Parallelize the delly execution on SV type (#111)

* parallelize delly on SV type

* removed the delly_sv_types param

* fix concat subwf after module update

* fix bam_sv_calling tests

CHANGELOG.md

@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 1. Added the samplesheet to the pipeline output as `OUTDIR/samplesheet.csv`
+2. Added parallelization on SV type to the delly flow
 
 ### `Changes`
 
@@ -19,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 6. Removed the old output publishing code and used the new workflow output definitions instead
 7. Bumped the minimal nextflow version to 24.10.0
 8. VCFanno will now run when `--vcfanno_toml` has been given and `--annotate` has not been given. You still need to supply `--annotate` to get the full annotation, but this can be used check for common variants without having to perform full annotation.
+9. Removed the `--delly_sv_types` parameter.
 
 ### `Fixed`
 

assets/svync/delly.yaml

@@ -16,6 +16,11 @@ info:
       DEL: -~sub:$INFO/END,$POS
       INS: $INFO/SVLEN
       TRA: 1
+  SVINSSEQ:
+    value: $INFO/CONSENSUS
+    number: 1
+    type: string
+    description: The sequence of the insertion
   CIEND:
     value: $INFO/CIEND
     number: 2

conf/modules.config

@@ -49,8 +49,17 @@ process {
     //
 
     withName: "^.*BAM_VARIANT_CALLING_DELLY:DELLY_CALL\$" {
-        ext.args = {"--svtype ${params.delly_sv_types} --map-qual ${params.delly_map_qual} --min-clique-size ${params.delly_min_clique_size}"}
-        ext.suffix = "vcf"
+        tag = { "${meta.id}.${meta.sv_type}" }
+        ext.args = {"--svtype ${meta.sv_type} --map-qual ${params.delly_map_qual} --min-clique-size ${params.delly_min_clique_size}"}
+        ext.prefix = { "${meta.id}.${meta.sv_type}" }
+    }
+
+    withName: "^.*BAM_VARIANT_CALLING_DELLY:BCFTOOLS_CONCAT\$" {
+        ext.args = {"--output-type z"}
+    }
+
+    withName: "^.*BAM_VARIANT_CALLING_DELLY:BCFTOOLS_SORT\$" {
+        ext.args = {"--output-type z --write-index=tbi"}
         ext.prefix = { "${meta.id}.delly" }
     }
 
@@ -274,6 +283,11 @@ process {
 
     withName: "^.*VCF_CONCAT_BCFTOOLS:BCFTOOLS_CONCAT\$" {
         ext.args = "--output-type z --allow-overlaps"
+        ext.prefix = { "${meta.id}.concat" }
+    }
+
+    withName: "^.*VCF_CONCAT_BCFTOOLS:BCFTOOLS_SORT\$" {
+        ext.args = "--output-type z --write-index=tbi"
     }
 
     /*

modules.json

@@ -23,7 +23,7 @@
                     },
                     "bcftools/concat": {
                         "branch": "master",
-                        "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
                         "installed_by": ["modules"]
                     },
                     "bcftools/filter": {
@@ -48,9 +48,8 @@
                     },
                     "delly/call": {
                         "branch": "master",
-                        "git_sha": "92bf2a8afa318a64f9d333cf87b510c662fd4274",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/delly/call/delly-call.diff"
+                        "git_sha": "699f066b2d90f079378205ce557f9ea75d90dbf9",
+                        "installed_by": ["modules"]
                     },
                     "ensemblvep/download": {
                         "branch": "master",
@@ -131,7 +130,7 @@
                     },
                     "svync": {
                         "branch": "master",
-                        "git_sha": "3df1a372b844c98c31ec3446faac7c75e64518a3",
+                        "git_sha": "916a4cbc4f831d501860495b157c4857833e22a7",
                         "installed_by": ["modules"]
                     },
                     "tabix/bgziptabix": {