28 change hdr to hrd

.gitignore

@@ -0,0 +1,20 @@
+*.code-workspace
+*.pyc
+*.pyo
+.*.sw?
+.DS_Store
+.nextflow*
+.nf-test.log
+.nf-test/
+.screenrc
+__pycache__
+output/
+results*/
+test.xml
+test_output/
+tests/data/
+work/
+.github/CODEOWNERS-tmp
+bin/python_modules/__init__.pyc
+bin/python_modules/Options.pyc
+bin/python_modules/Tabfile.pyc

conf/dkfz_cluster_hg37.config

@@ -57,7 +57,6 @@ params {
     mapability_file            = "${params.data_path}/databases/UCSC/wgEncodeCrgMapabilityAlign100mer_chr.bedGraph.gz"
     replication_time_file      = "${params.data_path}/databases/ENCODE/ReplicationTime_10cellines_mean_10KB.Rda"
     gc_content_file            = "${params.data_path}/stats/hg19_GRch37_100genomes_gc_content_10kb.txt"
-    gene_annotation_file       = "${params.data_path}/tools_data/ACEseq/INFORM_druggable_genes.csv"
 
     // get breakpoints/ PSCBS gaps
     centromer_file             = "${params.data_path}/stats/hg19_gaps.txt"

conf/dkfz_cluster_hg38.config

@@ -58,7 +58,6 @@ params {
     mapability_file            = "${params.data_path}/stats/mappability_m2e2/GRCh38_Mappability_Align_100mer_m2e2.ALT_HLA.bedGraph.gz"
     replication_time_file      = "${params.data_path}/databases/ENCODE/RepliSeq/time_mean_10KB.Rda"
     gc_content_file            = "${params.data_path}/stats/gc_content_hg38.txt"
-    gene_annotation_file       = "${params.data_path}/tools_data/ACEseq/INFORM_druggable_genes.hg38.tsv"
 
     // get breakpoints/ PSCBS gaps
     centromer_file             = "assets/hg38/gap_with_centromeres.header.txt"

conf/modules.config

@@ -158,7 +158,7 @@ process {
             mode: params.publish_dir_mode
         ]
     }
-    withName: 'ESTIMATE_HDRSCORE' {
+    withName: 'ESTIMATE_HRDSCORE' {
         publishDir = [
             path:  {"${params.outdir}/${meta.id}"},
             pattern: "*{.txt}",

conf/test.config

@@ -64,7 +64,6 @@ params {
     mapability_file            = "${projectDir}/testdata/annotations/mappability5.test.bed.gz"
     replication_time_file      = "${projectDir}/testdata/annotations/ReplicationTime_10cellines_mean_10KB.Rda"
     gc_content_file            = "assets/hg19/hg19_GRch37_100genomes_gc_content_10kb.txt"
-    gene_annotation_file       = "${projectDir}/testdata/annotations/druggable_genes.csv"
 
     // get breakpoints/ PSCBS gaps
     centromer_file             = "assets/hg19/hg19_gaps.txt"

conf/test_full.config

@@ -58,7 +58,6 @@ params {
     mapability_file            = "${params.data_path}/databases/UCSC/wgEncodeCrgMapabilityAlign100mer_chr.bedGraph.gz"
     replication_time_file      = "${params.data_path}/databases/ENCODE/ReplicationTime_10cellines_mean_10KB.Rda"
     gc_content_file            = "${params.data_path}/stats/hg19_GRch37_100genomes_gc_content_10kb.txt"
-    gene_annotation_file       = "${params.data_path}/tools_data/ACEseq/INFORM_druggable_genes.csv"
 
     // get breakpoints/ PSCBS gaps
     centromer_file             = "${params.data_path}/stats/hg19_gaps.txt"

conf/test_hg37.config

@@ -63,7 +63,6 @@ params {
     mapability_file            = "${projectDir}/testdata/annotations/mappability5.test.bed.gz"
     replication_time_file      = "${projectDir}/testdata/annotations/ReplicationTime_10cellines_mean_10KB.Rda"
     gc_content_file            = "assets/hg19/hg19_GRch37_100genomes_gc_content_10kb.txt"
-    gene_annotation_file       = "${projectDir}/testdata/annotations/druggable_genes.csv"
 
     // get breakpoints/ PSCBS gaps
     centromer_file             = "assets/hg19/hg19_gaps.txt"

conf/test_nocontrol_hg37.config

@@ -57,7 +57,6 @@ params {
     mapability_file            = "${params.data_path}/databases/UCSC/wgEncodeCrgMapabilityAlign100mer_chr.bedGraph.gz"
     replication_time_file      = "${params.data_path}/databases/ENCODE/ReplicationTime_10cellines_mean_10KB.Rda"
     gc_content_file            = "${params.data_path}/stats/hg19_GRch37_100genomes_gc_content_10kb.txt"
-    gene_annotation_file       = "${params.data_path}/tools_data/ACEseq/INFORM_druggable_genes.csv"
 
