Merge pull request #19 from ramprasadn/germlinecnvcallerupdate

update Germlinecnvcaller subworkflow

conf/modules/germlinecnvcaller_cohort.config

@@ -36,6 +36,14 @@ process {
         ]
     }
 
+    withName: '.*GERMLINECNVCALLER_COHORT:GATK4_BEDTOINTERVALLIST_TARGETS' {
+        ext.when = { params.analysis_type.equals("wes") && params.target_interval_list.equals(null) && params.target_bed }
+    }
+
+    withName: '.*GERMLINECNVCALLER_COHORT:GATK4_BEDTOINTERVALLIST_EXCLUDE' {
+        ext.when = { params.analysis_type.equals("wes") && params.exclude_interval_list.equals(null) && params.exclude_bed }
+    }
+
     withName: '.*GERMLINECNVCALLER_COHORT:GATK4_PREPROCESSINTERVALS' {
         ext.args = { ["--imr OVERLAPPING_ONLY",
                         "--padding ${params.padding}",

docs/usage.md

@@ -111,10 +111,18 @@ If you wish to share such profile (such as upload as supplementary material for
 
 If you are running the pipeline to generate references for the GATK's germlinecnvcalling workflow, you should ensure that you have provided all the mandatory options specified in the table below.
 
-| Mandatory                 | Optional |
-| ------------------------- | -------- |
-| fasta/genomes             | fai      |
-| ploidy_priors<sup>1</sup> | dict     |
+| Mandatory                 | Optional                          |
+| ------------------------- | --------------------------------- |
+| fasta/genomes             | fai                               |
+| ploidy_priors<sup>1</sup> | dict                              |
+|                           | target_bed/target_interval_list   |
+|                           | exclude_bed/exclude_interval_list |
+|                           | bin_length                        |
+|                           | mappable_regions                  |
+|                           | padding                           |
+|                           | readcount_format                  |
+|                           | scatter_content                   |
+|                           | segmental_duplications            |
 
 <sup>1</sup> To learn more about this file, see [this comment](https://gatk.broadinstitute.org/hc/en-us/community/posts/360074399831/comments/13441240230299) on GATK forum.<br />
 

main.nf

@@ -16,7 +16,6 @@ nextflow.enable.dsl = 2
     IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
-
 include { CREATEPANELREFS         } from './workflows/createpanelrefs'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_createpanelrefs_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_createpanelrefs_pipeline'
@@ -31,9 +30,13 @@ include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_crea
 
 //   This is an example of how to use getGenomeAttribute() to fetch parameters
 //   from igenomes.config using `--genome`
-params.fasta = getGenomeAttribute('fasta')
-params.fai   = getGenomeAttribute('fai')
-params.dict  = getGenomeAttribute('dict')
+params.fasta                 = getGenomeAttribute('fasta')
+params.fai                   = getGenomeAttribute('fai')
+params.dict                  = getGenomeAttribute('dict')
+params.target_bed            = getGenomeAttribute('target_bed')
+params.target_interval_list  = getGenomeAttribute('target_interval_list')
+params.exclude_bed           = getGenomeAttribute('exclude_bed')
+params.exclude_interval_list = getGenomeAttribute('exclude_interval_list')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

modules.json

@@ -15,6 +15,11 @@
                         "git_sha": "42ae163c3c6eb23646189c30c07a889ad39c9b0e",
                         "installed_by": ["modules"]
                     },
+                    "gatk4/bedtointervallist": {
+                        "branch": "master",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": ["modules"]
+                    },
                     "gatk4/collectreadcounts": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",

nextflow.config

@@ -23,6 +23,7 @@ params {
     tools                      = null // No default, must be specified
 
     // Germlinecnvcaller options
+    analysis_type              = 'wgs'
     bin_length                 = 1000
     mappable_regions           = null
     padding                    = 0

