diff --git a/tests/test.nf.test b/tests/test.nf.test index 0e188f09..bf910a3e 100644 --- a/tests/test.nf.test +++ b/tests/test.nf.test @@ -58,12 +58,13 @@ nextflow_pipeline { def stable_content_mapstats = getAllFilesFromDir("$outputDir/mapstats" , true , ['**/*.html', '**/mapped_reads_gc-content_distribution.txt', '**/genome_gc_content_per_window.png'], null , ['**/*.{bed,json,txt,log,css,png,js}'] ) def stable_name_mapstats = getAllFilesFromDir("$outputDir/mapstats" , true , null , null , ['**/*.html', '**/mapped_reads_gc-content_distribution.txt', '**/genome_gc_content_per_window.png'] ) + // MultiQC + def stable_name_multiqc = getAllFilesFromDir("$outputDir/multiqc" , true , null , null , ['*', '**/*'] ) + // Preprocessing def stable_content_preprocessing = getAllFilesFromDir("$outputDir/preprocessing" , true , ['**/*.{zip,log}', '**/*fastp.html'], null , ['**/*'] ) def stable_name_preprocessing = getAllFilesFromDir("$outputDir/preprocessing" , true , null , null , ['**/*.{zip,log}', '**/*fastp.html'] ) - // TODO MultiQC - // TODO assertAll( { assert workflow.success }, @@ -74,20 +75,15 @@ nextflow_pipeline { // Checking changes to contents of each section { assert snapshot( stable_content_bamfiltering , stable_name_bamfiltering*.name ).match("bam_filtering") }, { assert snapshot( stable_content_baminputstats ).match("bam_input_stats") }, + { assert snapshot( stable_content_damageestimation, stable_name_damageestimation*.name ).match("damage_estimation") }, { assert snapshot( stable_content_deduplication , stable_name_deduplication*.name ).match("deduplication") }, { assert snapshot( stable_content_final_bams , stable_name_final_bams*.name ).match("final_bams") }, // NOTE: The snapshot section for mapping cannot be named 'mapping'. See https://github.com/askimed/nf-test/issues/279 { assert snapshot( stable_content_mapping , stable_name_mapping*.name ).match("mapping_output") }, { assert snapshot( stable_content_mapstats , stable_name_mapstats*.name ).match("mapstats") }, - { assert snapshot( stable_content_damageestimation, stable_name_damageestimation*.name ).match("damage_estimation") }, + { assert snapshot( stable_name_multiqc*.name ).match("multiqc") }, { assert snapshot( stable_content_preprocessing , stable_name_preprocessing*.name ).match("preprocessing") }, - // // MultiQC - // { assert snapshot( - // path("$outputDir/multiqc/multiqc_report.html").exists() - // ).match("multiqc") - // }, - // Versions { assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() }, diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap index 1f535ea6..0332e54c 100644 --- a/tests/test.nf.test.snap +++ b/tests/test.nf.test.snap @@ -534,11 +534,11 @@ [ "JK2782_JK2782_TGGCCGATCAACGA_L1.fastp.json:md5,f9ac29dc38bd5e51beb9ea5a8a8e22f3", "JK2802_JK2802_AGAATAACCTACCA_L2.fastp.json:md5,582794e200f2ddf0aad317ab42f88e79", - "JK2782_JK2782_TGGCCGATCAACGA_L1_fastqc.html:md5,9ef46c888ba9b9fde3d6100249bbf2cb", - "JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.html:md5,bdae5c26be457bd61a5f40e3378e79fe", - "JK2782_JK2782_TGGCCGATCAACGA_L1_1_fastqc.html:md5,cfdadc1f8e2a3ff6238d404c2f69eb65", - "JK2782_JK2782_TGGCCGATCAACGA_L1_2_fastqc.html:md5,93c488b52c8addf9b12fb3275b7555aa", - "JