Merge pull request #404 from nf-core/update_sentieon_wgsmetricsalgo

Replace local version of SENTIEON_WGSMETRICS with nf-core version
nf-core · Aug 17, 2023 · 42c0676 · 42c0676
2 parents bc20d53 + cc653d3
commit 42c0676
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Showing 6 changed files with 164 additions and 61 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Installed the nf-core version of the sentieon/dedup module. The dedup module also contains a call to Sentieon's LocusCollector [#401](https://github.com/nf-core/raredisease/pull/401)
 - Removing Sentieon-based BQSR. Recent Illumina sequencers tend to provide well-calibrated BQs, so BQSR may not provide much benefit [#402](https://github.com/nf-core/raredisease/pull/402)
 - Installed the nf-core version of the sentieon/dnamodelapply module [#403](https://github.com/nf-core/raredisease/pull/403)
+- Installed the nf-core version of the sentieon/wgsmetricsalgo module [#404](https://github.com/nf-core/raredisease/pull/404)
 
 ### `Fixed`
 

diff --git a/modules.json b/modules.json
@@ -370,6 +370,11 @@
                         "git_sha": "b28e4dde755117e8dab5d6e85e292f145b8b53c3",
                         "installed_by": ["modules"]
                     },
+                    "sentieon/wgsmetrics": {
+                        "branch": "master",
+                        "git_sha": "b1e9314b919f498e116bfc1417b7185185e99261",
+                        "installed_by": ["modules"]
+                    },
                     "smncopynumbercaller": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",

diff --git a/modules/local/sentieon/wgsmetricsalgo.nf b/modules/local/sentieon/wgsmetricsalgo.nf
diff --git a/modules/nf-core/sentieon/wgsmetrics/main.nf b/modules/nf-core/sentieon/wgsmetrics/main.nf
diff --git a/modules/nf-core/sentieon/wgsmetrics/meta.yml b/modules/nf-core/sentieon/wgsmetrics/meta.yml
diff --git a/subworkflows/local/qc_bam.nf b/subworkflows/local/qc_bam.nf
@@ -10,8 +10,8 @@ include { MOSDEPTH                                               } from '../../m
 include { UCSC_WIGTOBIGWIG                                       } from '../../modules/nf-core/ucsc/wigtobigwig/main'
 include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS   } from '../../modules/nf-core/picard/collectwgsmetrics/main'
 include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS_Y } from '../../modules/nf-core/picard/collectwgsmetrics/main'
-include { SENTIEON_WGSMETRICSALGO as SENTIEON_WGSMETRICS         } from '../../modules/local/sentieon/wgsmetricsalgo'
-include { SENTIEON_WGSMETRICSALGO as SENTIEON_WGSMETRICS_Y       } from '../../modules/local/sentieon/wgsmetricsalgo'
+include { SENTIEON_WGSMETRICS                                                        } from '../../modules/nf-core/sentieon/wgsmetrics/main'
+include { SENTIEON_WGSMETRICS as SENTIEON_WGSMETRICS_Y           } from '../../modules/nf-core/sentieon/wgsmetrics/main'
 
 workflow QC_BAM {
 
@@ -52,8 +52,8 @@ workflow QC_BAM {
         PICARD_COLLECTWGSMETRICS ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_wgs )
         PICARD_COLLECTWGSMETRICS_Y ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_y )
 
-        SENTIEON_WGSMETRICS ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_wgs )
-        SENTIEON_WGSMETRICS_Y ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_y )
+        SENTIEON_WGSMETRICS ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_wgs.map{ interval -> [[:], interval]} )
+        SENTIEON_WGSMETRICS_Y ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_y.map{ interval -> [[:], interval]} )
 
         ch_cov   = Channel.empty().mix(PICARD_COLLECTWGSMETRICS.out.metrics, SENTIEON_WGSMETRICS.out.wgs_metrics)
         ch_cov_y = Channel.empty().mix(PICARD_COLLECTWGSMETRICS_Y.out.metrics, SENTIEON_WGSMETRICS_Y.out.wgs_metrics)