Merge pull request #156 from CenterForMedicalGeneticsGhent/update-pro…

…files update profiles seqplorer, hypercap and seqcap
nf-cmgg · Dec 11, 2023 · 32b4fe0 · 32b4fe0
2 parents 8105456 + 2d29367
commit 32b4fe0
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,10 +3,18 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.5.0dev [date]
+## v1.4.1dev [date]
 
 ### New Features
 
+1. Added the `--output_suffix` option to add a custom suffix to the basename of the output files.
+
+### Improvements
+
+1. Updated the seqplorer profile so that the output filenames are correct for easy import
+2. Changed the separator in `--vcfanno_resources` to `;`
+   instead of `,` to allow commas in glob patterns.
+
 ## v1.4.0 - Kingly Kortrijk - [December 6 2023]
 
 ### New Features

diff --git a/conf/HyperCap.config b/conf/HyperCap.config
diff --git a/conf/hypercap.config b/conf/hypercap.config
@@ -0,0 +1,12 @@
+/*
+========================================================================================
+    Nextflow config file for HyperCap runs
+========================================================================================
+*/
+
+params {
+    callers             = "vardict"
+    scatter_count       = 5
+
+    output_suffix       = "-vardict-decomposed-annotated"
+}
diff --git a/conf/modules.config b/conf/modules.config
@@ -44,6 +44,8 @@ def individual_validation = { "${params.outdir}/${meta.sample}/validation/${getG
 
 def callers = params.callers.tokenize(",")
 
+def final_prefix = params.output_suffix ? { "${meta.id}${params.output_suffix}" } : { "${meta.id}.${getGenotypedCaller(meta.caller)}" }
+
 process {
 
     publishDir = [
@@ -76,7 +78,7 @@ process {
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ] // SAVE
-        ext.prefix = { "${meta.id}.${getGenotypedCaller(meta.caller)}" }
+        ext.prefix = final_prefix
     }
 
     /*
@@ -251,7 +253,7 @@ process {
                 }
 
                 withName: "^.*:GVCF_JOINT_GENOTYPE_GATK4:VCF_CONCAT_BCFTOOLS:BCFTOOLS_CONCAT\$" {
-                    ext.prefix = {"${meta.id}.${getGenotypedCaller(meta.caller)}"}
+                    ext.prefix = final_prefix
                     ext.args = "--allow-overlaps --output-type z"
                     publishDir = [
                         enabled: enableOutput("original"),
@@ -269,7 +271,7 @@ process {
                     }
 
                     withName: "^.*:CRAM_CALL_GENOTYPE_GATK4:VCF_FILTER_BCFTOOLS:FILTER_2\$" {
-                        ext.prefix = {"${meta.id}.${getGenotypedCaller(meta.caller)}"}
+                        ext.prefix = final_prefix
                         ext.args = {'--output-type z --soft-filter \'GATKCutoffIndel\' -e \'TYPE="indel" && (ReadPosRankSum < -20.0 || QD < 2.0 || FS > 200.0 || SOR > 10.0 || (QD < 10.0 && AD[0:1] / (AD[0:1] + AD[0:0]) < 0.25 && ReadPosRankSum < 0.0))\' -m \'+\''}
                         publishDir = [
                             enabled: enableOutput("filter"),
@@ -370,7 +372,7 @@ process {
                 enabled: enableOutput("normalize"),
                 mode: params.publish_dir_mode,
                 path: final_output,
-                saveAs: { filename -> filename.endsWith('.vcf.gz') ? "${meta.id}.${getGenotypedCaller(meta.caller)}.vcf.gz" : null }
+                saveAs: { filename -> filename.endsWith('.vcf.gz') ? filename.replaceAll(".normalized.vcf.gz\$", ".vcf.gz") : null }
             ] // SAVE
         }
 
