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AratzAratz
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Fix group reports for paired reads
1 parent 00470cb commit 13b2bd5

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2 files changed

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-3
lines changed

2 files changed

+95
-3
lines changed

‎tests/MiSeq_PairedEnd.main.nf.test.snap‎

Lines changed: 94 additions & 2 deletions
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@@ -1,7 +1,7 @@
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{
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"MiSeq data test": {
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"content": [
4-
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8,
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{
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"FASTQC": {
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"fastqc": "0.12.1"
@@ -116,6 +116,83 @@
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"multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
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"multiqc/global_report/multiqc_plots/svg/general_stats_table.svg",
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"multiqc/global_report/multiqc_report.html",
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"multiqc/group_reports",
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"multiqc/group_reports/Bpacificus",
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"multiqc/group_reports/Bpacificus/multiqc_data",
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"multiqc/group_reports/Bpacificus/multiqc_data/fastq_screen_plot.txt",
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"multiqc/group_reports/Bpacificus/multiqc_data/fastqc-status-check-heatmap.txt",
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"multiqc/group_reports/Bpacificus/multiqc_data/fastqc_adapter_content_plot.txt",
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"multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_base_n_content_plot.txt",
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"multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_base_sequence_quality_plot.txt",
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"multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
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"multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
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"multiqc/group_reports/Bpacificus/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt",
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"multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_counts_plot.txt",
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"multiqc/group_reports/Bpacificus/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
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"multiqc/group_reports/Bpacificus/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
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"multiqc/group_reports/Bpacificus/multiqc_data/multiqc.log",
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"multiqc/group_reports/Bpacificus/multiqc_data/multiqc_SAMPLE_PAIRED_END_1_1.txt",
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"multiqc/group_reports/Bpacificus/multiqc_data/multiqc_SAMPLE_PAIRED_END_2_2.txt",
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"multiqc/group_reports/Bpacificus/multiqc_data/multiqc_citations.txt",
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"multiqc/group_reports/Bpacificus/multiqc_data/multiqc_data.json",
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"multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastq_screen.txt",
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"multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastqc.txt",
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"multiqc/group_reports/Bpacificus/multiqc_data/multiqc_general_stats.txt",
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"multiqc/group_reports/Bpacificus/multiqc_data/multiqc_software_versions.txt",
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"multiqc/group_reports/Bpacificus/multiqc_data/multiqc_sources.txt",
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"multiqc/group_reports/Bpacificus/multiqc_plots",
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"multiqc/group_reports/Bpacificus/multiqc_plots/pdf",
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"multiqc/group_reports/Bpacificus/multiqc_plots/pdf/SAMPLE_PAIRED_END_1_1.pdf",
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"multiqc/group_reports/Bpacificus/multiqc_plots/pdf/SAMPLE_PAIRED_END_2_2.pdf",
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"multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf",
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"multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-pct.pdf",
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"multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
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"multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
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"multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
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"multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
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"multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
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"multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
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"multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
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"multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
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"multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
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"multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
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"multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
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"multiqc/group_reports/Bpacificus/multiqc_plots/pdf/general_stats_table.pdf",
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"multiqc/group_reports/Bpacificus/multiqc_plots/png",
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"multiqc/group_reports/Bpacificus/multiqc_plots/png/SAMPLE_PAIRED_END_1_1.png",
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"multiqc/group_reports/Bpacificus/multiqc_plots/png/SAMPLE_PAIRED_END_2_2.png",
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"multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-cnt.png",
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"multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-pct.png",
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"multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc-status-check-heatmap.png",
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"multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_adapter_content_plot.png",
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"multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
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"multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
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"multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
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"multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
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"multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png",
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"multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png",
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"multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png",
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"multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
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"multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
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"multiqc/group_reports/Bpacificus/multiqc_plots/png/general_stats_table.png",
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"multiqc/group_reports/Bpacificus/multiqc_plots/svg",
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"multiqc/group_reports/Bpacificus/multiqc_plots/svg/SAMPLE_PAIRED_END_1_1.svg",
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"multiqc/group_reports/Bpacificus/multiqc_plots/svg/SAMPLE_PAIRED_END_2_2.svg",
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"multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-cnt.svg",
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"multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-pct.svg",
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"multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
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"multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
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"multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
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"multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
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"multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
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"multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
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"multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
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"multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
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"multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg",
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"multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
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"multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
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"multiqc/group_reports/Bpacificus/multiqc_plots/svg/general_stats_table.svg",
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"multiqc/group_reports/Bpacificus/multiqc_report.html",
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"pipeline_info",
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"pipeline_info/nf_core_seqinspector_software_mqc_versions.yml",
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"seqfu_stats",
@@ -148,6 +225,21 @@
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"multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
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"multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
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"multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
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"fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd",
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"fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b",
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"fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445",
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"fastqc_per_base_n_content_plot.txt:md5,4eca1ef40d4d3d318b82e68e9fa3c589",
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"fastqc_per_base_sequence_quality_plot.txt:md5,218757a51c3de79a39a704c979df03da",
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"fastqc_per_sequence_gc_content_plot_Counts.txt:md5,a4035ac9f0a0c07574130758b06630d7",
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"fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,637b937e023c84115ec06b529cc8ec1b",
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"fastqc_per_sequence_quality_scores_plot.txt:md5,47d60153a430e2b8da51655704c2b31b",
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"fastqc_sequence_counts_plot.txt:md5,10737092a3473fba81fbe49555512b2b",
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"fastqc_sequence_duplication_levels_plot.txt:md5,6412f57686de02e1f1c3751a7ca2be8b",
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"multiqc_SAMPLE_PAIRED_END_1_1.txt:md5,f6a5c7426b2c70dba8566b1f27d27fbf",
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"multiqc_SAMPLE_PAIRED_END_2_2.txt:md5,f531e01892d985ca20fc4924dec7b9f2",
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"multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
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"multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5",
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"multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984",
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"SAMPLE_PAIRED_END_1_1.tsv:md5,bbd911ff3fa43212dfd4c5a5872dbdb6",
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"SAMPLE_PAIRED_END_1_1_mqc.txt:md5,cd60f746b6749cc66213d031af1b931c",
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"SAMPLE_PAIRED_END_2_2.tsv:md5,152566a128dd657da33465b4966b5799",
@@ -158,6 +250,6 @@
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"nf-test": "0.9.0",
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"nextflow": "24.10.4"
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},
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"timestamp": "2025-03-25T10:33:30.467558"
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"timestamp": "2025-03-25T12:00:04.338174"
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}
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}

‎workflows/seqinspector.nf‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -188,7 +188,7 @@ workflow SEQINSPECTOR {
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.map { file -> [ (file =~ /\[TAG:(.+)\]/)[0][1], file ] }
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.join(mqc_by_tag)
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.multiMap { sample_tag, config, samples ->
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samples_per_tag: samples
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samples_per_tag: samples.flatten()
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config: config
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}
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