Fixed pharokka snap

nf-core · Feb 16, 2024 · 711f59a · 711f59a
1 parent 7218318
commit 711f59a
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Showing 3 changed files with 37 additions and 36 deletions.
diff --git a/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap b/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap
diff --git a/tests/main.nf.test b/tests/main.nf.test
@@ -10,9 +10,10 @@ nextflow_pipeline {
         when {
             params {
                 outdir                      = "$outputDir"
+                assembly_min_length         = 3000
                 mash_screen_min_score       = 1
                 mash_screen_winner_take_all = true
-                genomad_min_score           = 0.01
+                genomad_min_score           = 0.7
                 genomad_max_fdr             = 1
                 genomad_disable_nn          = true
                 genomad_sensitivity         = 0.1
@@ -41,9 +42,9 @@ nextflow_pipeline {
                     path("${params.outdir}/VirusMicrodiversity/instrain/profile/test2.IS/output/test2.IS_gene_info.tsv"),
                     path("${params.outdir}/pipeline_info/software_versions.yml")
                     ).match() },
-                { assert path("${outputDir}/VirusLifestyle/bacphlip/all_samples_anicluster_representatives.fna.bacphlip").readLines().size() == 4 },
-                { assert path("${outputDir}/VirusAbundance/coverm/contig/all_samples_alignment_results.tsv").readLines().size() == 4 },
-                { assert path("${params.outdir}/VirusMicrodiversity/instrain/compare/all_samples.IS_compare/output/all_samples.IS_compare_pooled_SNV_data.tsv").readLines().size() == 15 },
+                { assert path("${outputDir}/VirusLifestyle/bacphlip/all_samples_anicluster_representatives.fna.bacphlip").readLines().size() == 3 },
+                { assert path("${outputDir}/VirusAbundance/coverm/contig/all_samples_alignment_results.tsv").readLines().size() == 3 },
+                { assert path("${params.outdir}/VirusMicrodiversity/instrain/compare/all_samples.IS_compare/output/all_samples.IS_compare_pooled_SNV_data.tsv").readLines().size() == 11 },
                 { assert new File("$outputDir/ReadQuality/fastqc/test1_1_fastqc.html").exists() },
                 { assert new File("$outputDir/ReadQuality/fastqc/test1_2_fastqc.html").exists() },
                 { assert new File("$outputDir/VirusAbundance/bowtie2/align/test1.bam").exists() },

diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap