Merge pull request #8 from maxulysse/mutect2

Adding PON with Mutect2

.gitignore

@@ -7,3 +7,4 @@ results/
 testing*
 testing/
 work/
+.nf-test.log

CHANGELOG.md

@@ -12,6 +12,7 @@ Initial release of nf-core/createpanelrefs, created with the [nf-core](https://n
 - [#5](https://github.com/nf-core/createpanelrefs/pull/5) - `CNVKIT` can be used to create a PON
 - [#5](https://github.com/nf-core/createpanelrefs/pull/5) - Usage of nf-validation
 - [#5](https://github.com/nf-core/createpanelrefs/pull/5) - Usage of nf-test
+- [#8](https://github.com/nf-core/createpanelrefs/pull/8) - `Mutect2` can be used to create a PON
 
 ### `Fixed`
 

conf/igenomes.config

@@ -280,7 +280,6 @@ params {
         'GATK.GRCh38' {
             bwa              = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/"
             bwamem2          = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/"
-            cf_chrom_len     = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len"
             dbsnp            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz"
             dbsnp_tbi        = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi"
             dict             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict"

conf/modules/mutect2.config

@@ -0,0 +1,19 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+process {
+
+    withName: '.*BAM_CREATE_SOM_PON_GATK:GATK4_MUTECT2' {
+        ext.args = "--max-mnp-distance 0"
+    }
+
+}

conf/test.config

@@ -20,17 +20,20 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input = "${projectDir}/tests/csv/1.0.0/cram.csv"
+    input = "${projectDir}/tests/csv/1.0.0/bam.csv"
 
     // Main options
     tools = 'cnvkit'
 
     //Germlinecnvcaller options
-    gcnv_scatter_content = 2
-    gcnv_ploidy_priors   = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv"
+    gcnv_scatter_content    = 2
+    gcnv_ploidy_priors      = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv"
 
     // Small reference genome
-    genome            = null
-    igenomes_ignore   = true
-    fasta             = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta"
+    genome                  = null
+    igenomes_ignore         = true
+    fasta                   = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta"
+    dict                    = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.dict"
+    fai                     = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai"
+    target_bed              = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed"
 }

modules.json

@@ -30,6 +30,11 @@
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
+                    "gatk4/createsomaticpanelofnormals": {
+                        "branch": "master",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
+                        "installed_by": ["bam_create_som_pon_gatk"]
+                    },
                     "gatk4/determinegermlinecontigploidy": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
@@ -40,6 +45,11 @@
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
+                    "gatk4/genomicsdbimport": {
+                        "branch": "master",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "installed_by": ["bam_create_som_pon_gatk"]
+                    },
                     "gatk4/germlinecnvcaller": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
@@ -50,6 +60,11 @@
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
+                    "gatk4/mutect2": {
+                        "branch": "master",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
+                        "installed_by": ["bam_create_som_pon_gatk"]
+                    },
                     "gatk4/preprocessintervals": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
@@ -79,6 +94,11 @@
             },
             "subworkflows": {
                 "nf-core": {
+                    "bam_create_som_pon_gatk": {
+                        "branch": "master",
+                        "git_sha": "b0783b07beb65cac505fa6202e8f670437637b45",
+                        "installed_by": ["subworkflows"]
+                    },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",