     // get breakpoints/ PSCBS gaps
     centromer_file             = "${params.data_path}/stats/hg19_gaps.txt"

modules/local/estimate_hdrscore.nf → modules/local/estimate_hrdscore.nf

@@ -1,4 +1,4 @@
-process ESTIMATE_HDRSCORE {
+process ESTIMATE_HRDSCORE {
     tag "$meta.id"
     label 'process_single'
 
@@ -11,7 +11,6 @@ process ESTIMATE_HDRSCORE {
     each path(blacklist)
     each path(centromers)
     each path(cytobands)
-    val(chr_prefix)
 
     output:
     tuple val(meta), path("*.txt")        , emit: txt
@@ -22,7 +21,6 @@ process ESTIMATE_HDRSCORE {
 
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def chrprefix = chr_prefix == "chr" ? "chr": "no"
 
     """
     estimateHRDScore.sh \\

modules/local/generate_plots.nf

@@ -13,7 +13,7 @@ process GENERATE_PLOTS {
 
     output:
     path('*.png')   
-    tuple val(meta), path('*.txt')                   , emit: hdr_estimate_files 
+    tuple val(meta), path('*.txt')                   , emit: hrd_estimate_files 
     tuple val(meta), path("*_cnv_parameter_*.txt")   , emit: cnv_params
     path  "versions.yml"                             , emit: versions
 

subworkflows/local/hdr_estimation.nf → subworkflows/local/hrd_estimation.nf

@@ -3,35 +3,33 @@
 //
 
 params.options = [:]
-include { ESTIMATE_HDRSCORE       } from '../../modules/local/estimate_hdrscore.nf'              addParams( options: params.options )
+include { ESTIMATE_HRDSCORE       } from '../../modules/local/estimate_hrdscore.nf'              addParams( options: params.options )
 
-workflow HDR_ESTIMATION {
+workflow HRD_ESTIMATION {
     take:
     json_report   // channel: [val(meta), path(.json)]
     hdr_files     // channel: [val(meta), [path(.txt), path(.txt)..]]
     blacklist     // channel: [blacklist.txt]
     sexfile       // channel: [val(meta), path(sexfile.txt)]
     centromers    // channel: [centromers.txt] 
     cytobands     // channel: [cytobands.txt]
-    chrprefix     // channel: [chromosome prefix value]
 
 
     main:
     versions = Channel.empty()
 
     //
-    // MODULE:ESTIMATE_HDRSCORE
+    // MODULE:ESTIMATE_HRDSCORE
     //
     // RUN parseJson.py
     input_ch =  json_report.join(hdr_files)
-    ESTIMATE_HDRSCORE(
+    ESTIMATE_HRDSCORE(
         input_ch.join(sexfile),
         blacklist,
         centromers,
-        cytobands,
-        chrprefix
+        cytobands
     )
-    versions  = versions.mix(ESTIMATE_HDRSCORE.out.versions) 
+    versions  = versions.mix(ESTIMATE_HRDSCORE.out.versions) 
 
     emit:
     versions

subworkflows/local/purity_evaluation.nf

@@ -69,7 +69,7 @@ workflow PURITY_EVALUATION {
         ch_input,
         chrlength
     )
-    hdr_files = GENERATE_PLOTS.out.hdr_estimate_files
+    hrd_files = GENERATE_PLOTS.out.hrd_estimate_files
     versions  = versions.mix(GENERATE_PLOTS.out.versions)
 
     //
@@ -83,6 +83,6 @@ workflow PURITY_EVALUATION {
 
     emit:
     json_report
-    hdr_files
+    hrd_files
     versions
 }

workflows/aceseq.nf

@@ -77,7 +77,7 @@ include { SNV_CALLING              } from '../subworkflows/local/snv_calling'
 include { PREPROCESSING            } from '../subworkflows/local/preprocessing'
 include { SEGMENTATION             } from '../subworkflows/local/segmentation'
 include { PURITY_EVALUATION        } from '../subworkflows/local/purity_evaluation'
-include { HDR_ESTIMATION           } from '../subworkflows/local/hdr_estimation'
+include { HRD_ESTIMATION           } from '../subworkflows/local/hrd_estimation'
 include { PHASING_X                } from '../subworkflows/local/phasing_x'
 include { PHASING_Y                } from '../subworkflows/local/phasing_y'
 
@@ -261,18 +261,18 @@ workflow ACESEQ {
         ch_versions     = ch_versions.mix(PURITY_EVALUATION.out.versions)
 
         //
-        // SUBWORKFLOW: HDR_ESTIMATION: 
+        // SUBWORKFLOW: HRD_ESTIMATION: 
         //
 
-        HDR_ESTIMATION(
+        HRD_ESTIMATION(
             PURITY_EVALUATION.out.json_report,
-            PURITY_EVALUATION.out.hdr_files,
+            PURITY_EVALUATION.out.hrd_files,
             blacklist,
             SNV_CALLING.out.ch_sex,
             centromers,
-            cytobands,
-            chrprefix
+            cytobands
         )
+        ch_versions     = ch_versions.mix(HRD_ESTIMATION.out.versions)
     }
     else{
         println "Only quality check is performed since runQualityCheckOnly is set to ${params.runQualityCheckOnly}"