add some new custom profiles (#229)

* add some new custom profiles * fix tests * fix utils_nfschema_plugin test * fix somalier relate tests * fix rgtools pedfilter test * be more specific for bcftools norm * fix bcftools annotate test * fix vep tests * fix vep tests * make annotation wf local * remove snpeff/snpeff * prettier
nf-cmgg · Nov 22, 2024 · fb6a4e3 · fb6a4e3
1 parent 0957b03
commit fb6a4e3
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Showing 35 changed files with 1,422 additions and 1,176 deletions.
diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
@@ -27,7 +27,7 @@ jobs:
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
-        
+
       - name: Parse version
         id: version
         run: |

diff --git a/conf/seqcap.config → conf/copgt.config b/conf/seqcap.config → conf/copgt.config
@@ -1,12 +1,11 @@
 /*
 ========================================================================================
-    Nextflow config file for SeqCap runs
+    Nextflow config file for WES runs
 ========================================================================================
 */
 
 params {
-    callers   = "vardict"
-    filter    = true
-    normalize = true
-    scatter_count = 14
+    caller        = "haplotypecaller"
+    only_call     = true
+    scatter_count = 8
 }
diff --git a/conf/hypercap.config b/conf/hypercap.config
@@ -8,6 +8,4 @@ params {
     callers             = "vardict"
     scatter_count       = 5
     only_pass           = true
-
-    output_suffix       = "-vardict-decomposed-annotated"
 }
diff --git a/conf/modules.config b/conf/modules.config
@@ -240,7 +240,7 @@ process {
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     */
 
-    withName: "^.*BCFTOOLS_NORM\$" {
+    withName: "^.*GERMLINE:BCFTOOLS_NORM\$" {
         ext.prefix = {"${meta.id}.normalized"}
         ext.args = "-m-"
     }

diff --git a/conf/wes.config b/conf/wes.config
@@ -0,0 +1,10 @@
+/*
+========================================================================================
+    Nextflow config file for WES runs
+========================================================================================
+*/
+
+params {
+    callers             = "haplotypecaller"
+    scatter_count       = 8
+}
diff --git a/modules.json b/modules.json
@@ -14,7 +14,7 @@
                     "bcftools/concat": {
                         "branch": "master",
                         "git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d",
-                        "installed_by": ["vcf_annotate_ensemblvep_snpeff"]
+                        "installed_by": ["modules"]
                     },
                     "bcftools/filter": {
                         "branch": "master",
@@ -29,7 +29,7 @@
                     "bcftools/pluginscatter": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["vcf_annotate_ensemblvep_snpeff"]
+                        "installed_by": ["modules"]
                     },
                     "bcftools/query": {
                         "branch": "master",
@@ -44,7 +44,7 @@
                     "bcftools/sort": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["vcf_annotate_ensemblvep_snpeff"]
+                        "installed_by": ["modules"]
                     },
                     "bcftools/stats": {
                         "branch": "master",
@@ -86,7 +86,7 @@
                     "ensemblvep/vep": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["vcf_annotate_ensemblvep_snpeff"],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff"
                     },
                     "gatk4/calibratedragstrmodel": {
@@ -180,11 +180,6 @@
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
-                    "snpeff/snpeff": {
-                        "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["vcf_annotate_ensemblvep_snpeff"]
-                    },
                     "somalier/extract": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
@@ -199,7 +194,7 @@
                     "tabix/bgzip": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["vcf_annotate_ensemblvep_snpeff"]
+                        "installed_by": ["modules"]
                     },
                     "tabix/bgziptabix": {
                         "branch": "master",
@@ -209,7 +204,7 @@
                     "tabix/tabix": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules", "vcf_annotate_ensemblvep_snpeff"]
+                        "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
@@ -248,12 +243,7 @@
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
-                        "installed_by": ["subworkflows"]
-                    },
-                    "vcf_annotate_ensemblvep_snpeff": {
-                        "branch": "master",
-                        "git_sha": "1b2fdf082b2ea7976b112e149a474d816094724c",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }
                 }