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.html:md5,d91b50b71a4102be9b0460bf5ae1cb3f" + "JK2782_JK2782_TGGCCGATCAACGA_L1_fastqc.html:md5,216c34977465c92bdb711531169e13ce", + "JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.html:md5,a09e8cd893fd8bae563a3f7ba220584c", + "JK2782_JK2782_TGGCCGATCAACGA_L1_1_fastqc.html:md5,975c5fccdaa5e0f99d573a6e5a3c8582", + "JK2782_JK2782_TGGCCGATCAACGA_L1_2_fastqc.html:md5,180fb58f703c6c5106ad95859e486298", + "JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.html:md5,b9e9718a0f9cf3cb3d99abea1f45fe86" ], [ "JK2782_JK2782_TGGCCGATCAACGA_L1.fastp.html", @@ -556,7 +556,7 @@ "nf-test": "0.8.4", "nextflow": "24.10.0" }, - "timestamp": "2024-12-06T11:48:14.351935" + "timestamp": "2024-12-11T12:39:48.728259" }, "damage_estimation": { "content": [ @@ -709,6 +709,182 @@ }, "timestamp": "2024-12-06T11:48:13.991772" }, + "multiqc": { + "content": [ + [ + "multiqc", + "multiqc_data", + "fastp-insert-size-plot.txt", + "fastp-seq-content-gc-plot_Read_1_After_filtering.txt", + "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt", + "fastp-seq-content-gc-plot_Read_2_Before_filtering.txt", + "fastp-seq-content-n-plot_Read_1_After_filtering.txt", + "fastp-seq-content-n-plot_Read_1_Before_filtering.txt", + "fastp-seq-content-n-plot_Read_2_Before_filtering.txt", + "fastp-seq-quality-plot_Read_1_After_filtering.txt", + "fastp-seq-quality-plot_Read_1_Before_filtering.txt", + "fastp-seq-quality-plot_Read_2_Before_filtering.txt", + "fastp_filtered_reads_plot.txt", + "fastqc-status-check-heatmap.txt", + "fastqc_adapter_content_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "fiveprime_misinc_plot.txt", + "length-distribution-Forward.txt", + "length-distribution-Reverse.txt", + "mapdamage-fiveprime_misinc_plot.txt", + "mapdamage-length-distribution-Forward.txt", + "mapdamage-length-distribution-Reverse.txt", + "mapdamage-threeprime_misinc_plot.txt", + "multiqc.log", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_general_stats.txt", + "multiqc_sources.txt", + "preseq_complexity_plot_molecules.txt", + "qualimap_coverage_histogram.txt", + "qualimap_gc_content.txt", + "qualimap_genome_fraction.txt", + "samtools-flagstat-dp_Percentage_of_total.txt", + "samtools-flagstat-dp_Read_counts.txt", + "threeprime_misinc_plot.txt", + "multiqc_plots", + "pdf", + "fastp-insert-size-plot.pdf", + "fastp-seq-content-gc-plot_Read_1_After_filtering.pdf", + "fastp-seq-content-gc-plot_Read_1_Before_filtering.pdf", + "fastp-seq-content-gc-plot_Read_2_Before_filtering.pdf", + "fastp-seq-content-n-plot_Read_1_After_filtering.pdf", + "fastp-seq-content-n-plot_Read_1_Before_filtering.pdf", + "fastp-seq-content-n-plot_Read_2_Before_filtering.pdf", + "fastp-seq-quality-plot_Read_1_After_filtering.pdf", + "fastp-seq-quality-plot_Read_1_Before_filtering.pdf", + "fastp-seq-quality-plot_Read_2_Before_filtering.pdf", + "fastp_filtered_reads_plot-cnt.pdf", + "fastp_filtered_reads_plot-pct.pdf", + "fastqc-status-check-heatmap.pdf", + "fastqc_adapter_content_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf", + "fiveprime_misinc_plot.pdf", + "general_stats_table.pdf", + "length-distribution-Forward.pdf", + "length-distribution-Reverse.pdf", + "mapdamage-fiveprime_misinc_plot.pdf", + "mapdamage-length-distribution-Forward.pdf", + "mapdamage-length-distribution-Reverse.pdf", + "mapdamage-threeprime_misinc_plot.pdf", + "preseq_complexity_plot_molecules.pdf", + "qualimap_coverage_histogram.pdf", + "qualimap_gc_content.pdf", + "qualimap_genome_fraction.pdf", + "samtools-flagstat-dp_Percentage_of_total.pdf", + "samtools-flagstat-dp_Read_counts.pdf", + "threeprime_misinc_plot.pdf", + "png", + "fastp-insert-size-plot.png", + "fastp-seq-content-gc-plot_Read_1_After_filtering.png", + "fastp-seq-content-gc-plot_Read_1_Before_filtering.png", + "fastp-seq-content-gc-plot_Read_2_Before_filtering.png", + "fastp-seq-content-n-plot_Read_1_After_filtering.png", + "fastp-seq-content-n-plot_Read_1_Before_filtering.png", + "fastp-seq-content-n-plot_Read_2_Before_filtering.png", + "fastp-seq-quality-plot_Read_1_After_filtering.png", + "fastp-seq-quality-plot_Read_1_Before_filtering.png", + "fastp-seq-quality-plot_Read_2_Before_filtering.png", + "fastp_filtered_reads_plot-cnt.png", + "fastp_filtered_reads_plot-pct.png", + "fastqc-status-check-heatmap.png", + "fastqc_adapter_content_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png", + "fiveprime_misinc_plot.png", + "general_stats_table.png", + "length-distribution-Forward.png", + "length-distribution-Reverse.png", + "mapdamage-fiveprime_misinc_plot.png", + "mapdamage-length-distribution-Forward.png", + "mapdamage-length-distribution-Reverse.png", + "mapdamage-threeprime_misinc_plot.png", + "preseq_complexity_plot_molecules.png", + "qualimap_coverage_histogram.png", + "qualimap_gc_content.png", + "qualimap_genome_fraction.png", + "samtools-flagstat-dp_Percentage_of_total.png", + "samtools-flagstat-dp_Read_counts.png", + "threeprime_misinc_plot.png", + "svg", + "fastp-insert-size-plot.svg", + "fastp-seq-content-gc-plot_Read_1_After_filtering.svg", + "fastp-seq-content-gc-plot_Read_1_Before_filtering.svg", + "fastp-seq-content-gc-plot_Read_2_Before_filtering.svg", + "fastp-seq-content-n-plot_Read_1_After_filtering.svg", + "fastp-seq-content-n-plot_Read_1_Before_filtering.svg", + "fastp-seq-content-n-plot_Read_2_Before_filtering.svg", + "fastp-seq-quality-plot_Read_1_After_filtering.svg", + "fastp-seq-quality-plot_Read_1_Before_filtering.svg", + "fastp-seq-quality-plot_Read_2_Before_filtering.svg", + "fastp_filtered_reads_plot-cnt.svg", + "fastp_filtered_reads_plot-pct.svg", + "fastqc-status-check-heatmap.svg", + "fastqc_adapter_content_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg", + "fiveprime_misinc_plot.svg", + "general_stats_table.svg", + "length-distribution-Forward.svg", + "length-distribution-Reverse.svg", + "mapdamage-fiveprime_misinc_plot.svg", + "mapdamage-length-distribution-Forward.svg", + "mapdamage-length-distribution-Reverse.svg", + "mapdamage-threeprime_misinc_plot.svg", + "preseq_complexity_plot_molecules.svg", + "qualimap_coverage_histogram.svg", + "qualimap_gc_content.svg", + "qualimap_genome_fraction.svg", + "samtools-flagstat-dp_Percentage_of_total.svg", + "samtools-flagstat-dp_Read_counts.svg", + "threeprime_misinc_plot.svg", + "multiqc_report.html" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.10.0" + }, + "timestamp": "2024-12-11T12:39:48.786989" + }, "mapping_output": { "content": [ [