Merge branch 'dev' of github.com:oist/plessy_pairwiseGenomeComparison into dev

Author: U13bs1125

Diff for: conf/test.config

@@ -21,10 +21,9 @@ 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 = 'https://raw.githubusercontent.com/U13bs1125/test-datasets/pairgenomealign/testsamplesheet.csv'
-    
-    //Target genome
+    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

Diff for: workflows/pairalign.nf

@@ -5,8 +5,11 @@
 */
 
 include { ASSEMBLYSCAN           } from '../modules/nf-core/assemblyscan/main'
-include { LAST_LASTDB                 } from '../modules/nf-core/last/lastdb/main'
-include { LAST_TRAIN                 } from '../modules/nf-core/last/train/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'
 include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
@@ -50,9 +53,29 @@ workflow PAIRALIGN {
     //
     LAST_TRAIN (
          ch_samplesheet,
-         LAST_LASTDB.out.index
+         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)