Merge pull request #47 from nf-core/16-add-survivor-merge

16 add survivor merge

conf/modules.config

@@ -192,7 +192,7 @@ process {
         ext.when   = { params.method.split(',').contains('svanalyzer') }
         publishDir = [
             path: {"${params.outdir}/${meta.id}/svanalyzer_bench"},
-            pattern: "*{.vcf,distances,log,report}",
+            pattern: "*{.vcf.gz,tbi,distances,log,report}",
             mode: params.publish_dir_mode
         ]
     }
@@ -242,7 +242,7 @@ process {
     withName: MERGE_REPORTS {
         ext.prefix = {"${meta.benchmark_tool}.${meta.vartype}"}
         publishDir = [
-            path: {"${params.outdir}/summary"},
+            path: {"${params.outdir}/summary/tables"},
             pattern: "*{txt}",
             mode: params.publish_dir_mode
         ]
@@ -255,6 +255,28 @@ process {
             mode: params.publish_dir_mode
         ]
     }
+
+    withName: TABIX_BGZIP_BENCH{
+        ext.prefix = {input.toString() - ".vcf.gz"}
+    }
+
+    withName: SURVIVOR_MERGE {
+        ext.prefix = {"${meta.id}.${meta.vartype}.${meta.tag}"}
+        publishDir = [
+            path: {"${params.outdir}/summary/merged_vcf"},
+            pattern: "*{vcf}",
+            mode: params.publish_dir_mode
+        ]
+    }
+    withName: BCFTOOLS_QUERY {
+        ext.prefix = {"${meta.id}.${meta.vartype}.${meta.tag}"}
+        ext.args  = {"-f '%CHROM\t%POS\t%INFO/SVTYPE\t%INFO/SVLEN\t%INFO/SUPP_VEC\t%INFO/SUPP\t%ID[\t%SAMPLE]'" }
+        publishDir = [
+            path: {"${params.outdir}/summary/merged_vcf"},
+            pattern: "*{.txt}",
+            mode: params.publish_dir_mode
+        ]
+    }
 }
 //
 // Don't publish results for these processes

conf/test_full.config

@@ -27,7 +27,7 @@ params {
 
     // Processes
     analysis             = 'germline'
-    method               = 'rtgtools,happy,truvari,svanalyzer'  //
+    method               = 'happy,truvari,svanalyzer'  //
     similarity           = 0
     preprocess           = "normalization,deduplication,prepy"
     //variant_filtering    = "include"           // null, include, exclude

modules.json

@@ -15,6 +15,11 @@
                         "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
                         "installed_by": ["modules"]
                     },
+                    "bcftools/query": {
+                        "branch": "master",
+                        "git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f",
+                        "installed_by": ["modules"]
+                    },
                     "bcftools/reheader": {
                         "branch": "master",
                         "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
@@ -75,6 +80,11 @@
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
+                    "survivor/merge": {
+                        "branch": "master",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": ["modules"]
+                    },
                     "survivor/stats": {
                         "branch": "master",
                         "git_sha": "398375d72766cac92c4ffcf6927cac2d65310cfd",

modules/local/visualize_tagged/environment.yml

@@ -0,0 +1,7 @@
+name: plots
+channels:
+  - conda-forge
+dependencies:
+  - r-base=4.1.*
+  - r-ggplot2=3.3.*
+  - r-reshape2=1.4.*

modules/local/visualize_tagged/main.nf

@@ -0,0 +1,43 @@
+process VISUALIZE_TAGGED {
+    tag "$meta.benchmark_tool"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.4--r43hdfd78af_0':
+        'biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(vcf)
+
+    output:
+    tuple val(meta),path("*.txt"), emit: plots
+    path "versions.yml"          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.benchmark_tool}"
+
+    """
+    grep -o 'SUPP_VEC=[^,;]*' $vcf | awk -F'=' '{print \$2}' | sed -e 's/\\(.\\)/\\1 /g' > ${vcf}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
+    END_VERSIONS
+    """
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.benchmark_tool}"
+    """
+    touch ${vcf}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
+    END_VERSIONS
+    """
+}