Replace local version of SENTIEON_READWRITER with nf-core version

nf-core · Aug 14, 2023 · 219fc42 · 219fc42
1 parent ea6528b
commit 219fc42
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Showing 5 changed files with 162 additions and 57 deletions.
diff --git a/modules.json b/modules.json
@@ -350,6 +350,11 @@
                         "git_sha": "b9172e8c26a3db5009f7872654c44587e254f094",
                         "installed_by": ["modules"]
                     },
+                    "sentieon/readwriter": {
+                        "branch": "master",
+                        "git_sha": "b28e4dde755117e8dab5d6e85e292f145b8b53c3",
+                        "installed_by": ["modules"]
+                    },
                     "smncopynumbercaller": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",

diff --git a/modules/local/sentieon/readwriter.nf b/modules/local/sentieon/readwriter.nf
diff --git a/modules/nf-core/sentieon/readwriter/main.nf b/modules/nf-core/sentieon/readwriter/main.nf
diff --git a/modules/nf-core/sentieon/readwriter/meta.yml b/modules/nf-core/sentieon/readwriter/meta.yml
diff --git a/subworkflows/local/alignment/align_sentieon.nf b/subworkflows/local/alignment/align_sentieon.nf
@@ -7,8 +7,7 @@ include { SENTIEON_DATAMETRICS    } from '../../../modules/local/sentieon/datame
 include { SENTIEON_LOCUSCOLLECTOR } from '../../../modules/local/sentieon/locuscollector'
 include { SENTIEON_DEDUP          } from '../../../modules/local/sentieon/dedup'
 include { SENTIEON_BQSR           } from '../../../modules/local/sentieon/bqsr'
-include { SENTIEON_READWRITER     } from '../../../modules/local/sentieon/readwriter'
-
+include { SENTIEON_READWRITER     } from '../../../modules/nf-core/sentieon/readwriter/main'
 workflow ALIGN_SENTIEON {
     take:
         ch_reads_input     // channel: [mandatory] [ val(meta), path(reads_input) ]
@@ -41,7 +40,7 @@ workflow ALIGN_SENTIEON {
                 }
             .set{ merge_bams_in }
 
-        SENTIEON_READWRITER (merge_bams_in.multiple)
+        SENTIEON_READWRITER ( merge_bams_in.multiple, ch_genome_fasta, ch_genome_fai )
         ch_bam_bai = merge_bams_in.single.mix(SENTIEON_READWRITER.out.bam_bai)
 
         SENTIEON_DATAMETRICS (ch_bam_bai, ch_genome_fasta, ch_genome_fai )