Get testing working

nf-core · May 23, 2024 · 526ef0d · 526ef0d
1 parent 3e2377c
commit 526ef0d
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Showing 7 changed files with 33 additions and 19 deletions.
diff --git a/conf/test.config b/conf/test.config
@@ -22,7 +22,9 @@ params {
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input         = params.pipelines_testdata_base_path + 'createtaxdb/samplesheets/test.csv'
+    input            = params.pipelines_testdata_base_path + 'createtaxdb/samplesheets/test.csv'
+
+    dbname           = "database"
 
     build_diamond    = true
     build_kaiju      = true

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -18,4 +18,12 @@ params {
     // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
+
+    build_diamond    = true
+    build_kaiju      = true
+    build_malt       = true
+    build_centrifuge = true
+    build_kraken2    = true
+    build_bracken    = true
+
 }
diff --git a/nextflow.config b/nextflow.config
@@ -54,7 +54,7 @@ params {
     validate_params                  = true
 
     // General parameters
-    dbname                   = "database"
+    dbname                   = null
     save_concatenated_fastas = false
 
     accession2taxid = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -10,7 +10,7 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["input", "outdir"],
+            "required": ["input", "outdir", "dbname"],
             "properties": {
                 "input": {
                     "type": "string",
@@ -43,7 +43,6 @@
                 },
                 "dbname": {
                     "type": "string",
-                    "default": "database",
                     "description": "Specify name that resulting databases will be prefixed with.",
                     "fa_icon": "fas fa-id-badge"
                 },
@@ -149,7 +148,8 @@
                 "build_bracken": {
                     "type": "boolean",
                     "fa_icon": "fas fa-save",
-                    "description": "Generate Bracken files required for abundance estimation."
+                    "description": "Turn on extending of Kraken2 database to include Bracken files. Requires nucleotide FASTA File input.",
+                    "help_text": "Bracken2 databases are simply just a Kraken2 database with two additional files.\n\nNote however this requires a Kraken2 database _with_ intermediate files still in it, thus can result in large database directories."
                 }
             },
             "fa_icon": "fas fa-database"

diff --git a/tests/test.nf.test b/tests/test.nf.test
@@ -21,9 +21,11 @@ nextflow_pipeline {
                         path("$outputDir/centrifuge/"),
                         path("$outputDir/diamond/database.dmnd"),
                         path("$outputDir/kaiju/database.fmi"),
-                        path("$outputDir/kraken2/db/hash.k2d"),
-                        file("$outputDir/kraken2/db/opts.k2d").name,
-                        path("$outputDir/kraken2/db/taxo.k2d"),
+                        path("$outputDir/kraken2/database/hash.k2d"),
+                        file("$outputDir/kraken2/database/opts.k2d").name,
+                        path("$outputDir/kraken2/database/taxo.k2d"),
+                        file("$outputDir/bracken/database/database100mers.kmer_distrib").name,
+                        file("$outputDir/bracken/database/database100mers.kraken").name,
                         path("$outputDir/malt/malt-build.log").readLines().last().contains('Peak memory'),
                         path("$outputDir/malt/malt_index/index0.idx"),
                         path("$outputDir/malt/malt_index/ref.db"),

diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap
@@ -12,6 +12,8 @@
             "hash.k2d:md5,01122a04dcef29ceb3baa68a9f6e6ef5",
             "opts.k2d",
             "taxo.k2d:md5,cd8170a8c5a1b763a9ac1ffa2107cc88",
+            "database100mers.kmer_distrib",
+            "database100mers.kraken",
             true,
             "index0.idx:md5,876139dc930e68992cd2625e08bba48a",
             "ref.db:md5,377073f58a9f9b85acca59fcf21744a9",
@@ -23,8 +25,8 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.02.0"
+            "nextflow": "24.04.1"
         },
-        "timestamp": "2024-04-11T10:59:28.687364796"
+        "timestamp": "2024-05-23T08:00:31.799820635"
     }
 }
diff --git a/workflows/createtaxdb.nf b/workflows/createtaxdb.nf
@@ -148,9 +148,9 @@ workflow CREATETAXDB {
         def k2_keepintermediates = params.kraken2_keepintermediate || params.build_bracken ? false : true
         FASTA_BUILD_ADD_KRAKEN2_BRACKEN ( CAT_CAT_DNA.out.file_out, ch_taxonomy_namesdmp, ch_taxonomy_nodesdmp, ch_accession2taxid, k2_keepintermediates, params.build_bracken )
         ch_versions = ch_versions.mix(FASTA_BUILD_ADD_KRAKEN2_BRACKEN.out.versions.first())
-        ch_kraken2_output = FASTA_BUILD_ADD_KRAKEN2_BRACKEN.out.db
+        ch_kraken2_bracken_output = FASTA_BUILD_ADD_KRAKEN2_BRACKEN.out.db
     } else {
-        ch_kraken2_output = Channel.empty()
+        ch_kraken2_bracken_output = Channel.empty()
     }
 
     // Module: Run MALT/BUILD
@@ -229,13 +229,13 @@ workflow CREATETAXDB {
     multiqc_report = MULTIQC.out.report.toList()
 
     emit:
-    versions            = ch_collated_versions
-    multiqc_report      = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
-    centrifuge_database = ch_centrifuge_output
-    diamond_database    = ch_diamond_output
-    kaiju_database      = ch_kaiju_output
-    kraken2_database    = ch_kraken2_output
-    malt_database       = ch_malt_output
+    versions                    = ch_collated_versions
+    multiqc_report              = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
+    centrifuge_database         = ch_centrifuge_output
+    diamond_database            = ch_diamond_output
+    kaiju_database              = ch_kaiju_output
+    kraken2_bracken_database    = ch_kraken2_bracken_output
+    malt_database               = ch_malt_output
 }
 
 /*