From e4cfa09c0899163863ed5cd9bb06f1a6193a64ae Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 26 Aug 2024 20:03:54 +0200 Subject: [PATCH] update tests and snapshots --- tests/default.nf.test.snap | 60 ++++----- tests/featurecounts_group_type.nf.test.snap | 60 ++++----- tests/hisat2.nf.test | 8 +- tests/hisat2.nf.test.snap | 72 +++++------ tests/min_mapped_reads.nf.test.snap | 62 +++++----- tests/remove_ribo_rna.nf.test.snap | 76 ++++++------ tests/skip_qc.nf.test.snap | 60 ++++----- tests/skip_trimming.nf.test.snap | 60 ++++----- tests/star_rsem.nf.test.snap | 128 ++++++++++---------- 9 files changed, 293 insertions(+), 293 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index ba779ac75..e625d1637 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -227,42 +227,42 @@ }, "star_salmon/samtools_stats": { "content": [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,e3689e1939a931a656ab14b5a40d27a9", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,990280b423241cd1d3e9ab3410841ee8", - "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,30b35c766650cfb3af89fa09c8654b59", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,451eeb9f3caea89d069f26a77a3ac9e9", - "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,a093ff94182b1cd6a206b019e43c8281", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,d0e0e89c8af100c2adfa7cbf0021f8a2", - "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "WT_REP1.markdup.sorted.bam.flagstat:md5,501ff3ad52e73a6168814545bb99abf8", - "WT_REP1.markdup.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f", - "WT_REP1.sorted.bam.flagstat:md5,694fa7255da6612e0503f37b41cdbade", - "WT_REP1.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f", - "WT_REP2.markdup.sorted.bam.flagstat:md5,3530fb25cc5dfe72cc39053264b3b0cc", - "WT_REP2.markdup.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68", - "WT_REP2.sorted.bam.flagstat:md5,e1b514b8f09016ac33e31c25c8e5a447", - "WT_REP2.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.sorted.bam.stats", + "WT_REP1.markdup.sorted.bam.flagstat", + "WT_REP1.markdup.sorted.bam.idxstats", "WT_REP1.markdup.sorted.bam.stats", + "WT_REP1.sorted.bam.flagstat", + "WT_REP1.sorted.bam.idxstats", "WT_REP1.sorted.bam.stats", + "WT_REP2.markdup.sorted.bam.flagstat", + "WT_REP2.markdup.sorted.bam.idxstats", "WT_REP2.markdup.sorted.bam.stats", + "WT_REP2.sorted.bam.flagstat", + "WT_REP2.sorted.bam.idxstats", "WT_REP2.sorted.bam.stats" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T12:44:57.974787" + "timestamp": "2024-08-26T18:42:17.143005" }, "Params: default - stub": { "content": [ @@ -320,8 +320,6 @@ "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", "featurecounts_biotype_plot-cnt.png:md5,4c66fce934b018143e7b8f6a1383d3f6", "featurecounts_biotype_plot-pct.png:md5,9191dc2dd130f22ad404d27e045d2304", - "picard_deduplication-cnt.png:md5,52297225fca30daa61d3271754bdbc1a", - "picard_deduplication-pct.png:md5,b2aa123cc65c933ca630d89c6f098550", "qualimap_gene_coverage_profile_Counts.png:md5,ac424dc7e5444a32e482bd5048ac4432", "qualimap_gene_coverage_profile_Normalised.png:md5,62e5a2146daec985b8c2de02e3b57c1e", "rseqc_infer_experiment_plot.png:md5,60c3cafb671fad2cf5f695615230eb8f", @@ -332,8 +330,6 @@ "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", - "samtools_alignment_plot-cnt.png:md5,84f0e82efcef1221c5c2d292b4d4431c", - "samtools_alignment_plot-pct.png:md5,7836b2057272b390f75c890e26034ec2", "multiqc_report.html", "cutadapt_filtered_reads_plot-cnt.pdf", "cutadapt_filtered_reads_plot-pct.pdf", @@ -417,6 +413,8 @@ "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", + "picard_deduplication-cnt.png", + "picard_deduplication-pct.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", @@ -437,6 +435,8 @@ "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", "samtools-stats-dp.png", + "samtools_alignment_plot-cnt.png", + "samtools_alignment_plot-pct.png", "star_alignment_plot-cnt.png", "star_alignment_plot-pct.png", "star_salmon_deseq2_clustering-plot.png", @@ -519,7 +519,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:21:24.616733" + "timestamp": "2024-08-26T18:42:16.932219" }, "fastqc/raw": { "content": [ @@ -694,9 +694,7 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,56be7f0813c3cbea0f68f61d9b355b71", - "multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", - "picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -707,7 +705,6 @@ "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", - "samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", @@ -716,6 +713,7 @@ "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", "multiqc_general_stats.txt", + "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", "multiqc_rseqc_infer_experiment.txt", "multiqc_rseqc_junction_annotation.txt", @@ -738,6 +736,7 @@ "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", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", @@ -757,6 +756,7 @@ "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", "samtools-stats-dp.txt", + "samtools_alignment_plot.txt", "star_alignment_plot.txt", "star_summary_table.txt" ], @@ -764,7 +764,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:21:24.483792" + "timestamp": "2024-08-26T18:42:16.785525" }, "star_salmon/deseq2_qc": { "content": [ diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 078ab9d3d..b1160d39d 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -122,9 +122,7 @@ "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", - "picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -135,7 +133,6 @@ "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", - "samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", @@ -144,6 +141,7 @@ "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", "multiqc_general_stats.txt", + "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", "multiqc_rseqc_infer_experiment.txt", "multiqc_rseqc_junction_annotation.txt", @@ -166,6 +164,7 @@ "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", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", @@ -185,6 +184,7 @@ "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", "samtools-stats-dp.txt", + "samtools_alignment_plot.txt", "star_alignment_plot.txt", "star_summary_table.txt" ], @@ -192,7 +192,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:29:22.875142" + "timestamp": "2024-08-26T18:50:10.937365" }, "trimgalore": { "content": [ @@ -367,42 +367,42 @@ }, "star_salmon/samtools_stats": { "content": [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,e3689e1939a931a656ab14b5a40d27a9", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,990280b423241cd1d3e9ab3410841ee8", - "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,30b35c766650cfb3af89fa09c8654b59", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,451eeb9f3caea89d069f26a77a3ac9e9", - "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,a093ff94182b1cd6a206b019e43c8281", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,d0e0e89c8af100c2adfa7cbf0021f8a2", - "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "WT_REP1.markdup.sorted.bam.flagstat:md5,501ff3ad52e73a6168814545bb99abf8", - "WT_REP1.markdup.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f", - "WT_REP1.sorted.bam.flagstat:md5,694fa7255da6612e0503f37b41cdbade", - "WT_REP1.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f", - "WT_REP2.markdup.sorted.bam.flagstat:md5,3530fb25cc5dfe72cc39053264b3b0cc", - "WT_REP2.markdup.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68", - "WT_REP2.sorted.bam.flagstat:md5,e1b514b8f09016ac33e31c25c8e5a447", - "WT_REP2.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.sorted.bam.stats", + "WT_REP1.markdup.sorted.bam.flagstat", + "WT_REP1.markdup.sorted.bam.idxstats", "WT_REP1.markdup.sorted.bam.stats", + "WT_REP1.sorted.bam.flagstat", + "WT_REP1.sorted.bam.idxstats", "WT_REP1.sorted.bam.stats", + "WT_REP2.markdup.sorted.bam.flagstat", + "WT_REP2.markdup.sorted.bam.idxstats", "WT_REP2.markdup.sorted.bam.stats", + "WT_REP2.sorted.bam.flagstat", + "WT_REP2.sorted.bam.idxstats", "WT_REP2.sorted.bam.stats" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T14:18:39.635582" + "timestamp": "2024-08-26T18:50:11.105038" }, "salmon/deseq2_qc": { "content": [ @@ -469,8 +469,6 @@ "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054", "fastqc_sequence_duplication_levels_plot-1.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", - "picard_deduplication-cnt.png:md5,52297225fca30daa61d3271754bdbc1a", - "picard_deduplication-pct.png:md5,b2aa123cc65c933ca630d89c6f098550", "qualimap_gene_coverage_profile_Counts.png:md5,ac424dc7e5444a32e482bd5048ac4432", "qualimap_gene_coverage_profile_Normalised.png:md5,62e5a2146daec985b8c2de02e3b57c1e", "rseqc_infer_experiment_plot.png:md5,60c3cafb671fad2cf5f695615230eb8f", @@ -481,8 +479,6 @@ "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", - "samtools_alignment_plot-cnt.png:md5,84f0e82efcef1221c5c2d292b4d4431c", - "samtools_alignment_plot-pct.png:md5,7836b2057272b390f75c890e26034ec2", "multiqc_report.html", "cutadapt_filtered_reads_plot-cnt.pdf", "cutadapt_filtered_reads_plot-pct.pdf", @@ -564,6 +560,8 @@ "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", + "picard_deduplication-cnt.png", + "picard_deduplication-pct.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", @@ -584,6 +582,8 @@ "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", "samtools-stats-dp.png", + "samtools_alignment_plot-cnt.png", + "samtools_alignment_plot-pct.png", "star_alignment_plot-cnt.png", "star_alignment_plot-pct.png", "star_salmon_deseq2_clustering-plot.png", @@ -664,7 +664,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:29:22.943986" + "timestamp": "2024-08-26T18:50:11.011282" }, "star_salmon/picard_metrics": { "content": [ diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 67ae1187e..9577086ea 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -240,8 +240,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_data/salmon_plot.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-stats-dp.txt").name - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools_alignment_plot.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-stats-dp.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools_alignment_plot.txt").name ).match("multiqc_data") }, { assert snapshot( path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), @@ -426,7 +426,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/general_stats_table.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_deseq2_clustering-plot.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_deseq2_pca-plot.svg").name + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_deseq2_pca-plot.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_pe_plot-cnt.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_pe_plot-pct.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_se_plot-cnt.svg").name, @@ -464,7 +464,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-stats-dp.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name ).match("multiqc_plots") }, { assert snapshot( // Metrics are not stable diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index c3c508b2e..4e82775d6 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -150,9 +150,7 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,d35ad008181f0f7be84d5770d17a3a65", - "multiqc_picard_dups.txt:md5,71d5bafee1a4916951349018f387f7a0", "multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49", - "picard_deduplication.txt:md5,b54a144d4f23ade2221d7ca1af1997f4", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -163,7 +161,6 @@ "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", - "samtools_alignment_plot.txt:md5,b6ba3cc94a91b3d0a84c3fa721914744", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "hisat2_pe_plot.txt", @@ -181,6 +178,7 @@ "multiqc_hisat2_deseq2_clustering-plot_3.txt", "multiqc_hisat2_deseq2_clustering-plot_4.txt", "multiqc_hisat2_deseq2_pca-plot.txt", + "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", "multiqc_rseqc_infer_experiment.txt", "multiqc_rseqc_junction_annotation.txt", @@ -196,6 +194,7 @@ "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", + "picard_deduplication.txt", "qualimap_genomic_origin.txt", "rseqc_bam_stat.txt", "rseqc_inner_distance.txt", @@ -213,13 +212,14 @@ "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", - "samtools-stats-dp.txt" + "samtools-stats-dp.txt", + "samtools_alignment_plot.txt" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:35:09.357006" + "timestamp": "2024-08-26T19:01:52.559836" }, "hisat2/picard_metrics": { "content": [ @@ -277,42 +277,42 @@ }, "hisat2/samtools_stats": { "content": [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,e04029ba0b7c9a5007b1e21190416ab3", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,58ac8d961ffe5af5140e597ce46d1ac2", - "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,acdfa72b8fb5785abeddaabdab1ed8ca", - "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,58ac8d961ffe5af5140e597ce46d1ac2", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,b0b719dd29053aa37010082b6a0bb8d1", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,05a67765b944740c60f263a42a5fd65d", - "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,0f82cf321c7ac21d11c29b7e8fd6893b", - "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,05a67765b944740c60f263a42a5fd65d", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,cb40075ffa2e6f66d8b4b5025fd62004", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,a72f0d10ac28ec362a79435db766251f", - "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,92d7610422de90da2e76f99461721b7f", - "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,a72f0d10ac28ec362a79435db766251f", - "WT_REP1.markdup.sorted.bam.flagstat:md5,cb3229294e384dba57b00ddab95e5cc9", - "WT_REP1.markdup.sorted.bam.idxstats:md5,93da4c4f281b38c0f783cb4b7e93a6d0", - "WT_REP1.sorted.bam.flagstat:md5,c55ed3c6ea5f4134036fa8a09c20a1ee", - "WT_REP1.sorted.bam.idxstats:md5,93da4c4f281b38c0f783cb4b7e93a6d0", - "WT_REP2.markdup.sorted.bam.flagstat:md5,a0702469e2d220391604e1b72100cad1", - "WT_REP2.markdup.sorted.bam.idxstats:md5,ea45aa47d0b2b85d8aed7072e6ea36b5", - "WT_REP2.sorted.bam.flagstat:md5,b33836e522593ca0aed7c3b10973d5ed", - "WT_REP2.sorted.bam.idxstats:md5,ea45aa47d0b2b85d8aed7072e6ea36b5", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.sorted.bam.stats", + "WT_REP1.markdup.sorted.bam.flagstat", + "WT_REP1.markdup.sorted.bam.idxstats", "WT_REP1.markdup.sorted.bam.stats", + "WT_REP1.sorted.bam.flagstat", + "WT_REP1.sorted.bam.idxstats", "WT_REP1.sorted.bam.stats", + "WT_REP2.markdup.sorted.bam.flagstat", + "WT_REP2.markdup.sorted.bam.idxstats", "WT_REP2.markdup.sorted.bam.stats", + "WT_REP2.sorted.bam.flagstat", + "WT_REP2.sorted.bam.idxstats", "WT_REP2.sorted.bam.stats" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T13:55:07.609425" + "timestamp": "2024-08-26T19:01:52.753084" }, "salmon/deseq2_qc": { "content": [ @@ -400,8 +400,6 @@ "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", "featurecounts_biotype_plot-cnt.png:md5,138e00d2fe0af27f2979cf7bdff83b46", "featurecounts_biotype_plot-pct.png:md5,3b7550efe9068f3ada2cc64e311f3338", - "picard_deduplication-cnt.png:md5,fd520fbb1fda9104eb4d39d42df385d0", - "picard_deduplication-pct.png:md5,dbced4008901ab031eda6d0d96ca038b", "qualimap_gene_coverage_profile_Counts.png:md5,1aa39028b017760d0b09f1b6f8c1fa3a", "qualimap_gene_coverage_profile_Normalised.png:md5,1cd382a79b89564a006afe431aa3916d", "rseqc_infer_experiment_plot.png:md5,73f5b860029912da9c3f6a887238d251", @@ -412,8 +410,6 @@ "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", - "samtools_alignment_plot-cnt.png:md5,142e06e9daa0fe938f1e9162e1e850a2", - "samtools_alignment_plot-pct.png:md5,bbffb494310e6dff84d9fe7bc99e34fe", "multiqc_report.html", "cutadapt_filtered_reads_plot-cnt.pdf", "cutadapt_filtered_reads_plot-pct.pdf", @@ -448,6 +444,8 @@ "featurecounts_biotype_plot-cnt.pdf", "featurecounts_biotype_plot-pct.pdf", "general_stats_table.pdf", + "hisat2_deseq2_clustering-plot.pdf", + "hisat2_deseq2_pca-plot.pdf", "hisat2_pe_plot-cnt.pdf", "hisat2_pe_plot-pct.pdf", "hisat2_se_plot-cnt.pdf", @@ -457,8 +455,6 @@ "qualimap_gene_coverage_profile_Counts.pdf", "qualimap_gene_coverage_profile_Normalised.pdf", "qualimap_genomic_origin-cnt.pdf", - "hisat2_deseq2_clustering-plot.pdf", - "hisat2_deseq2_pca-plot.pdf", "qualimap_genomic_origin-pct.pdf", "rseqc_bam_stat.pdf", "rseqc_infer_experiment_plot.pdf", @@ -504,6 +500,8 @@ "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", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", @@ -524,6 +522,8 @@ "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", "samtools-stats-dp.png", + "samtools_alignment_plot-cnt.png", + "samtools_alignment_plot-pct.png", "cutadapt_filtered_reads_plot-cnt.svg", "cutadapt_filtered_reads_plot-pct.svg", "cutadapt_trimmed_sequences_plot_3_Counts.svg", @@ -557,6 +557,8 @@ "featurecounts_biotype_plot-cnt.svg", "featurecounts_biotype_plot-pct.svg", "general_stats_table.svg", + "hisat2_deseq2_clustering-plot.svg", + "hisat2_deseq2_pca-plot.svg", "hisat2_pe_plot-cnt.svg", "hisat2_pe_plot-pct.svg", "hisat2_se_plot-cnt.svg", @@ -594,15 +596,13 @@ "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg", "samtools-stats-dp.svg", "samtools_alignment_plot-cnt.svg", - "samtools_alignment_plot-pct.svg", - "hisat2_deseq2_clustering-plot.svg", - "hisat2_deseq2_pca-plot.svg" + "samtools_alignment_plot-pct.svg" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:35:09.426445" + "timestamp": "2024-08-26T19:01:52.649421" }, "fastqc/raw": { "content": [ diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 8d6d24c80..99789ff7c 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -185,36 +185,36 @@ }, "star_salmon/samtools_stats": { "content": [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,e3689e1939a931a656ab14b5a40d27a9", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,990280b423241cd1d3e9ab3410841ee8", - "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,30b35c766650cfb3af89fa09c8654b59", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,451eeb9f3caea89d069f26a77a3ac9e9", - "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,a093ff94182b1cd6a206b019e43c8281", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,d0e0e89c8af100c2adfa7cbf0021f8a2", - "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "WT_REP1.sorted.bam.flagstat:md5,694fa7255da6612e0503f37b41cdbade", - "WT_REP1.