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Fix test. and snapshot.
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@TCLamnidis
TCLamnidis committed Jan 24, 2025
1 parent 5ed2b0b commit 80007d7
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Showing 2 changed files with 49 additions and 12 deletions.
3 changes: 1 addition & 2 deletions tests/test.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -86,8 +86,7 @@ nextflow_pipeline {
{ assert snapshot( stable_content_preprocessing , stable_name_preprocessing*.name ).match("preprocessing") },

// Versions
{ assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },

{ assert new File("$outputDir/pipeline_info/nf_core_eager_software_mqc_versions.yml").exists() },

)
}
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58 changes: 48 additions & 10 deletions tests/test.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -226,12 +226,15 @@
"multiqc",
"multiqc_data",
"fastp-insert-size-plot.txt",
"fastp-seq-content-gc-plot_Merged_and_filtered.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_Merged_and_filtered.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_Merged_and_filtered.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",
Expand All @@ -256,9 +259,16 @@
"mapdamage-threeprime_misinc_plot.txt",
"multiqc.log",
"multiqc_citations.txt",
"multiqc_damageprofiler_metrics.txt",
"multiqc_data.json",
"multiqc_fastp.txt",
"multiqc_fastqc.txt",
"multiqc_general_stats.txt",
"multiqc_qualimap_bamqc_genome_results.txt",
"multiqc_samtools_flagstat.txt",
"multiqc_software_versions.txt",
"multiqc_sources.txt",
"preseq.txt",
"preseq_complexity_plot_molecules.txt",
"qualimap_coverage_histogram.txt",
"qualimap_gc_content.txt",
Expand All @@ -269,12 +279,15 @@
"multiqc_plots",
"pdf",
"fastp-insert-size-plot.pdf",
"fastp-seq-content-gc-plot_Merged_and_filtered.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_Merged_and_filtered.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_Merged_and_filtered.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",
Expand Down Expand Up @@ -309,12 +322,15 @@
"threeprime_misinc_plot.pdf",
"png",
"fastp-insert-size-plot.png",
"fastp-seq-content-gc-plot_Merged_and_filtered.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_Merged_and_filtered.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_Merged_and_filtered.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",
Expand Down Expand Up @@ -349,12 +365,15 @@
"threeprime_misinc_plot.png",
"svg",
"fastp-insert-size-plot.svg",
"fastp-seq-content-gc-plot_Merged_and_filtered.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_Merged_and_filtered.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_Merged_and_filtered.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",
Expand Down Expand Up @@ -415,7 +434,7 @@
"nf-test": "0.8.4",
"nextflow": "24.10.0"
},
"timestamp": "2024-12-06T16:19:51.141013"
"timestamp": "2025-01-24T10:16:05.866524"
},
"mapstats": {
"content": [
Expand Down Expand Up @@ -532,13 +551,13 @@
"preprocessing": {
"content": [
[
"JK2782_JK2782_TGGCCGATCAACGA_L1.fastp.json:md5,f9ac29dc38bd5e51beb9ea5a8a8e22f3",
"JK2802_JK2802_AGAATAACCTACCA_L2.fastp.json:md5,582794e200f2ddf0aad317ab42f88e79",
"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.json:md5,63c38066b91b7a7d581ed44775319404",
"JK2802_JK2802_AGAATAACCTACCA_L2.fastp.json:md5,0257faf7f1e9e1d586bbf0831340b793",
"JK2782_JK2782_TGGCCGATCAACGA_L1_fastqc.html:md5,1eebe49a7160dd41c21d8daae66f13ca",
"JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.html:md5,e0cd5701ece6563da2e1c360b0394f14",
"JK2782_JK2782_TGGCCGATCAACGA_L1_1_fastqc.html:md5,91bcb103c2669b75794571670c79d9fc",
"JK2782_JK2782_TGGCCGATCAACGA_L1_2_fastqc.html:md5,fcbe19f1a2c8797ad6654b45fc877a49",
"JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.html:md5,439ada6a5b364e591d4cff60fbc51496"
],
[
"JK2782_JK2782_TGGCCGATCAACGA_L1.fastp.html",
Expand All @@ -556,7 +575,7 @@
"nf-test": "0.8.4",
"nextflow": "24.10.0"
},
"timestamp": "2024-12-11T12:39:48.728259"
"timestamp": "2025-01-24T10:16:06.27333"
},
"damage_estimation": {
"content": [
Expand Down Expand Up @@ -715,12 +734,15 @@
"multiqc",
"multiqc_data",
"fastp-insert-size-plot.txt",
"fastp-seq-content-gc-plot_Merged_and_filtered.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_Merged_and_filtered.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_Merged_and_filtered.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",
Expand All @@ -745,9 +767,16 @@
"mapdamage-threeprime_misinc_plot.txt",
"multiqc.log",
"multiqc_citations.txt",
"multiqc_damageprofiler_metrics.txt",
"multiqc_data.json",
"multiqc_fastp.txt",
"multiqc_fastqc.txt",
"multiqc_general_stats.txt",
"multiqc_qualimap_bamqc_genome_results.txt",
"multiqc_samtools_flagstat.txt",
"multiqc_software_versions.txt",
"multiqc_sources.txt",
"preseq.txt",
"preseq_complexity_plot_molecules.txt",
"qualimap_coverage_histogram.txt",
"qualimap_gc_content.txt",
Expand All @@ -758,12 +787,15 @@
"multiqc_plots",
"pdf",
"fastp-insert-size-plot.pdf",
"fastp-seq-content-gc-plot_Merged_and_filtered.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_Merged_and_filtered.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_Merged_and_filtered.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",
Expand Down Expand Up @@ -798,12 +830,15 @@
"threeprime_misinc_plot.pdf",
"png",
"fastp-insert-size-plot.png",
"fastp-seq-content-gc-plot_Merged_and_filtered.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_Merged_and_filtered.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_Merged_and_filtered.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",
Expand Down Expand Up @@ -838,12 +873,15 @@
"threeprime_misinc_plot.png",
"svg",
"fastp-insert-size-plot.svg",
"fastp-seq-content-gc-plot_Merged_and_filtered.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_Merged_and_filtered.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_Merged_and_filtered.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",
Expand Down Expand Up @@ -883,7 +921,7 @@
"nf-test": "0.8.4",
"nextflow": "24.10.0"
},
"timestamp": "2024-12-11T12:39:48.786989"
"timestamp": "2025-01-24T10:16:06.096234"
},
"mapping_output": {
"content": [
Expand Down

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