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Check existence of Multiqc output files. reorder tests to match alpha…
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…numeric ordering of directories in output
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@TCLamnidis
TCLamnidis committed Dec 11, 2024
1 parent 997fb5b commit 82cb639
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Showing 2 changed files with 187 additions and 15 deletions.
14 changes: 5 additions & 9 deletions tests/test.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -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 },
Expand All @@ -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() },

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188 changes: 182 additions & 6 deletions tests/test.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -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": [
Expand Down Expand Up @@ -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": [
[
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