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f", - "WT_REP2.sorted.bam.flagstat:md5,e1b514b8f09016ac33e31c25c8e5a447", - "WT_REP2.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.sorted.bam.stats", + "WT_REP1.sorted.bam.flagstat", + "WT_REP1.sorted.bam.idxstats", "WT_REP1.sorted.bam.stats", + "WT_REP2.sorted.bam.flagstat", + "WT_REP2.sorted.bam.idxstats", "WT_REP2.sorted.bam.stats" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T13:06:37.230258" + "timestamp": "2024-08-26T19:09:21.84327" }, "multiqc_plots": { "content": [ @@ -242,8 +242,6 @@ "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", "featurecounts_biotype_plot-cnt.png:md5,95b10627fff1af0a209b8e380f4a4d0b", "featurecounts_biotype_plot-pct.png:md5,f9c1cf03824ff9ba7da8537ecd93945b", - "picard_deduplication-cnt.png:md5,b09ea843c14ec1d0370fa56c8ce29e87", - "picard_deduplication-pct.png:md5,6bdbd89afeff028594ad2a5a38e9b2a7", "qualimap_gene_coverage_profile_Counts.png:md5,2d54a60bef3dfa978da48c1b6872c41c", "qualimap_gene_coverage_profile_Normalised.png:md5,a85a901be4c08c9dfcfd9fc87d890c1e", "rseqc_infer_experiment_plot.png:md5,5ce01a7b923f4e6433b76dd88ca22f42", @@ -254,8 +252,6 @@ "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", - "samtools_alignment_plot-cnt.png:md5,84f0e82efcef1221c5c2d292b4d4431c", - "samtools_alignment_plot-pct.png:md5,7836b2057272b390f75c890e26034ec2", "multiqc_report.html", "cutadapt_filtered_reads_plot-cnt.pdf", "cutadapt_filtered_reads_plot-pct.pdf", @@ -340,26 +336,30 @@ "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", - "rseqc_bam_stat.png", + "picard_deduplication-cnt.png", + "picard_deduplication-pct.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", + "rseqc_bam_stat.png", + "rseqc_inner_distance_plot_Counts.png", + "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", "rseqc_junction_annotation_junctions_plot_Events-pct.png", "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png", "rseqc_junction_annotation_junctions_plot_Junctions-pct.png", - "rseqc_read_distribution_plot-cnt.png", - "rseqc_read_distribution_plot-pct.png", - "rseqc_inner_distance_plot_Counts.png", - "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_saturation_plot_All_Junctions.png", "rseqc_junction_saturation_plot_Known_Junctions.png", "rseqc_junction_saturation_plot_Novel_Junctions.png", + "rseqc_read_distribution_plot-cnt.png", + "rseqc_read_distribution_plot-pct.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", "samtools-stats-dp.png", + "samtools_alignment_plot-cnt.png", + "samtools_alignment_plot-pct.png", "star_alignment_plot-cnt.png", "star_alignment_plot-pct.png", "star_salmon_deseq2_clustering-plot.png", @@ -443,7 +443,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:42:10.506344" + "timestamp": "2024-08-26T19:09:21.766479" }, "Params: --min_mapped_reads 90 - stub": { "content": [ @@ -634,9 +634,7 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,f3c566d2eaf6bf2ffe5ad12036ce3500", - "multiqc_picard_dups.txt:md5,6dff325f1bf12d9de88a11af272be755", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", - "picard_deduplication.txt:md5,bcf1670f90e552256db4de7fa65d5306", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -647,7 +645,6 @@ "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", - "samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", @@ -656,6 +653,7 @@ "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", "multiqc_general_stats.txt", + "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", "multiqc_rseqc_infer_experiment.txt", "multiqc_rseqc_junction_annotation.txt", @@ -678,6 +676,7 @@ "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", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", @@ -697,6 +696,7 @@ "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", "samtools-stats-dp.txt", + "samtools_alignment_plot.txt", "star_alignment_plot.txt", "star_summary_table.txt" ], @@ -704,7 +704,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:42:10.446106" + "timestamp": "2024-08-26T19:09:21.700284" }, "star_salmon/deseq2_qc": { "content": [ diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 9e1c4be55..a90fd3388 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -227,42 +227,42 @@ }, "star_salmon/samtools_stats": { "content": [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,9cb85f4008ba88f43e15fae47baad525", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,ba4001c9dec79a99b79e3162ba939f85", - "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,8ac0db45c52a28d167582874992e5833", - "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,ba4001c9dec79a99b79e3162ba939f85", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,0496e26c6be67b341255761a447b1569", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,fd9be758f872e026a22b3ed86628daed", - "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,12fb0d3b2c65e4738f30d530a329efb1", - "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,fd9be758f872e026a22b3ed86628daed", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,2df8940452346d9d82b95206d4b304e1", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,b42aae33316d4a5a58459143eab2e4f0", - "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,3535e1cbe40f90e3749dad930251dd9f", - "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,b42aae33316d4a5a58459143eab2e4f0", - "WT_REP1.markdup.sorted.bam.flagstat:md5,d931e8e7fd82c493d12e78f404b13f2c", - "WT_REP1.markdup.sorted.bam.idxstats:md5,d2c9dce1a6fcf97a65e3b4313d8a29ef", - "WT_REP1.sorted.bam.flagstat:md5,7bffb4d7dff374febb1ca99c1436ebf7", - "WT_REP1.sorted.bam.idxstats:md5,d2c9dce1a6fcf97a65e3b4313d8a29ef", - "WT_REP2.markdup.sorted.bam.flagstat:md5,ca4330f24cf0d98ceb18c617294aed9e", - "WT_REP2.markdup.sorted.bam.idxstats:md5,47d975efef6048ae120f71124e2b378f", - "WT_REP2.sorted.bam.flagstat:md5,41d560c31aa88088efffe62d0f488583", - "WT_REP2.sorted.bam.idxstats:md5,47d975efef6048ae120f71124e2b378f", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.sorted.bam.stats", + "WT_REP1.markdup.sorted.bam.flagstat", + "WT_REP1.markdup.sorted.bam.idxstats", "WT_REP1.markdup.sorted.bam.stats", + "WT_REP1.sorted.bam.flagstat", + "WT_REP1.sorted.bam.idxstats", "WT_REP1.sorted.bam.stats", + "WT_REP2.markdup.sorted.bam.flagstat", + "WT_REP2.markdup.sorted.bam.idxstats", "WT_REP2.markdup.sorted.bam.stats", + "WT_REP2.sorted.bam.flagstat", + "WT_REP2.sorted.bam.idxstats", "WT_REP2.sorted.bam.stats" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T13:19:36.4571" + "timestamp": "2024-08-26T19:21:47.319657" }, "multiqc_plots": { "content": [ @@ -289,8 +289,6 @@ "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", "featurecounts_biotype_plot-cnt.png:md5,ed2c5826034fcf2417afe79902897c45", "featurecounts_biotype_plot-pct.png:md5,96abf028d347f568289b3a741aa8c08d", - "picard_deduplication-cnt.png:md5,015a79422216c364e1d8ae4389b63838", - "picard_deduplication-pct.png:md5,73b0c4736e772c7daeae10f09dd73d21", "qualimap_gene_coverage_profile_Counts.png:md5,fb739f4297a156f0913f21f20090f598", "qualimap_gene_coverage_profile_Normalised.png:md5,710960caa692f0d0eceadcc83650cf00", "rseqc_infer_experiment_plot.png:md5,49f1faa0849545b8a75af2657d0ee5fa", @@ -301,8 +299,6 @@ "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,f12bcf930eac8ed45da7b4668b1169c8", "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,ff8e0f61b02f8c9abcce5e83214c87fd", "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,1a029e5d23f82d537470363a065b644a", - "samtools_alignment_plot-cnt.png:md5,788eabe2733b62baa802695e558f7198", - "samtools_alignment_plot-pct.png:md5,4c05880be8fd1968d11fb5d621fdac16", "sortmerna-detailed-plot-cnt.png:md5,3875997f21c98e8906cd182d959e0020", "sortmerna-detailed-plot-pct.png:md5,971398875e5cbd50313b6fee7eeb302c", "multiqc_report.html", @@ -390,6 +386,8 @@ "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", + "picard_deduplication-cnt.png", + "picard_deduplication-pct.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", @@ -410,6 +408,8 @@ "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", "samtools-stats-dp.png", + "samtools_alignment_plot-cnt.png", + "samtools_alignment_plot-pct.png", "star_alignment_plot-cnt.png", "star_alignment_plot-pct.png", "star_salmon_deseq2_clustering-plot.png", @@ -494,7 +494,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:55:04.146511" + "timestamp": "2024-08-26T19:21:47.217167" }, "Params: --remove_ribo_rna - stub": { "content": [ @@ -700,9 +700,7 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,54f0eef4ab0ecf6a03505b18752b43cd", - "multiqc_picard_dups.txt:md5,5e93e7e4ecaeed2550bffa44dc32184b", "multiqc_samtools_idxstats.txt:md5,413ba06f3d8e4ab0dbde8ef8952c4b32", - "picard_deduplication.txt:md5,32d912bd78e7d99276a52e13575d08aa", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -713,7 +711,6 @@ "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", - "samtools_alignment_plot.txt:md5,207e0c3f557679f37350577364b8956d", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", @@ -722,17 +719,11 @@ "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.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", - "qualimap_genomic_origin.txt", - "qualimap_rnaseq_genome_results.txt", - "rseqc_bam_stat.txt", - "rseqc_junction_annotation_junctions_plot_Events.txt", - "rseqc_junction_annotation_junctions_plot_Junctions.txt", - "rseqc_read_distribution_plot.txt", - "rseqc_read_dups_plot.txt", - "multiqc_rseqc_infer_experiment.txt", "multiqc_salmon.txt", "multiqc_salmon_deseq2_clustering-plot.txt", "multiqc_salmon_deseq2_clustering-plot_1.txt", @@ -752,18 +743,27 @@ "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", + "qualimap_rnaseq_genome_results.txt", + "rseqc_bam_stat.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", + "rseqc_read_distribution_plot.txt", "rseqc_read_dups.txt", + "rseqc_read_dups_plot.txt", "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "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" @@ -772,7 +772,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:55:04.076927" + "timestamp": "2024-08-26T19:21:47.111212" }, "star_salmon/deseq2_qc": { "content": [ diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 514f7b216..397229679 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -111,30 +111,30 @@ "multiqc_citations.txt:md5,ef51c78faebdd32bad296ba14406b41e", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", - "picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", - "samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", "junction_saturation_novel.txt", "multiqc_data.json", "multiqc_general_stats.txt", + "multiqc_picard_dups.txt", "multiqc_salmon.txt", "multiqc_samtools_flagstat.txt", "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", "multiqc_star.txt", + "picard_deduplication.txt", "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", "samtools-stats-dp.txt", + "samtools_alignment_plot.txt", "star_alignment_plot.txt", "star_summary_table.txt" ], @@ -142,7 +142,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T12:11:57.852981" + "timestamp": "2024-08-26T19:28:48.798947" }, "references": { "content": [ @@ -207,42 +207,42 @@ }, "star_salmon/samtools_stats": { "content": [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,e3689e1939a931a656ab14b5a40d27a9", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,990280b423241cd1d3e9ab3410841ee8", - "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,30b35c766650cfb3af89fa09c8654b59", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,451eeb9f3caea89d069f26a77a3ac9e9", - "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,a093ff94182b1cd6a206b019e43c8281", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,d0e0e89c8af100c2adfa7cbf0021f8a2", - "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "WT_REP1.markdup.sorted.bam.flagstat:md5,501ff3ad52e73a6168814545bb99abf8", - "WT_REP1.markdup.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f", - "WT_REP1.sorted.bam.flagstat:md5,694fa7255da6612e0503f37b41cdbade", - "WT_REP1.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f", - "WT_REP2.markdup.sorted.bam.flagstat:md5,3530fb25cc5dfe72cc39053264b3b0cc", - "WT_REP2.markdup.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68", - "WT_REP2.sorted.bam.flagstat:md5,e1b514b8f09016ac33e31c25c8e5a447", - "WT_REP2.