nextflow_schema.json

@@ -11,13 +11,38 @@
             "description": "Options used by the germlinecnvcaller subworkflow",
             "default": "",
             "properties": {
+                "analysis_type": {
+                    "type": "string",
+                    "default": "wgs",
+                    "description": "Specifies which analysis type for the pipeline- either 'wgs' or 'wes'.",
+                    "fa_icon": "fas fa-align-center",
+                    "enum": ["wgs", "wes"]
+                },
                 "bin_length": {
                     "type": "number",
                     "default": 1000,
                     "description": "Length (in bp) of the bins. If zero, no binning will be performed.",
                     "fa_icon": "fas fa-sort-numeric-down",
                     "help_text": "Used by GATK's PreprocessIntervals. GATK recommends a bin length of 1000 for WGS analysis, and 0 for WES analysis. "
                 },
+                "exclude_bed": {
+                    "type": "string",
+                    "exists": true,
+                    "format": "path",
+                    "fa_icon": "fas fa-file",
+                    "pattern": "^\\S+\\.bed$",
+                    "description": "Path to directory for a bed file containing regions to be exluded from the analysis.",
+                    "help_text": "If the regions you would like to exclude are in bed format, use this option. If you have an interval_list file, use `exclude_interval_list` parameter instead."
+                },
+                "exclude_interval_list": {
+                    "type": "string",
+                    "exists": true,
+                    "format": "path",
+                    "fa_icon": "fas fa-file",
+                    "pattern": "^\\S+\\._interval_list$",
+                    "description": "Path to directory for exclude_interval_list file.",
+                    "help_text": "If the regions you would like to exclude are in interval_list format, use this option. If you have a bed file, use `exclude` parameter instead."
+                },
                 "mappable_regions": {
                     "type": "string",
                     "exists": true,
@@ -63,6 +88,24 @@
                     "format": "file-path",
                     "fa_icon": "fas fa-file",
                     "help_text": "Used by GATK's AnnotateIntervals."
+                },
+                "target_bed": {
+                    "type": "string",
+                    "exists": true,
+                    "format": "path",
+                    "fa_icon": "fas fa-file",
+                    "pattern": "^\\S+\\.bed$",
+                    "description": "Path to directory for target bed file.",
+                    "help_text": "If the regions you would like to analyse are in bed format, use this option. If you have an interval_list file, use `target_interval_list` parameter instead."
+                },
+                "target_interval_list": {
+                    "type": "string",
+                    "exists": true,
+                    "format": "path",
+                    "fa_icon": "fas fa-file",
+                    "pattern": "^\\S+\\._interval_list$",
+                    "description": "Path to directory for target interval_list file.",
+                    "help_text": "If the regions you would like to analyse are in interval_list format, use this option. If you have a bed file, use `target_bed` parameter instead."
                 }
             }
         },

subworkflows/local/germlinecnvcaller_cohort.nf

@@ -1,21 +1,27 @@
-include { GATK4_ANNOTATEINTERVALS             } from '../../modules/nf-core/gatk4/annotateintervals/main'
-include { GATK4_COLLECTREADCOUNTS             } from '../../modules/nf-core/gatk4/collectreadcounts/main'
-include { GATK4_DETERMINEGERMLINECONTIGPLOIDY } from '../../modules/nf-core/gatk4/determinegermlinecontigploidy/main'
-include { GATK4_FILTERINTERVALS               } from '../../modules/nf-core/gatk4/filterintervals/main'
-include { GATK4_GERMLINECNVCALLER             } from '../../modules/nf-core/gatk4/germlinecnvcaller/main'
-include { GATK4_INTERVALLISTTOOLS             } from '../../modules/nf-core/gatk4/intervallisttools/main'
-include { GATK4_PREPROCESSINTERVALS           } from '../../modules/nf-core/gatk4/preprocessintervals/main'
-include { PICARD_CREATESEQUENCEDICTIONARY     } from '../../modules/nf-core/picard/createsequencedictionary/main'
-include { SAMTOOLS_FAIDX                      } from '../../modules/nf-core/samtools/faidx/main'
-include { SAMTOOLS_INDEX                      } from '../../modules/nf-core/samtools/index/main'
+include { GATK4_ANNOTATEINTERVALS                                    } from '../../modules/nf-core/gatk4/annotateintervals/main'
+include { GATK4_BEDTOINTERVALLIST as GATK4_BEDTOINTERVALLIST_TARGETS } from '../../modules/nf-core/gatk4/bedtointervallist/main'
+include { GATK4_BEDTOINTERVALLIST as GATK4_BEDTOINTERVALLIST_EXCLUDE } from '../../modules/nf-core/gatk4/bedtointervallist/main'
+include { GATK4_COLLECTREADCOUNTS                                    } from '../../modules/nf-core/gatk4/collectreadcounts/main'
+include { GATK4_DETERMINEGERMLINECONTIGPLOIDY                        } from '../../modules/nf-core/gatk4/determinegermlinecontigploidy/main'
+include { GATK4_FILTERINTERVALS                                      } from '../../modules/nf-core/gatk4/filterintervals/main'
+include { GATK4_GERMLINECNVCALLER                                    } from '../../modules/nf-core/gatk4/germlinecnvcaller/main'
+include { GATK4_INTERVALLISTTOOLS                                    } from '../../modules/nf-core/gatk4/intervallisttools/main'
+include { GATK4_PREPROCESSINTERVALS                                  } from '../../modules/nf-core/gatk4/preprocessintervals/main'
+include { PICARD_CREATESEQUENCEDICTIONARY                            } from '../../modules/nf-core/picard/createsequencedictionary/main'
+include { SAMTOOLS_FAIDX                                             } from '../../modules/nf-core/samtools/faidx/main'
+include { SAMTOOLS_INDEX                                             } from '../../modules/nf-core/samtools/index/main'
 