@@ -380,7 +382,7 @@ process {
                 enabled: enableOutput("normalize"),
                 mode: params.publish_dir_mode,
                 path: final_output,
-                saveAs: { filename -> filename.endsWith('.vcf.gz.tbi') ? "${meta.id}.${getGenotypedCaller(meta.caller)}.vcf.gz.tbi" : null }
+                saveAs: { filename -> filename.endsWith('.vcf.gz.tbi') ? filename.replaceAll(".normalized.vcf.gz.tbi\$", ".vcF.gz.tbi") : null }
             ] // SAVE
         }
     }
@@ -395,7 +397,7 @@ process {
 
         withName: "^.*:VCF_EXTRACT_RELATE_SOMALIER:SOMALIER_RELATE\$" {
             ext.args = { ped ? "" : "--infer"}
-            ext.prefix = { "${meta.sample ?: meta.id}.${getGenotypedCaller(meta.caller)}" }
+            ext.prefix = final_prefix
             publishDir = [
                 overwrite: true,
                 enabled: true,
@@ -416,14 +418,14 @@ process {
             }
 
             withName: "^.*:VCF_PED_RTGTOOLS:BCFTOOLS_ANNOTATE\$" {
-                ext.prefix = { "${meta.sample ?: meta.id}.${getGenotypedCaller(meta.caller)}.pedheader" }
+                ext.prefix = final_prefix
                 ext.args = "--output-type z"
                 publishDir = [
                     enabled: enableOutput("add_ped"),
                     overwrite: true,
                     path: final_output,
                     mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename.replace(".pedheader", "") }
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
                 ] // SAVE
             }
         }
@@ -476,7 +478,7 @@ process {
                     mode: params.publish_dir_mode,
                     saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
                 ] // SAVE
-                ext.prefix = { "${meta.id}.${getGenotypedCaller(meta.caller)}" }
+                ext.prefix = final_prefix
             }
 
             if (params.vcfanno){
@@ -488,7 +490,7 @@ process {
                         mode: params.publish_dir_mode,
                         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
                     ] // SAVE
-                    ext.prefix = { "${meta.id}.${getGenotypedCaller(meta.caller)}" }
+                    ext.prefix = final_prefix
                 }
             }
 
@@ -536,8 +538,8 @@ process {
         */
 
         if(params.gemini){
-            withName: VCF2DB{
-                ext.prefix = { "${meta.sample ?: meta.id}.${getGenotypedCaller(meta.caller)}" }
+            withName: "^.*:VCF2DB\$" {
+                ext.prefix = final_prefix
                 publishDir = [
                     overwrite: true,
                     path: final_output,
@@ -547,13 +549,13 @@ process {
             }
         }
 
-        withName: TABIX_FINAL {
+        withName: "^.*:TABIX_FINAL\$" {
             publishDir = [
                 enabled: true,
                 overwrite: true,
                 path: final_output,
                 mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.id}.${getGenotypedCaller(meta.caller)}.vcf.gz.tbi" }
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ] // SAVE
         }
     }
@@ -568,17 +570,6 @@ process {
         cache = false
     }
 
-    withName: MULTIQC {
-        publishDir = [
-            overwrite: true,
-            path: { "${params.outdir}/multiqc_reports" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ] // SAVE => Fix the location problem
-        errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
-        ext.args      = { params.multiqc_config ? "--config $multiqc_custom_config" : "" }
-    }
-
     withName: 'MULTIQC' {
         ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
         publishDir = [

diff --git a/conf/SeqCap.config → conf/seqcap.config b/conf/SeqCap.config → conf/seqcap.config
diff --git a/conf/seqplorer.config b/conf/seqplorer.config
@@ -5,19 +5,18 @@
 */
 
 params {
-    filter          = true
-    decompose       = true
-    normalize       = true
+    filter              = true
+    normalize           = true
+    gemini              = true
 
+    vcfanno             = true
     annotate            = true
-    vep_dbnsfp          = true
+    vep_merged          = true
     vep_spliceai        = true
     vep_mastermind      = true
     vep_eog             = true
     vep_maxentscan      = true
     vep_spliceregion    = true
 
-
-    gemini          = true
-
+    output_suffix       = "-gatk4-haplotype-joint-decomposed-annotated"
 }
diff --git a/conf/test.config b/conf/test.config
@@ -50,6 +50,6 @@ params {
     // VCFanno
     vcfanno           = true
     vcfanno_config    = "${projectDir}/assets/vcfanno.toml"
-    vcfanno_resources = "https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz,https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz.tbi"
+    vcfanno_resources = "https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz;https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz.tbi"
 
