Merge pull request #24 from oist/addedmodules

Running more modules
oist · Apr 26, 2024 · cd517dd · cd517dd
2 parents ecb5bb4 + d845557
commit cd517dd
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Showing 3 changed files with 20 additions and 3 deletions.
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -17,7 +17,7 @@
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?a\\.gz$",
+                "pattern": "^\\S+\\.f(ast)?a(\\.gz)?$",
                 "errorMessage": "Fasta file for genomes must be provided, cannot contain spaces and must have extension '.fa.gz' or '.fasta.gz'"
             }
         },

diff --git a/conf/test.config b/conf/test.config
@@ -22,7 +22,10 @@ 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  = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
+    input  = 'https://raw.githubusercontent.com/U13bs1125/test-datasets/pairgenomealign/testsamplesheet.csv'
+
+    // Target
+    target = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta'
 
     // Genome references
     genome = 'R64-1-1'

diff --git a/workflows/pairalign.nf b/workflows/pairalign.nf
@@ -5,8 +5,10 @@
 */
 
 include { ASSEMBLYSCAN           } from '../modules/nf-core/assemblyscan/main'
+include { LAST_DOTPLOT           } from '../modules/nf-core/last/dotplot/main'
 include { LAST_LASTAL            } from '../modules/nf-core/last/lastal/main'
 include { LAST_LASTDB            } from '../modules/nf-core/last/lastdb/main'
+include { LAST_SPLIT             } from '../modules/nf-core/last/split/main'
 include { LAST_TRAIN             } from '../modules/nf-core/last/train/main'
 include { MULTIQC                } from '../modules/nf-core/multiqc/main'
 include { paramsSummaryMap       } from 'plugin/nf-validation'
@@ -54,14 +56,26 @@ workflow PAIRALIGN {
          LAST_LASTDB.out.index.map { row -> row[1] }  // Remove metadata map
     )
 
-    //
     // MODULE: lastal
     //
     LAST_LASTAL (
         ch_samplesheet.join(LAST_TRAIN.out.param_file),
         LAST_LASTDB.out.index.map { row -> row[1] }  // Remove metadata map
     )
 
+    // MODULE: last_split
+    //
+    LAST_SPLIT (
+         LAST_LASTAL.out.maf
+    )
+
+    // MODULE: last_dotplot
+    //
+    LAST_DOTPLOT (
+         LAST_SPLIT.out.maf,
+         'png'
+    )
+
     // Collate and save software versions
     //
     softwareVersionsToYAML(ch_versions)