\.(pdf|svg)/,
         /dupradar-section-plot\.pdf/,
         /dupradar-section-plot\.svg/,
         /fail_mapped_samples_table.*/,
@@ -277,23 +276,11 @@ class UTILS {
         /RAP1_UNINDUCED_REP2\.txt/,
         /WT_REP1\.txt/,
         /WT_REP2\.txt/,
-        /deseq2\.dds\.RData/,
-        /deseq2\.pca\.vals\.txt/,
-        /deseq2\.plots\.pdf/,
-        /deseq2\.sample\.dists\.txt/,
-        /deseq2\.size_factors\.RData/,
+        /deseq2.*/,
 
         // 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/,
-        /kallisto\.merged\.gene_lengths\.tsv/,
-        /kallisto\.merged\.gene_tpm\.tsv/,
-        /kallisto\.merged\.transcript_counts\.tsv/,
-        /kallisto\.merged\.transcript_lengths\.tsv/,
-        /kallisto\.merged\.transcript_tpm\.tsv/,
         /run_info\.json/,
 
         // To exclude from salmon quant
@@ -304,27 +291,14 @@ class UTILS {
         /quant\.genes\.sf/,
         /quant\.sf/,
 
-        // To exclude from salmon
-        /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/,
+        // To exclude from kallisto|salmon aligners
+        /(kallisto|salmon)\.merged.*/,
 
         // To exclude bigwig
         /.*\.(forward|reverse)\.bigWig/,
 
         // To exlude dupradar
-        /.*_duprateExpBoxplot\.pdf/,
-        /.*_expressionHist\.pdf/,
-        /.*_duprateExpDens\.pdf/,
+        /.*_(duprateExpBoxplot|duprateExpDens|expressionHist)\.pdf/,
 
         // To exclude featurecounts
         /.*\.featureCounts\.txt\.summary/,

diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap
@@ -315,8 +315,6 @@
                 "star_salmon_deseq2_pca-plot.pdf",
                 "star_summary_table.pdf",
                 "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",
@@ -855,6 +853,8 @@
                 "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",
+                "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",
                 "dupradar-section-plot.png:md5,eacbc664cc29a7a59a6aa366b4618582",
@@ -1046,7 +1046,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-18T13:07:21.624648"
+        "timestamp": "2024-09-19T10:41:32.333555"
     },
     "Params: --min_mapped_reads 90 - stub": {
         "content": [

diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap
@@ -324,8 +324,6 @@
                 "star_salmon_deseq2_pca-plot.pdf",
                 "star_summary_table.pdf",
                 "png",
-                "cutadapt_filtered_reads_plot-cnt.png",
-                "cutadapt_filtered_reads_plot-pct.png",
                 "fail_strand_check_table.png",
                 "fastqc_adapter_content_plot.png",
                 "fastqc_per_base_n_content_plot-1.png",
@@ -979,6 +977,8 @@
                 "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",
+                "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",
                 "dupradar-section-plot.png:md5,62ee84d3b32bdbfb9766fa970680f92c",
@@ -1232,7 +1232,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-18T17:38:19.910241"
+        "timestamp": "2024-09-19T10:54:06.730344"
     },
     "Params: --remove_ribo_rna - stub": {
         "content": [

diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap
@@ -111,8 +111,6 @@
                 "general_stats_table.pdf",
                 "salmon_plot.pdf",
                 "png",
-                "cutadapt_filtered_reads_plot-cnt.png",
-                "cutadapt_filtered_reads_plot-pct.png",
                 "fastqc_per_base_n_content_plot.png",
                 "fastqc_per_base_sequence_quality_plot.png",
                 "fastqc_sequence_length_distribution_plot.png",
@@ -232,6 +230,8 @@
                 "multiqc_citations.txt:md5,f789abe663d4b4214f0ddeb413a7f150",
                 "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
                 "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
+                "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",
@@ -279,7 +279,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-17T19:13:06.946699"
+        "timestamp": "2024-09-19T10:58:01.584391"
     },
     "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": {
         "content": [

diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap
@@ -256,8 +256,6 @@
                 "star_alignment_plot-pct.pdf",
                 "star_summary_table.pdf",
                 "png",
-                "cutadapt_filtered_reads_plot-cnt.png",
-                "cutadapt_filtered_reads_plot-pct.png",
                 "fastqc_per_base_n_content_plot.png",
                 "fastqc_per_base_sequence_quality_plot.png",
                 "fastqc_sequence_length_distribution_plot.png",
@@ -573,6 +571,8 @@
                 "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",
+                "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",
@@ -677,6 +677,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-17T19:23:30.52516"
+        "timestamp": "2024-09-19T11:04:14.333102"
     }
 }
diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap
@@ -313,8 +313,6 @@
                 "star_rsem_deseq2_clustering-plot.pdf",
                 "star_rsem_deseq2_pca-plot.pdf",
                 "png",
-                "cutadapt_filtered_reads_plot-cnt.png",
-                "cutadapt_filtered_reads_plot-pct.png",
                 "fail_strand_check_table.png",
                 "fastqc_adapter_content_plot.png",
                 "fastqc_per_base_n_content_plot-1.png",
@@ -918,6 +916,8 @@
                 "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
                 "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3e67e07b5c978fa363965e8e90356eef",
                 "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,a83e44c5a22e014d377c41419175784c",
+                "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",
                 "dupradar-section-plot.png:md5,f76a34d2eb6f2351729d79efc1434ee8",
@@ -1143,7 +1143,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-19T09:17:34.302993"
+        "timestamp": "2024-09-19T11:19:40.881884"
     },
     "Params: --aligner star_rsem - stub": {
         "content": [