Merge pull request #338 from genomic-medicine-sweden/update-prp-to-ve…

…rsion-010

Updated JASEN to support PRP v0.10.0

CHANGELOG.md

@@ -13,14 +13,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added `samplelist_nanopore.csv` for running long-read test data
 - Added location of documentation to `README` 
 - Added `cdmDir` to config
+- Added process for adding IGV annotation tracks with PRP.
+- Updated how `mycobacterium_tuberculosis` workflow adds IGV annotation tracks.
 
 ### Fixed
 
 - Fixed `--qc` argument filepath to be full filepath to output
+- Fixed tbprofiler url in container Makefile
+- Fixed TB installation steps in main Makefile
 
 ### Changed
 
 - Updated TbProfiler to version 6.3
+- Updated PRP to version 0.10.0
+- Removed delly annotation
+- Updated vcf args in prp module
 
 ## [0.8.0]
 

Makefile

@@ -602,11 +602,11 @@ $(KPNEU_CGMLST_DIR)/alleles_rereffed: | $(KPNEU_CGMLST_DIR)/alleles/unpacking.do
 # M. tuberculosis
 # -----------------------------
 MTUBE_GENOMES_DIR := $(ASSETS_DIR)/genomes/mycobacterium_tuberculosis
-# MTUBE_TBDB_DIR := $(ASSETS_DIR)/tbdb
-# MTUBE_TBPROFILER_DBS_DIR := $(ASSETS_DIR)/tbprofiler_dbs
+MTUBE_TBDB_DIR := $(ASSETS_DIR)/tbdb
+MTUBE_TBPROFILER_DBS_DIR := $(ASSETS_DIR)/tbprofiler_dbs
 MTUBE_REFSEQ_ACC := GCF_000195955.2
 
-mtuberculosis_all: mtuberculosis_download_reference mtuberculosis_faidx_reference mtuberculosis_bwaidx_reference #mtuberculosis_converged_who_fohm_tbdb mtuberculosis_bgzip_bed mtuberculosis_index_bed
+mtuberculosis_all: mtuberculosis_download_reference mtuberculosis_faidx_reference mtuberculosis_bwaidx_reference mtuberculosis_converged_who_fohm_tbdb mtuberculosis_bgzip_bed mtuberculosis_index_bed
 
 mtuberculosis_download_reference: $(MTUBE_GENOMES_DIR)/$(MTUBE_REFSEQ_ACC).fasta
 

configs/nextflow.base.config

@@ -77,6 +77,7 @@ profiles {
 	mycobacterium_tuberculosis {
 		params.species = 'mycobacterium tuberculosis'
 		params.speciesDir = 'mtuberculosis'
+		params.resistantLociName = 'resistance_loci'
 		params.referenceGenome = "${params.root}/assets/genomes/mycobacterium_tuberculosis/GCF_000195955.2.fasta"
 		params.referenceGenomeIdx = "${params.root}/assets/genomes/mycobacterium_tuberculosis/GCF_000195955.2.fasta.fai"
 		params.referenceGenomeGff = "${params.root}/assets/genomes/mycobacterium_tuberculosis/GCF_000195955.2.gff"
@@ -106,6 +107,10 @@ process {
 	memory='1 GB'
 	cpus=2
 
+	withName: add_igv_track {
+		container = "${params.containerDir}/bonsai-prp.sif"
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
+	}
 	withName: amrfinderplus {
 		container = "${params.containerDir}/ncbi-amrfinderplus.sif"
 		cpus = 4

configs/nextflow.ci.config

@@ -81,6 +81,7 @@ profiles {
 	mycobacterium_tuberculosis {
 		params.species = 'mycobacterium tuberculosis'
 		params.speciesDir = 'mtuberculosis'
+		params.resistantLociName = 'resistance_loci'
 		params.referenceGenome = "${params.root}/assets/genomes/mycobacterium_tuberculosis/GCF_000195955.2.fasta"
 		params.referenceGenomeIdx = "${params.root}/assets/genomes/mycobacterium_tuberculosis/GCF_000195955.2.fasta.fai"
 		params.referenceGenomeGff = "${params.root}/assets/genomes/mycobacterium_tuberculosis/GCF_000195955.2.gff"
@@ -95,6 +96,10 @@ process {
 	memory='1 GB'
 	cpus=2
 