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.sorted.bam.stats", + "WT_REP1.markdup.sorted.bam.flagstat", + "WT_REP1.markdup.sorted.bam.idxstats", "WT_REP1.markdup.sorted.bam.stats", + "WT_REP1.sorted.bam.flagstat", + "WT_REP1.sorted.bam.idxstats", "WT_REP1.sorted.bam.stats", + "WT_REP2.markdup.sorted.bam.flagstat", + "WT_REP2.markdup.sorted.bam.idxstats", "WT_REP2.markdup.sorted.bam.stats", + "WT_REP2.sorted.bam.flagstat", + "WT_REP2.sorted.bam.idxstats", "WT_REP2.sorted.bam.stats" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T12:23:34.122811" + "timestamp": "2024-08-26T19:28:48.898246" }, "salmon": { "content": [ @@ -280,14 +280,10 @@ "fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", "fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", - "picard_deduplication-cnt.png:md5,52297225fca30daa61d3271754bdbc1a", - "picard_deduplication-pct.png:md5,b2aa123cc65c933ca630d89c6f098550", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,d5d8a85b7ad72a0cb93d9283ea12b23f", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d", - "samtools_alignment_plot-cnt.png:md5,84f0e82efcef1221c5c2d292b4d4431c", - "samtools_alignment_plot-pct.png:md5,7836b2057272b390f75c890e26034ec2", "multiqc_report.html", "cutadapt_filtered_reads_plot-cnt.pdf", "cutadapt_filtered_reads_plot-pct.pdf", @@ -326,10 +322,14 @@ "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", + "picard_deduplication-cnt.png", + "picard_deduplication-pct.png", "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", "samtools-stats-dp.png", + "samtools_alignment_plot-cnt.png", + "samtools_alignment_plot-pct.png", "star_alignment_plot-cnt.png", "star_alignment_plot-pct.png", "star_summary_table.png", @@ -370,7 +370,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T12:11:57.881376" + "timestamp": "2024-08-26T19:28:48.850602" }, "star_salmon/picard_metrics": { "content": [ diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 2d36963fa..f71775121 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -108,9 +108,7 @@ "multiqc_citations.txt:md5,1f80cefb6f0103d9a316c396a9441a90", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_featurecounts_biotype_plot.txt:md5,567475905baa63091cfd0560fb297e10", - "multiqc_picard_dups.txt:md5,825db93f9329a134414feff0a3ce601c", "multiqc_samtools_idxstats.txt:md5,adf5f32fa1485ad0f4dacdfedc7b4bbc", - "picard_deduplication.txt:md5,b14cb08fecb135e93b8dd4e16f9e44fd", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -121,7 +119,6 @@ "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,a557130553131c893398532377d3b525", - "samtools_alignment_plot.txt:md5,8a3a4dfbbfc068f150836ab6e163424a", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", "junction_saturation_novel.txt", @@ -129,6 +126,7 @@ "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", "multiqc_general_stats.txt", + "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", "multiqc_rseqc_infer_experiment.txt", "multiqc_rseqc_junction_annotation.txt", @@ -151,6 +149,7 @@ "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", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", @@ -170,6 +169,7 @@ "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", "samtools-stats-dp.txt", + "samtools_alignment_plot.txt", "star_alignment_plot.txt", "star_summary_table.txt" ], @@ -177,7 +177,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T17:04:58.433949" + "timestamp": "2024-08-26T19:36:32.752543" }, "star_salmon/rseqc": { "content": [ @@ -364,42 +364,42 @@ }, "star_salmon/samtools_stats": { "content": [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,1c541ffc31671136810db9586f150155", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,cc2766e4a48241322c2528aa61f7d208", - "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,94c8742a1292d77da53a27c535483247", - "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,cc2766e4a48241322c2528aa61f7d208", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,083e57d9f4bbb14e0b46622bbaeaae8c", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,e27c453209fefead3f703e3ab1c0b3f7", - "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,b67e1eb8b5bc947d670ac81ef8f3aeda", - "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,e27c453209fefead3f703e3ab1c0b3f7", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,36cebb6188f9fd742562493e6a6640fe", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,79cebfe8ad6602dffd2199f5472b28d0", - "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,ef6a9825af30377b0781a4d4a29b932b", - "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,79cebfe8ad6602dffd2199f5472b28d0", - "WT_REP1.markdup.sorted.bam.flagstat:md5,6d3457815eb053088f68f84efcd20280", - "WT_REP1.markdup.sorted.bam.idxstats:md5,0da68758394dbc7470b2a2ea50bb8814", - "WT_REP1.sorted.bam.flagstat:md5,b1909dcb78af39009545b03fe1584cc5", - "WT_REP1.sorted.bam.idxstats:md5,0da68758394dbc7470b2a2ea50bb8814", - "WT_REP2.markdup.sorted.bam.flagstat:md5,5cd1d564776bee679329d90de069b2d6", - "WT_REP2.markdup.sorted.bam.idxstats:md5,22d51757c5b252c030984f169a131237", - "WT_REP2.sorted.bam.flagstat:md5,84f3a9290292d1a47ed095616b506ebd", - "WT_REP2.sorted.bam.idxstats:md5,22d51757c5b252c030984f169a131237", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.sorted.bam.stats", + "WT_REP1.markdup.sorted.bam.flagstat", + "WT_REP1.markdup.sorted.bam.idxstats", "WT_REP1.markdup.sorted.bam.stats", + "WT_REP1.sorted.bam.flagstat", + "WT_REP1.sorted.bam.idxstats", "WT_REP1.sorted.bam.stats", + "WT_REP2.markdup.sorted.bam.flagstat", + "WT_REP2.markdup.sorted.bam.idxstats", "WT_REP2.markdup.sorted.bam.stats", + "WT_REP2.sorted.bam.flagstat", + "WT_REP2.sorted.bam.idxstats", "WT_REP2.sorted.bam.stats" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T15:27:30.577354" + "timestamp": "2024-08-26T19:36:32.899658" }, "salmon/deseq2_qc": { "content": [ @@ -456,8 +456,6 @@ "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", "featurecounts_biotype_plot-cnt.png:md5,dcb37b4ce2fff5ca2e22767b172e55a8", "featurecounts_biotype_plot-pct.png:md5,b15370ba2c056815939251f820d9e2af", - "picard_deduplication-cnt.png:md5,e01e21b8894cdc3c540d82619aa66f62", - "picard_deduplication-pct.png:md5,b6cb33b941cbc71c22167d01d61b38f8", "qualimap_gene_coverage_profile_Counts.png:md5,8312f777db61509caa66d1f53a4b6b07", "qualimap_gene_coverage_profile_Normalised.png:md5,66acb12427130766801a8376f95ed88b", "rseqc_infer_experiment_plot.png:md5,c3108e35020ee93a77a62ea0167613b2", @@ -468,8 +466,6 @@ "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d", "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,64f2501f91db6dd0edd5e49c0b9ca8b7", "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,52f30fc3448f43735ce9eca54b306c8e", - "samtools_alignment_plot-cnt.png:md5,267822d4de67c0c7bc543c704bec1cbe", - "samtools_alignment_plot-pct.png:md5,17f1dbee7ed2fa1039596175d9f34b42", "multiqc_report.html", "dupradar-section-plot.pdf", "fail_strand_check_table.pdf", @@ -533,6 +529,8 @@ "fastqc_per_base_sequence_quality_plot.