 }
diff --git a/main.nf b/main.nf
@@ -33,7 +33,8 @@ params.mastermind           = WorkflowMain.getGenomeAttribute(params, 'mastermin
 params.mastermind_tbi       = WorkflowMain.getGenomeAttribute(params, 'mastermind_tbi')
 params.eog                  = WorkflowMain.getGenomeAttribute(params, 'eog')
 params.eog_tbi              = WorkflowMain.getGenomeAttribute(params, 'eog_tbi')
-
+params.vcfanno_resources    = WorkflowMain.getGenomeAttribute(params, 'vcfanno_resources')
+params.vcfanno_config       = WorkflowMain.getGenomeAttribute(params, 'vcfanno_config')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/nextflow.config b/nextflow.config
@@ -27,6 +27,7 @@ params {
     callers                    = "haplotypecaller"
     vardict_min_af             = 0.1   // Minimum allele frequency for VarDict
     normalize                  = false
+    output_suffix              = ""
 
     // Module specific parameters
     dragstr                    = false
@@ -51,9 +52,7 @@ params {
 
     // VCFanno parameters
     vcfanno                    = false
-    vcfanno_config             = null
     vcfanno_lua                = null
-    vcfanno_resources          = null
 
     // References
     genome                     = "GRCh38"
@@ -231,8 +230,8 @@ profiles {
     WES             { includeConfig 'conf/WES.config'           }
     WGS             { includeConfig 'conf/WGS.config'           }
     seqplorer       { includeConfig 'conf/seqplorer.config'     }
-    SeqCap          { includeConfig 'conf/SeqCap.config'     }
-    HyperCap        { includeConfig 'conf/HyperCap.config'     }
+    seqcap          { includeConfig 'conf/seqcap.config'        }
+    hypercap        { includeConfig 'conf/hypercap.config'      }
 
 }
 
@@ -296,7 +295,7 @@ manifest {
     description     = 'A nextflow pipeline for calling and annotating variants'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.5.0dev'
+    version         = '1.4.1dev'
     doi             = ''
 }
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -239,6 +239,10 @@
                 "normalize": {
                     "type": "boolean",
                     "description": "Normalize the VCF after joint genotyping (will run on the decomposed VCF when --decompose is also used)"
+                },
+                "output_suffix": {
+                    "type": "string",
+                    "description": "A custom suffix to add to the basename of the output files"
                 }
             },
             "required": ["scatter_count"]
@@ -610,7 +614,7 @@
                 },
                 "vcfanno_resources": {
                     "type": "string",
-                    "description": "A comma-seperated list of resource files for VCFanno, please also supply their indices using this parameter"
+                    "description": "A semicolon-seperated list of resource files for VCFanno, please also supply their indices using this parameter"
                 }
             },
             "help_text": "Annotation will only run when `--annotate true` is specified."

diff --git a/tests/full_gvcf.nf.test b/tests/full_gvcf.nf.test
@@ -19,7 +19,7 @@ nextflow_pipeline {
 
                 vcfanno           = true
                 vcfanno_config    = "https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml"
-                vcfanno_resources = "https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz,https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz.tbi"
+                vcfanno_resources = "https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz;https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz.tbi"
 
             }
         }

diff --git a/tests/full_wes.nf.test b/tests/full_wes.nf.test
@@ -18,7 +18,7 @@ nextflow_pipeline {
 
                 vcfanno           = true
                 vcfanno_config    = "https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml"
-                vcfanno_resources = "https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz,https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz.tbi"
+                vcfanno_resources = "https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz;https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz.tbi"
 
             }
         }

diff --git a/tests/full_wgs.nf.test b/tests/full_wgs.nf.test
@@ -20,7 +20,7 @@ nextflow_pipeline {
 
                 vcfanno           = true
                 vcfanno_config    = "https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml"
-                vcfanno_resources = "https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz,https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz.tbi"
+                vcfanno_resources = "https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz;https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz.tbi"
 
             }
         }