 workflow GERMLINECNVCALLER_COHORT {
     take:
-        ch_user_dict     // channel: [mandatory] [ val(meta), path(dict) ]
-        ch_user_fai      // channel: [mandatory] [ val(meta), path(fai) ]
-        ch_fasta         // channel: [mandatory] [ val(meta), path(fasta) ]
-        ch_input         // channel: [mandatory] [ val(meta), path(bam/cram), path(bai/crai) ]
-        ch_ploidy_priors // channel: [mandatory] [ path(tsv) ]
+        ch_user_dict                  // channel: [mandatory] [ val(meta), path(dict) ]
+        ch_user_fai                   // channel: [mandatory] [ val(meta), path(fai) ]
+        ch_fasta                      // channel: [mandatory] [ val(meta), path(fasta) ]
+        ch_input                      // channel: [mandatory] [ val(meta), path(bam/cram), path(bai/crai) ]
+        ch_ploidy_priors              // channel: [mandatory] [ path(tsv) ]
+        ch_target_bed                 // channel: [mandatory] [ val(meta), path(bed) ]
+        ch_user_target_interval_list  // channel: [mandatory] [ val(meta), path(intervals) ]
+        ch_exclude_bed                // channel: [mandatory] [ val(meta), path(bed) ]
+        ch_user_exclude_interval_list // channel: [mandatory] [ val(meta), path(intervals) ]
 
     main:
         ch_versions = Channel.empty()
@@ -37,10 +43,42 @@ workflow GERMLINECNVCALLER_COHORT {
             .collect()
             .set { ch_fai }
 
+        GATK4_BEDTOINTERVALLIST_TARGETS (ch_target_bed, ch_dict) //Runs for wes analysis, when target_bed file is provided instead of target_interval_list
+        GATK4_BEDTOINTERVALLIST_EXCLUDE (ch_exclude_bed, ch_dict) //Runs for wes analysis, when exclude_bed file is provided instead of target_interval_list
+
+        ch_user_target_interval_list
+            .combine(GATK4_BEDTOINTERVALLIST_TARGETS.out.interval_list.ifEmpty(null))
+            .branch { it  ->
+                intervallistfrompath: it[2].equals(null)
+                    return [it[0], it[1]]
+                intervallistfrombed: !(it[2].equals(null))
+                    return [it[2], it[3]]
+            }
+            .set { ch_targets_for_mix }
+
+        ch_targets_for_mix.intervallistfrompath.mix(ch_targets_for_mix.intervallistfrombed)
+            .collect()
+            .set {ch_target_interval_list}
+
+        ch_user_exclude_interval_list
+            .combine(GATK4_BEDTOINTERVALLIST_EXCLUDE.out.interval_list.ifEmpty(null))
+            .branch { it  ->
+                intervallistfrompath: it[2].equals(null)
+                    return [it[0], it[1]]
+                intervallistfrombed: !(it[2].equals(null))
+                    return [it[2], it[3]]
+            }
+            .set { ch_exclude_for_mix }
+
+        ch_exclude_for_mix.intervallistfrompath.mix(ch_exclude_for_mix.intervallistfrombed)
+            .collect()
+            .set { ch_exclude_interval_list }
+
         GATK4_PREPROCESSINTERVALS ( ch_fasta,
                                     ch_fai,
                                     ch_dict,
-                                    [[:],[]], [[:],[]] )
+                                    ch_target_interval_list,
+                                    ch_exclude_interval_list)
 
         GATK4_ANNOTATEINTERVALS (   GATK4_PREPROCESSINTERVALS.out.interval_list,
                                     ch_fasta,
@@ -121,6 +159,8 @@ workflow GERMLINECNVCALLER_COHORT {
         ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions)
         ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first())
         ch_versions = ch_versions.mix(GATK4_PREPROCESSINTERVALS.out.versions)
+        ch_versions = ch_versions.mix(GATK4_BEDTOINTERVALLIST_TARGETS.out.versions)
+        ch_versions = ch_versions.mix(GATK4_BEDTOINTERVALLIST_EXCLUDE.out.versions)
         ch_versions = ch_versions.mix(GATK4_COLLECTREADCOUNTS.out.versions.first())
         ch_versions = ch_versions.mix(GATK4_ANNOTATEINTERVALS.out.versions)
         ch_versions = ch_versions.mix(GATK4_FILTERINTERVALS.out.versions)

tests/pipeline/germlinecnvcaller_cohort.nf.test

@@ -25,6 +25,10 @@ nextflow_workflow {
                                 [[ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam"),[]],
                                 [[ id:'test2' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam"),[]])
                 input[4] = Channel.fromPath(params.ploidy_priors)
+                input[5] = Channel.value([[:],[]])
+                input[6] = Channel.value([[:],[]])
+                input[7] = Channel.value([[:],[]])
+                input[8] = Channel.value([[:],[]])
                 """
             }
         }