Merge pull request #398 from asp8200/update_sentieon_bwamem_module

Installing and calling nf-core/modules version of sentieon/bwamem
nf-core · Aug 9, 2023 · ea6528b · ea6528b
2 parents b0e4832 + 78eaee6
commit ea6528b
Show file tree

Hide file tree

Showing 8 changed files with 160 additions and 75 deletions.
diff --git a/conf/modules/align_sentieon.config b/conf/modules/align_sentieon.config
@@ -16,6 +16,7 @@
 //
 
 process {
+
     withName: '.*ALIGN_SENTIEON:.*' {
         ext.when = params.aligner.equals("sentieon")
     }

diff --git a/conf/test.config b/conf/test.config
@@ -50,3 +50,10 @@ params {
     vep_filters          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt"
     vep_cache_version    = 107
 }
+
+process {
+    withLabel: 'sentieon' {
+        ext.sentieon_auth_mech_base64 = secrets.SENTIEON_AUTH_MECH_BASE64
+        ext.sentieon_auth_data_base64 = secrets.SENTIEON_AUTH_DATA_BASE64
+    }
+}
diff --git a/modules.json b/modules.json
@@ -345,6 +345,11 @@
                         "git_sha": "49af8ed458e28729e483bc96e5a57c28163b9ea0",
                         "installed_by": ["modules"]
                     },
+                    "sentieon/bwamem": {
+                        "branch": "master",
+                        "git_sha": "b9172e8c26a3db5009f7872654c44587e254f094",
+                        "installed_by": ["modules"]
+                    },
                     "smncopynumbercaller": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",

diff --git a/modules/local/sentieon/bwamem.nf b/modules/local/sentieon/bwamem.nf
diff --git a/modules/nf-core/sentieon/bwamem/main.nf b/modules/nf-core/sentieon/bwamem/main.nf
diff --git a/modules/nf-core/sentieon/bwamem/meta.yml b/modules/nf-core/sentieon/bwamem/meta.yml
diff --git a/subworkflows/local/alignment/align_sentieon.nf b/subworkflows/local/alignment/align_sentieon.nf
@@ -2,7 +2,7 @@
 // A subworkflow to annotate structural variants.
 //
 
-include { SENTIEON_BWAMEM         } from '../../../modules/local/sentieon/bwamem'
+include { SENTIEON_BWAMEM         } from '../../../modules/nf-core/sentieon/bwamem/main'
 include { SENTIEON_DATAMETRICS    } from '../../../modules/local/sentieon/datametrics'
 include { SENTIEON_LOCUSCOLLECTOR } from '../../../modules/local/sentieon/locuscollector'
 include { SENTIEON_DEDUP          } from '../../../modules/local/sentieon/dedup'
@@ -25,11 +25,10 @@ workflow ALIGN_SENTIEON {
         ch_bqsr_bai = Channel.empty()
         ch_bqsr_csv = Channel.empty()
 
-        SENTIEON_BWAMEM ( ch_reads_input, ch_genome_fasta, ch_genome_fai, ch_bwa_index )
+        SENTIEON_BWAMEM ( ch_reads_input, ch_bwa_index, ch_genome_fasta.map{ meta, fasta -> fasta }, ch_genome_fai.map{ meta, fai -> fai })
 
         SENTIEON_BWAMEM.out
-            .bam
-            .join(SENTIEON_BWAMEM.out.bai, failOnMismatch:true, failOnDuplicate:true)
+            .bam_and_bai
             .map{ meta, bam, bai ->
                 new_id   = meta.id.split('_')[0]
                 new_meta = meta + [id:new_id, read_group:"\'@RG\\tID:" + new_id + "\\tPL:" + val_platform + "\\tSM:" + new_id + "\'"]

diff --git a/subworkflows/local/mitochondria/align_and_call_MT.nf b/subworkflows/local/mitochondria/align_and_call_MT.nf
@@ -2,7 +2,7 @@
 // Align and call MT
 //
 
-include { SENTIEON_BWAMEM as SENTIEON_BWAMEM_MT                             } from '../../../modules/local/sentieon/bwamem'
+include { SENTIEON_BWAMEM as SENTIEON_BWAMEM_MT                             } from '../../../modules/nf-core/sentieon/bwamem/main'
 include { BWAMEM2_MEM as BWAMEM2_MEM_MT                                     } from '../../../modules/nf-core/bwamem2/mem/main'
 include { GATK4_MERGEBAMALIGNMENT as GATK4_MERGEBAMALIGNMENT_MT             } from '../../../modules/nf-core/gatk4/mergebamalignment/main'
 include { PICARD_ADDORREPLACEREADGROUPS as PICARD_ADDORREPLACEREADGROUPS_MT } from '../../../modules/nf-core/picard/addorreplacereadgroups/main'
@@ -32,10 +32,10 @@ workflow ALIGN_AND_CALL_MT {
 
         BWAMEM2_MEM_MT (ch_fastq, ch_bwamem2index, true)
 
-        SENTIEON_BWAMEM_MT ( ch_fastq, ch_fasta, ch_fai, ch_bwaindex )
+        SENTIEON_BWAMEM_MT ( ch_fastq, ch_bwaindex, ch_fasta.map{ meta, fasta -> fasta }, ch_fai.map{ meta, fai -> fai } )
 
         Channel.empty()
-            .mix(BWAMEM2_MEM_MT.out.bam, SENTIEON_BWAMEM_MT.out.bam)
+            .mix(BWAMEM2_MEM_MT.out.bam, SENTIEON_BWAMEM_MT.out.bam_and_bai.map{ meta, bam, bai -> [meta, bam] })
             .join(ch_ubam, failOnMismatch:true, failOnDuplicate:true)
             .set {ch_bam_ubam}