use sintax instead of dada to satisfy memory limit

nf-core · Mar 19, 2024 · 2756612 · 2756612
1 parent 54e28be
commit 2756612
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Showing 6 changed files with 11 additions and 11 deletions.
diff --git a/conf/test_iontorrent.config b/conf/test_iontorrent.config
@@ -22,9 +22,12 @@ params {
     // Input data
     FW_primer = "GTGARTCATCGARTCTTTG"
     RV_primer = "TCCTCSSCTTATTGATATGC"
-    dada_ref_taxonomy = "unite-fungi=8.2"
+    sintax_ref_taxonomy = "unite-fungi=8.2"
     input = "https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/Samplesheet_it_SE_ITS.tsv"
     iontorrent = true
     max_ee = 5
     skip_qiime = true
+
+    // Prevent default taxonomic classification
+    skip_dada_taxonomy = true
 }
diff --git a/conf/test_pacbio_its.config b/conf/test_pacbio_its.config
@@ -22,7 +22,7 @@ params {
     // Input data
     FW_primer = "CTTGGTCATTTAGAGGAAGTAA"
     RV_primer = "TCCTGAGGGAAACTTCG"
-    dada_ref_taxonomy = "unite-fungi=8.2"
+    sintax_ref_taxonomy = "unite-fungi=8.2"
     input = "https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/Samplesheet_pacbio_ITS.tsv"
     metadata = "https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/Metadata_pacbio_ITS.tsv"
     pacbio = true
@@ -31,4 +31,7 @@ params {
     addsh = true
     skip_qiime = true
     sbdiexport = true
+
+    // Prevent default taxonomic classification
+    skip_dada_taxonomy = true
 }
diff --git a/tests/pipeline/iontorrent.nf.test b/tests/pipeline/iontorrent.nf.test
@@ -27,11 +27,9 @@ nextflow_pipeline {
                 { assert snapshot(path("$outputDir/dada2/ASV_seqs.fasta"),
                                 path("$outputDir/dada2/ASV_table.tsv"),
                                 path("$outputDir/dada2/DADA2_stats.tsv"),
-                                path("$outputDir/dada2/ref_taxonomy.unite-fungi_8_3.txt"),
                                 path("$outputDir/dada2/DADA2_table.rds"),
                                 path("$outputDir/dada2/DADA2_table.tsv")).match("dada2") },
-                { assert new File("$outputDir/dada2/ASV_tax.unite-fungi_8_3.tsv").exists() },
-                { assert new File("$outputDir/dada2/ASV_tax_species.unite-fungi_8_3.tsv").exists() },
+                { assert new File("$outputDir/sintax/ASV_tax_sintax.unite-fungi_8_2.tsv").exists() },
                 { assert new File("$outputDir/fastqc/it1_fastqc.html").exists() },
                 { assert new File("$outputDir/fastqc/it2_fastqc.html").exists() },
                 { assert new File("$outputDir/fastqc/it3_fastqc.html").exists() },

diff --git a/tests/pipeline/iontorrent.nf.test.snap b/tests/pipeline/iontorrent.nf.test.snap
diff --git a/tests/pipeline/pacbio_its.nf.test b/tests/pipeline/pacbio_its.nf.test
@@ -31,12 +31,10 @@ nextflow_pipeline {
                 { assert new File("$outputDir/cutadapt/pb3.trimmed.cutadapt.log").exists() },
                 { assert snapshot(path("$outputDir/dada2/ASV_seqs.fasta"),
                                 path("$outputDir/dada2/ASV_table.tsv"),
-                                path("$outputDir/dada2/ref_taxonomy.unite-fungi_8_3.txt"),
                                 path("$outputDir/dada2/DADA2_stats.tsv"),
                                 path("$outputDir/dada2/DADA2_table.rds"),
                                 path("$outputDir/dada2/DADA2_table.tsv")).match("dada2") },
-                { assert new File("$outputDir/dada2/ASV_tax.unite-fungi_8_3.tsv").exists() },
-                { assert new File("$outputDir/dada2/ASV_tax_species.unite-fungi_8_3.tsv").exists() },
+                { assert new File("$outputDir/sintax/ASV_tax_sintax.unite-fungi_8_2.tsv").exists() },
                 { assert new File("$outputDir/fastqc/pb1_fastqc.html").exists() },
                 { assert new File("$outputDir/fastqc/pb2_fastqc.html").exists() },
                 { assert new File("$outputDir/fastqc/pb3_fastqc.html").exists() },
@@ -54,7 +52,7 @@ nextflow_pipeline {
                 { assert new File("$outputDir/SBDI/annotation.tsv").exists() },
                 { assert new File("$outputDir/SBDI/asv-table.tsv").exists() },
                 { assert new File("$outputDir/summary_report/summary_report.html").exists() },
-                { assert new File("$outputDir/phyloseq/dada2_phyloseq.rds").exists() }
+                { assert new File("$outputDir/phyloseq/sintax_phyloseq.rds").exists() }
             )
         }
     }

diff --git a/tests/pipeline/pacbio_its.nf.test.snap b/tests/pipeline/pacbio_its.nf.test.snap