+	withName: add_igv_track {
+		container = "${params.containerDir}/bonsai-prp.sif"
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
+	}
 	withName: amrfinderplus {
 		container = "${params.containerDir}/ncbi-amrfinderplus.sif"
 		cpus = 4

configs/nextflow.dev.config

@@ -94,6 +94,7 @@ profiles {
 		params.species = 'mycobacterium tuberculosis'
 		params.speciesDir = 'mtuberculosis'
 		params.symlinkDir = "/access/jasen/mtuberculosis/"
+		params.resistantLociName = 'resistance_loci'
 		params.referenceGenome = "${params.root}/assets/genomes/mycobacterium_tuberculosis/GCF_000195955.2.fasta"
 		params.referenceGenomeIdx = "${params.root}/assets/genomes/mycobacterium_tuberculosis/GCF_000195955.2.fasta.fai"
 		params.referenceGenomeGff = "${params.root}/assets/genomes/mycobacterium_tuberculosis/GCF_000195955.2.gff"
@@ -110,6 +111,10 @@ process {
 	memory='1 GB'
 	cpus=2
 
+	withName: add_igv_track {
+		container = "${params.containerDir}/bonsai-prp.sif"
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
+	}
 	withName: amrfinderplus {
 		container = "https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.11.11--h6e70893_0"
 		cpus = 4
@@ -276,7 +281,7 @@ process {
 	withName: tbprofiler_mergedb {
 		cpus = 16
 		memory = '12 GB'
-		container = "https://depot.galaxyproject.org/singularity/tb-profiler%3A6.3.0--pyhdfd78af_0"
+		container = "https://depot.galaxyproject.org/singularity/tb-profiler:6.3.0--pyhdfd78af_0"
 		publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/tbprofiler_mergedb", mode: 'copy', overwrite: true, pattern: '*.json' ], [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true, pattern: '*.{vcf.gz}' ], [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true, pattern: '*.bam*' ] ]
 		ext.args = "--external_db ${params.root}/assets/tbdb/converged_who_fohm_tbdb --calling_params '-q 15'"
 	}

configs/nextflow.hopper.config

@@ -92,6 +92,7 @@ profiles {
 	mycobacterium_tuberculosis {
 		params.species = 'mycobacterium tuberculosis'
 		params.speciesDir = 'mtuberculosis'
+		params.resistantLociName = 'resistance_loci'
 		params.symlinkDir = "/access/jasen/mtuberculosis/
 		params.referenceGenome = "${params.root}/assets/genomes/mycobacterium_tuberculosis/GCF_000195955.2.fasta"
 		params.referenceGenomeIdx = "${params.root}/assets/genomes/mycobacterium_tuberculosis/GCF_000195955.2.fasta.fai"
@@ -109,6 +110,10 @@ process {
 	memory='1 GB'
 	cpus=2
 
+	withName: add_igv_track {
+		container = "${params.containerDir}/bonsai-prp.sif"
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
+	}
 	withName: amrfinderplus {
 		container = "https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.11.11--h6e70893_0"
 		cpus = 4
@@ -117,7 +122,7 @@ process {
 		ext.args = "--plus"
 	}
 	withName: annotate_delly {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.9.3"
+		container = "${params.containerDir}/bonsai-prp.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true ]
 	}
 	withName: assembly_trim_clean {
@@ -291,7 +296,7 @@ process {
 	withName: tbprofiler_mergedb {
 		cpus = 16
 		memory = '12 GB'
-		container = "https://depot.galaxyproject.org/singularity/tb-profiler%3A6.3.0--pyhdfd78af_0"
+		container = "https://depot.galaxyproject.org/singularity/tb-profiler:6.3.0--pyhdfd78af_0"
 		publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/tbprofiler_mergedb", mode: 'copy', overwrite: true, pattern: '*.json' ], [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true, pattern: '*.{vcf.gz}' ], [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true, pattern: '*.bam*' ] ]
 		ext.args = "--external_db ${params.root}/assets/tbdb/converged_who_fohm_tbdb --calling_params '-q 15'"
 	}

