Adapt vcf to scout

CHANGELOG.md

@@ -3,25 +3,25 @@
 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).
 
-### Parameters
-
-| Old parameter | New parameter |
-| ------------- | ------------- |
-
-:::note
-Parameter has been updated if both old and new parameter information is present.
-Parameter has been added if just the new parameter information is present.
-Parameter has been removed if new parameter information isn't present.
-:::
-
 ## 2.0.2 - [XXXX-XX-XX]
 
 ### `Added`
 
+- Installed bcftools/norm [#127](https://github.com/genomic-medicine-sweden/tomte/pull/127)
+- Installed bcftools/annotate [#127](https://github.com/genomic-medicine-sweden/tomte/pull/127)
+
 ### `Fixed`
 
+- One line per call on vcf to make vcf suitable for Scout [#127](https://github.com/genomic-medicine-sweden/tomte/pull/127)
+- Added variant caller to vcf to make vcf suitable for Scout [#127](https://github.com/genomic-medicine-sweden/tomte/pull/127)
+- Normalised calls in vcf [#127](https://github.com/genomic-medicine-sweden/tomte/pull/127)
+
 ### `Parameters`
 
+### `Changed`
+
+- Updated template to v2.14.1 [#123](https://github.com/genomic-medicine-sweden/tomte/pull/123)
+
 ## 2.0.1 - Grinch [2024-04-25]
 
 ### `Added`

assets/foundin.hdr

@@ -0,0 +1 @@
+##INFO=<ID=FOUND_IN,Number=1,Type=String,Description="Program that called the variant">

conf/modules/allele_specific_calling.config

@@ -33,27 +33,33 @@ process {
     withName: '.*ALLELE_SPECIFIC_CALLING:BCFTOOLS_MERGE' {
         ext.args = '--output-type z'
         ext.prefix = { "${meta.id}" }
-        publishDir = [
-            path: { "${params.outdir}/bootstrapann" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
     }
 
     withName: '.*ALLELE_SPECIFIC_CALLING:RENAME_FILES' {
         ext.prefix = { "${meta.id}" }
+    }
+
+    withName: '.*ALLELE_SPECIFIC_CALLING:SPLIT_MULTIALLELICS' {
+        ext.prefix = { "${meta.id}_norm" }
+        ext.args = '--output-type z --multiallelics -both'
+    }
+
+    withName: '.*ALLELE_SPECIFIC_CALLING:REMOVE_DUPLICATES' {
+        ext.args = '--output-type z --rm-dup none'
+        ext.prefix = { "${meta.id}_split_rmdup" }
         publishDir = [
             path: { "${params.outdir}/bootstrapann" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
-    withName: '.*ALLELE_SPECIFIC_CALLING:TABIX_TABIX' {
+    withName: '.*ALLELE_SPECIFIC_CALLING:TABIX_REMOVE_DUP' {
         publishDir = [
             path: { "${params.outdir}/bootstrapann" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
+
 }

conf/modules/call_variants.config

@@ -60,5 +60,37 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
+        withName: '.*CALL_VARIANTS:SPLIT_MULTIALLELICS' {
+        ext.prefix = { "${meta.id}_norm" }
+        ext.args = '--output-type z --multiallelics -both'
+    }
+
+    withName: '.*CALL_VARIANTS:REMOVE_DUPLICATES' {
+        ext.args = '--output-type z --rm-dup none'
+        ext.prefix = { "${meta.id}_split_rmdup" }
+    }
+
+    withName: '.*CALL_VARIANTS:ADD_VARCALLER_TO_BED' {
+        ext.args2   = '-s 1 -b 2 -e 3'
+    }
+
+    withName: '.*CALL_VARIANTS:BCFTOOLS_ANNOTATE' {
+        ext.args = "-c CHROM,FROM,TO,FOUND_IN --output-type z"
+        ext.prefix = { "${meta.id}_split_rmdup_info" }
+        publishDir = [
+            path: { "${params.outdir}/call_variants" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+    withName: '.*CALL_VARIANTS:TABIX_ANNOTATE' {
+        publishDir = [
+            path: { "${params.outdir}/call_variants" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
 
 }

modules.json

@@ -5,6 +5,11 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
+                    "bcftools/annotate": {
+                        "branch": "master",
+                        "git_sha": "2ad29c2aed06d815d9f68ad7ba20b3b1c574ce9c",
+                        "installed_by": ["modules"]
+                    },
                     "bcftools/index": {
                         "branch": "master",
                         "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
@@ -21,6 +26,11 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/bcftools/mpileup/bcftools-mpileup.diff"
                     },
+                    "bcftools/norm": {
+                        "branch": "master",
+                        "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
+                        "installed_by": ["modules"]
+                    },
                     "bcftools/stats": {
                         "branch": "master",
                         "git_sha": "618364f55cb88f6c283f6c6c45c24d5f9f08f998",

modules/local/add_varcallername_to_bed.nf

@@ -0,0 +1,47 @@
+process ADD_VARCALLER_TO_BED {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' :
+        'biocontainers/tabix:1.11--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(chromsizes)
+
+    output:
+    tuple val(meta), path("*.gz"), path("*.tbi"), emit: gz_tbi
+    path  "versions.yml" ,                        emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def variant_caller = "${meta.id}"
+    """
+    awk '{print \$1"\t0\t"\$2"\t$variant_caller\"}' $chromsizes > ${variant_caller}.bed
+    bgzip --threads ${task.cpus} -c $args ${variant_caller}.bed > ${prefix}.bed.gz
+    tabix $args2 ${prefix}.bed.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bed.gz
+    touch ${prefix}.bed.gz.tbi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+    END_VERSIONS
+    """
+}