add to sentieon

nf-core · Nov 8, 2024 · 4ada05b · 4ada05b
1 parent b1c74b1
commit 4ada05b
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Showing 2 changed files with 20 additions and 4 deletions.
diff --git a/conf/modules/align_sentieon.config b/conf/modules/align_sentieon.config
@@ -30,6 +30,11 @@ process {
         ext.prefix = { "${meta.id}_merged.bam" }
     }
 
+    withName: '.*ALIGN:ALIGN_SENTIEON:EXTRACT_ALIGNMENTS' {
+        ext.prefix = { "${meta.id}_merged_extracted" }
+        ext.args2 = { params.restrict_to_contigs }
+    }
+
     withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_DEDUP' {
         ext.args4 = { $params.rmdup ? "--rmdup" : '' }
         ext.prefix = { "${meta.id}_dedup.bam" }

diff --git a/subworkflows/local/alignment/align_sentieon.nf b/subworkflows/local/alignment/align_sentieon.nf
@@ -2,10 +2,13 @@
 // A subworkflow to annotate structural variants.
 //
 
-include { SENTIEON_BWAMEM         } from '../../../modules/nf-core/sentieon/bwamem/main'
-include { SENTIEON_DATAMETRICS    } from '../../../modules/nf-core/sentieon/datametrics/main'
-include { SENTIEON_DEDUP          } from '../../../modules/nf-core/sentieon/dedup/main'
-include { SENTIEON_READWRITER     } from '../../../modules/nf-core/sentieon/readwriter/main'
+include { SENTIEON_BWAMEM                          } from '../../../modules/nf-core/sentieon/bwamem/main'
+include { SENTIEON_DATAMETRICS                     } from '../../../modules/nf-core/sentieon/datametrics/main'
+include { SENTIEON_DEDUP                           } from '../../../modules/nf-core/sentieon/dedup/main'
+include { SENTIEON_READWRITER                      } from '../../../modules/nf-core/sentieon/readwriter/main'
+include { SAMTOOLS_VIEW as EXTRACT_ALIGNMENTS      } from '../../../modules/nf-core/samtools/view/main'
+include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_EXTRACT } from '../../../modules/nf-core/samtools/index/main'
+
 workflow ALIGN_SENTIEON {
     take:
         ch_reads_input     // channel: [mandatory] [ val(meta), path(reads_input) ]
@@ -36,6 +39,14 @@ workflow ALIGN_SENTIEON {
         SENTIEON_READWRITER ( merge_bams_in.multiple, ch_genome_fasta, ch_genome_fai )
         ch_bam_bai = merge_bams_in.single.mix(SENTIEON_READWRITER.out.output_index)
 
+        // GET ALIGNMENT FROM PRIMARY CONTIGS
+        if (params.extract_alignments) {
+            EXTRACT_ALIGNMENTS( ch_bam_bai, ch_genome_fasta, [])
+            ch_bam_bai = EXTRACT_ALIGNMENTS.out.bam
+            SAMTOOLS_INDEX_EXTRACT ( EXTRACT_ALIGNMENTS.out.bam )
+            ch_bam_bai = EXTRACT_ALIGNMENTS.out.bam.join(SAMTOOLS_INDEX_EXTRACT.out.bai, failOnMismatch:true, failOnDuplicate:true)
+        }
+
         SENTIEON_DATAMETRICS ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, false )
 
         SENTIEON_DEDUP ( ch_bam_bai, ch_genome_fasta, ch_genome_fai )