configs/nextflow.ngp.config

@@ -103,6 +103,7 @@ profiles {
 	mycobacterium_tuberculosis {
 		params.species = 'mycobacterium tuberculosis'
 		params.speciesDir = 'mtuberculosis'
+		params.resistantLociName = 'resistance_loci'
 		params.referenceGenome = "${params.root}/assets/genomes/mycobacterium_tuberculosis/GCF_000195955.2.fasta"
 		params.referenceGenomeIdx = "${params.root}/assets/genomes/mycobacterium_tuberculosis/GCF_000195955.2.fasta.fai"
 		params.referenceGenomeGff = "${params.root}/assets/genomes/mycobacterium_tuberculosis/GCF_000195955.2.gff"
@@ -119,6 +120,10 @@ process {
 	memory='1 GB'
 	cpus=params.cpus_small
 
+	withName: add_igv_track {
+		container = "${params.containerDir}/bonsai-prp.sif"
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
+	}
 	withName: amrfinderplus {
 		container = "${params.containerDir}/ncbi-amrfinderplus.sif"
 		cpus = params.cpus_medium

container/Makefile

@@ -42,7 +42,7 @@ remote_containers := ncbi-amrfinderplus.sif \
 					virulencefinder.sif
 
 # URLs to Docker containers
-DOCKER_bonsai-prp := docker://clinicalgenomicslund/bonsai-prp:0.9.3
+DOCKER_bonsai-prp := docker://clinicalgenomicslund/bonsai-prp:0.10.0
 
 # URLs to remote containers
 URL_ncbi-amrfinderplus := https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.11.11--h6e70893_0
@@ -66,7 +66,7 @@ URL_skesa := https://depot.galaxyproject.org/singularity/skesa:2.5.1--hdcf5f25_0
 URL_snippy := https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2
 URL_sourmash := https://depot.galaxyproject.org/singularity/sourmash:4.8.2--hdfd78af_0
 URL_spades := https://depot.galaxyproject.org/singularity/spades:3.15.5--h95f258a_1
-URL_tb-profiler := https://depot.galaxyproject.org/singularity/tb-profiler%3A6.3.0--pyhdfd78af_0
+URL_tb-profiler := https://depot.galaxyproject.org/singularity/tb-profiler:6.3.0--pyhdfd78af_0
 URL_virulencefinder := https://depot.galaxyproject.org/singularity/virulencefinder:2.0.4--hdfd78af_1
 
 define log_message

nextflow-modules/modules/prp/main.nf

@@ -3,7 +3,7 @@ process create_analysis_result {
   scratch params.scratch
 
   input:
-    tuple val(sampleID), path(quast), path(postalignqc), path(mlst), path(cgmlst), path(amr), path(resistance), path(resfinderMeta), path(serotype), path(serotypefinderMeta), path(virulence), path(virulencefinderMeta), path(shigapass), path(bam), path(bai), path(runInfo), path(dellyVcf), path(mykrobe), path(tbprofiler), path(bracken)
+    tuple val(sampleID), path(quast), path(postalignqc), path(mlst), path(cgmlst), path(amr), path(resistance), path(resfinderMeta), path(serotype), path(serotypefinderMeta), path(virulence), path(virulencefinderMeta), path(shigapass), path(bam), path(bai), path(runInfo), path(vcf), path(mykrobe), path(tbprofiler), path(bracken)
     path referenceGenome
     path referenceGenomeIdx
     path referenceGenomeGff
@@ -18,7 +18,7 @@ process create_analysis_result {
     brackenArgs = bracken ? "--kraken ${bracken}" : ""
     bamArgs = bam ? "--bam ${params.outdir}/${params.speciesDir}/${params.bamDir}/${bam}" : ""
     cgmlstArgs = cgmlst ? "--cgmlst ${cgmlst}" : ""
-    dellyVcfArgs = dellyVcf ? "--sv-vcf ${params.outdir}/${params.speciesDir}/${params.vcfDir}/${dellyVcf}" : ""
+    vcfArgs = vcf ? "--vcf ${params.outdir}/${params.speciesDir}/${params.vcfDir}/${vcf}" : ""
     mlstArgs = mlst ? "--mlst ${mlst}" : ""
     mykrobeArgs = mykrobe ? "--mykrobe ${mykrobe}" : ""
     postalignqcArgs = postalignqc ? "--quality ${postalignqc}" : "" 
@@ -42,7 +42,7 @@ process create_analysis_result {
       ${bamArgs} \\
       ${brackenArgs} \\
       ${cgmlstArgs} \\
-      ${dellyVcfArgs} \\
+      ${vcfArgs} \\
       ${mlstArgs} \\
       ${mykrobeArgs} \\
       ${postalignqcArgs} \\
@@ -159,3 +159,28 @@ process annotate_delly {
     touch $output
     """
 }
+
+process add_igv_track {
+  tag "${sampleID}"
+  scratch params.scratch
+
+  input:
+    tuple val(sampleID), path(bonsaiInput)
+    val annotation
+    val trackName
+
+  output:
+    tuple val(sampleID), path(output), emit: json
+
+  script:
+    output = "${sampleID}_result.json"
+    """
+    prp add-igv-annotation-track --track-name ${trackName} --annotation-file ${annotation} --bonsai-input-file ${bonsaiInput} --output ${output}
+    """
+
+  stub:
+    output = "${sampleID}_result.json"
+    """
+    touch $output
+    """
+}