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", + "picard_deduplication-cnt.png", + "picard_deduplication-pct.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", @@ -553,6 +551,8 @@ "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", "samtools-stats-dp.png", + "samtools_alignment_plot-cnt.png", + "samtools_alignment_plot-pct.png", "star_alignment_plot-cnt.png", "star_alignment_plot-pct.png", "star_salmon_deseq2_clustering-plot.png", @@ -619,7 +619,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T17:04:58.556659" + "timestamp": "2024-08-26T19:36:32.816392" }, "star_salmon/picard_metrics": { "content": [ diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index beefc9b53..4d66a38db 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -82,23 +82,17 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,27bb37d346e8f0960c882a3676e219e8", - "multiqc_picard_dups.txt:md5,0e258d3ce451fa5233c81a631c807636", - "multiqc_rsem.txt:md5,426cfb38a96c0d7111336be3164171fb", "multiqc_samtools_idxstats.txt:md5,1cbc64fc9713831a6f45effc0cfe6a39", - "picard_deduplication.txt:md5,b6e23251b2007c0759c347aaa31d2a76", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,387c07f2a93e3d13048c4cd788d1fcc3", "qualimap_gene_coverage_profile_Normalised.txt:md5,35f0b71796622269bc51cf1e7a0650ab", "qualimap_rnaseq_cov_hist.txt:md5,a620cb9d1878e86e10e87500e98122f1", - "rsem_assignment_plot.txt:md5,136b1ca144da9a1b304ff3471ff44390", - "rsem_multimapping_rates.txt:md5,5d91bb56472834622e81e7919f746250", "rseqc_infer_experiment_plot.txt:md5,c0ddf72b026cdc54ad03e75eaa636f7e", "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", - "samtools_alignment_plot.txt:md5,911758be5fed6e87b16b288caa39db8e", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", @@ -107,6 +101,9 @@ "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", "multiqc_general_stats.txt", + "multiqc_picard_dups.txt", + "picard_deduplication.txt", + "multiqc_rsem.txt", "multiqc_rseqc_bam_stat.txt", "multiqc_rseqc_infer_experiment.txt", "multiqc_rseqc_junction_annotation.txt", @@ -131,6 +128,8 @@ "multiqc_star_rsem_deseq2_pca-plot.txt", "qualimap_genomic_origin.txt", "qualimap_rnaseq_genome_results.txt", + "rsem_assignment_plot.txt", + "rsem_multimapping_rates.txt", "rseqc_bam_stat.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", @@ -148,6 +147,7 @@ "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", "samtools-stats-dp.txt", + "samtools_alignment_plot.txt", "star_alignment_plot.txt", "star_summary_table.txt" ], @@ -155,46 +155,46 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T17:38:04.036713" + "timestamp": "2024-08-26T19:43:20.562966" }, "star_rsem/samtools_stats": { "content": [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,b4655647adf50bc443313ad150fe2afb", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,99f719593d131af1a215fbb5032acc1e", - "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,c2f5d38f0b54990850f4aee711080c99", - "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,99f719593d131af1a215fbb5032acc1e", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,8678d9c4f5280b7b2f7a69034c240551", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,d33f03663678f3c9a063a9cf55b1b1ec", - "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,25e061e1ffb777d0f7f405ffd26533b8", - "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,d33f03663678f3c9a063a9cf55b1b1ec", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,df6f55cec42df6fdf56f768af3cb8d24", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,37150ce5f3ee6d27ef1994a285ecf7be", - "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,4a55cc0140668a8d572e820159cecf55", - "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,37150ce5f3ee6d27ef1994a285ecf7be", - "WT_REP1.markdup.sorted.bam.flagstat:md5,35022e2aa70234da8122867da4207ccf", - "WT_REP1.markdup.sorted.bam.idxstats:md5,7be99ac4f46a81fa42302aea5da5db8e", - "WT_REP1.sorted.bam.flagstat:md5,afc212aa6cc3394a49d0c550ef202df5", - "WT_REP1.sorted.bam.idxstats:md5,7be99ac4f46a81fa42302aea5da5db8e", - "WT_REP2.markdup.sorted.bam.flagstat:md5,5d24f4ee7aef04aee46c2870c7b0d5c9", - "WT_REP2.markdup.sorted.bam.idxstats:md5,7cccd0ecf83b400e7da8afa93018749b", - "WT_REP2.sorted.bam.flagstat:md5,455fd491f2740a12f56fff9c9af44512", - "WT_REP2.sorted.bam.idxstats:md5,7cccd0ecf83b400e7da8afa93018749b", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.sorted.bam.stats", + "WT_REP1.markdup.sorted.bam.flagstat", + "WT_REP1.markdup.sorted.bam.idxstats", "WT_REP1.markdup.sorted.bam.stats", + "WT_REP1.sorted.bam.flagstat", + "WT_REP1.sorted.bam.idxstats", "WT_REP1.sorted.bam.stats", + "WT_REP2.markdup.sorted.bam.flagstat", + "WT_REP2.markdup.sorted.bam.idxstats", "WT_REP2.markdup.sorted.bam.stats", + "WT_REP2.sorted.bam.flagstat", + "WT_REP2.sorted.bam.idxstats", "WT_REP2.sorted.bam.stats" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T17:38:04.566101" + "timestamp": "2024-08-26T19:43:21.034611" }, "trimgalore": { "content": [ @@ -289,39 +289,39 @@ "content": [ "RAP1_IAA_30M_REP1.genes.results:md5,9f76f2687983812c29b108b1faadbb92", "RAP1_IAA_30M_REP1.isoforms.results:md5,7e8af74655cfa3533cdd8de305f101a4", - "RAP1_IAA_30M_REP1.cnt:md5,0dd947319d4be61a70c0972a341df022", - "RAP1_IAA_30M_REP1.model:md5,1f58eab071b48d7dd3563bf1cc49262f", - "RAP1_IAA_30M_REP1.theta:md5,75f1d4cd262c6f668e9851cc399d96be", "RAP1_UNINDUCED_REP1.genes.results:md5,0ebfda99b1e92d071d3d8f12f37d25cd", "RAP1_UNINDUCED_REP1.isoforms.results:md5,5fe29701e388c9ac813ab0e8f02e1e9b", - "RAP1_UNINDUCED_REP1.cnt:md5,722a818544a56ed0d86c2370831ecb18", - "RAP1_UNINDUCED_REP1.model:md5,262576fb8671db5c7debb045040c274a", - "RAP1_UNINDUCED_REP1.theta:md5,94a87800469746b15e219bb68c65f905", "RAP1_UNINDUCED_REP2.genes.results:md5,e6bed419600f1bdc30c59f2c2f0beec3", "RAP1_UNINDUCED_REP2.isoforms.results:md5,35ede7929d359424798d92398d6d9518", - "RAP1_UNINDUCED_REP2.cnt:md5,fa6b94589d49e68e53c19dee98d4f27b", - "RAP1_UNINDUCED_REP2.model:md5,34fb5bf5adf3a9e7ebee83533697dc88", - "RAP1_UNINDUCED_REP2.theta:md5,bd7a159324dc692dcc8ec7bec78167d9", "WT_REP1.genes.results:md5,8cd8c1d87970dbae9983250530a5915d", "WT_REP1.isoforms.results:md5,993a65e02daecd9457c529d118b6e8ac", - "WT_REP1.cnt:md5,938a5d93e8900fcf0771cbb9c6bdc33c", - "WT_REP1.model:md5,752de4891bcbba0072ca1966191fd8fc", - "WT_REP1.theta:md5,2a22bcd7d927e558c55a339ca18c2fe9", "WT_REP2.genes.results:md5,78387c8f57175756fda9c153790f3d37", "WT_REP2.isoforms.results:md5,89bd225b6702ec3edbe13d9443fce40f", - "WT_REP2.cnt:md5,667a6095dc7317aef8bc44d624dee544", - "WT_REP2.model:md5,d416932acda320ec20af45203c6038e9", - "WT_REP2.theta:md5,fe675b73daeca53bb506a009cca2efb6", "rsem.merged.gene_counts.tsv:md5,47f272199f24af4473c959df2a9149dc", "rsem.merged.gene_tpm.tsv:md5,a197b2d131dea75a83f9c219c23fb7a0", "rsem.merged.transcript_counts.tsv:md5,ffc75fd409d75edf5209e8e1af8ec8fc", - "rsem.merged.transcript_tpm.tsv:md5,b836618c69d111edf635ce7244ee85e5" + "rsem.merged.transcript_tpm.tsv:md5,b836618c69d111edf635ce7244ee85e5", + "RAP1_IAA_30M_REP1.cnt", + "RAP1_IAA_30M_REP1.model", + "RAP1_IAA_30M_REP1.theta", + "RAP1_UNINDUCED_REP1.cnt", + "RAP1_UNINDUCED_REP1.model", + "RAP1_UNINDUCED_REP1.theta", + "RAP1_UNINDUCED_REP2.cnt", + "RAP1_UNINDUCED_REP2.model", + "RAP1_UNINDUCED_REP2.theta", + "WT_REP1.cnt", + "WT_REP1.model", + "WT_REP1.theta", + "WT_REP2.cnt", + "WT_REP2.model", + "WT_REP2.theta" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T17:38:04.442121" + "timestamp": "2024-08-26T19:43:20.906583" }, "star_rsem/stringtie": { "content": [ @@ -374,9 +374,6 @@ }, "multiqc_plots": { "content": [ - "rsem_assignment_plot-cnt.pdf:md5,a1673a928363f38e45e3a1327338d367", - "rsem_assignment_plot-pct.pdf:md5,ce967bcc84c0a23c441514e51d759c16", - "rsem_multimapping_rates.pdf:md5,bace39413eb0e6143dd105dc503c8bb4", "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", @@ -400,12 +397,8 @@ "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", "featurecounts_biotype_plot-cnt.png:md5,b033cedf28f1b3f6f48f1ed793160679", "featurecounts_biotype_plot-pct.png:md5,1921c3931d871f8326a6a6c5c8278815", - "picard_deduplication-cnt.png:md5,a0e470143af7da76943152badf83ef1d", - "picard_deduplication-pct.png:md5,250f89fa9407e7cc8d467de6b212dff8", "qualimap_gene_coverage_profile_Counts.png:md5,04a262d5af169d6d771e48555adab37e", "qualimap_gene_coverage_profile_Normalised.png:md5,3bddc4f2a7d462996628e33daf490247", - "rsem_assignment_plot-cnt.png:md5,15fd495eeee0d791d8fe663c9a981b6a", - "rsem_assignment_plot-pct.png:md5,e38d64af2acd404fcdb72a55a6dd1986", "rsem_multimapping_rates.png:md5,e93d35b86e1be681eae9b6ad19e12350", "rseqc_infer_experiment_plot.png:md5,1a3a792e9a6e0c0f93c082594b24e566", "rseqc_read_dups_plot.png:md5,b79c01ce4697ebb7e0ebb4a3da5b44f7", @@ -415,11 +408,6 @@ "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,10d7c1023bcf922ac45e653a58ee13c8", "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,2edc4372d981aacfceb4f16da598d63a", "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,5d2286a4f77000c199ed22517338da4a", - "samtools_alignment_plot-cnt.png:md5,4640ff5819853aae35a7972dda40f6ab", - "samtools_alignment_plot-pct.png:md5,092bda5422215c1d2d7797e38802e599", - "rsem_assignment_plot-cnt.svg:md5,1791d7a84262b0299a8b81af0ac4eb59", - "rsem_assignment_plot-pct.svg:md5,64d6c83c006863f891689fcd535545b8", - "rsem_multimapping_rates.svg:md5,91e5caa077ff8ec40609d4b8f74daaf5", "multiqc_report.html", "cutadapt_filtered_reads_plot-cnt.pdf", "cutadapt_filtered_reads_plot-pct.pdf", @@ -460,6 +448,9 @@ "qualimap_gene_coverage_profile_Normalised.pdf", "qualimap_genomic_origin-cnt.pdf", "qualimap_genomic_origin-pct.pdf", + "rsem_assignment_plot-cnt.pdf", + "rsem_assignment_plot-pct.pdf", + "rsem_multimapping_rates.pdf", "rseqc_bam_stat.pdf", "rseqc_infer_experiment_plot.pdf", "rseqc_inner_distance_plot_Counts.pdf", @@ -503,8 +494,12 @@ "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", + "picard_deduplication-cnt.png", + "picard_deduplication-pct.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", + "rsem_assignment_plot-cnt.png", + "rsem_assignment_plot-pct.png", "rseqc_bam_stat.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", @@ -523,6 +518,8 @@ "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", "samtools-stats-dp.png", + "samtools_alignment_plot-cnt.png", + "samtools_alignment_plot-pct.png", "star_alignment_plot-cnt.png", "star_alignment_plot-pct.png", "star_rsem_deseq2_clustering-plot.png", @@ -567,6 +564,9 @@ "qualimap_gene_coverage_profile_Normalised.svg", "qualimap_genomic_origin-cnt.svg", "qualimap_genomic_origin-pct.svg", + "rsem_assignment_plot-cnt.svg", + "rsem_assignment_plot-pct.svg", + "rsem_multimapping_rates.svg", "rseqc_bam_stat.svg", "rseqc_infer_experiment_plot.svg", "rseqc_inner_distance_plot_Counts.svg", @@ -605,7 +605,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T17:38:04.178293" + "timestamp": "2024-08-26T19:43:20.672077" }, "star_rsem/picard_metrics": { "content": [ @@ -752,17 +752,17 @@ }, "star_rsem/log": { "content": [ - "RAP1_IAA_30M_REP1.log:md5,9b52ef81b57686c41c63d0d53c1a72d5", - "RAP1_UNINDUCED_REP1.log:md5,f0f9f92d686ce202ee464329a56b1f46", - "RAP1_UNINDUCED_REP2.log:md5,c9d68358d6f21024cb235b7191fa8290", - "WT_REP1.log:md5,cd3e07d999a1c8ffbce0a152004b7a12", - "WT_REP2.log:md5,39695fc38849c701844116f3209ccefc" + "RAP1_IAA_30M_REP1.log", + "RAP1_UNINDUCED_REP1.log", + "RAP1_UNINDUCED_REP2.log", + "WT_REP1.log", + "WT_REP2.log" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T17:38:04.313526" + "timestamp": "2024-08-26T19:43:20.787774" }, "Params: --aligner star_rsem - stub": { "content": [