workflows/mycobacterium_tuberculosis.nf

@@ -7,14 +7,15 @@ include { annotate_delly                        } from '../nextflow-modules/modu
 include { bracken                               } from '../nextflow-modules/modules/bracken/main.nf'
 include { copy_to_cron                          } from '../nextflow-modules/modules/cron/main.nf'
 include { create_analysis_result                } from '../nextflow-modules/modules/prp/main.nf'
+include { add_igv_track as add_variant_igv_track} from '../nextflow-modules/modules/prp/main.nf'
+include { add_igv_track as add_locus_igv_track  } from '../nextflow-modules/modules/prp/main.nf'
 include { create_cdm_input                      } from '../nextflow-modules/modules/prp/main.nf'
 include { create_yaml                           } from '../nextflow-modules/modules/yaml/main.nf'
 include { export_to_cdm                         } from '../nextflow-modules/modules/cmd/main.nf'
 include { kraken                                } from '../nextflow-modules/modules/kraken/main.nf'
 include { mykrobe                               } from '../nextflow-modules/modules/mykrobe/main.nf'
 include { post_align_qc                         } from '../nextflow-modules/modules/prp/main.nf'
 include { snippy                                } from '../nextflow-modules/modules/snippy/main.nf'
-include { tbprofiler as tbprofiler_tbdb         } from '../nextflow-modules/modules/tbprofiler/main.nf'
 include { tbprofiler as tbprofiler_mergedb      } from '../nextflow-modules/modules/tbprofiler/main.nf'
 include { CALL_BACTERIAL_BASE                   } from '../workflows/bacterial_base.nf'
 
@@ -97,7 +98,11 @@ workflow CALL_MYCOBACTERIUM_TUBERCULOSIS {
             create_analysis_result(combinedOutput, referenceGenome, referenceGenomeIdx, referenceGenomeGff)
         }
 
-        create_yaml(create_analysis_result.out.json.join(ch_sourmash), params.speciesDir)
+        // Add IGV annotation tracks
+        add_locus_igv_track(create_analysis_result.out.json, params.tbdbBed, params.resistantLociName)
+
+        // Create yaml for uploading results to Bonsai
+        create_yaml(add_locus_igv_track.out.json.join(ch_sourmash), params.speciesDir)
 
         ch_quast
             .join(ch_qc)
@@ -117,7 +122,7 @@ workflow CALL_MYCOBACTERIUM_TUBERCULOSIS {
         ch_versions = ch_versions.mix(tbprofiler_mergedb.out.versions)
 
     emit: 
-        pipeline_result = create_analysis_result.out.json
+        pipeline_result = add_locus_igv_track.out.json
         cdm             = export_to_cdm.out.cdm
         cron_yaml       = copy_to_cron.out.yaml
         cron_cdm        = copy_to_cron.out.cdm