diff --git a/bin/drop_config.py b/bin/drop_config.py new file mode 100755 index 00000000..537c9b97 --- /dev/null +++ b/bin/drop_config.py @@ -0,0 +1,173 @@ +#!/usr/bin/env python3 + +import argparse +from pathlib import Path +import yaml + + +def read_config(): + return yaml.safe_load( + """ + projectTitle: "DROP: Detection of RNA Outliers Pipeline" + root: # root directory of all intermediate output + htmlOutputPath: # path for HTML rendered reports + indexWithFolderName: true # whether the root base name should be part of the index name + + hpoFile: null # if null, downloads it from webserver + sampleAnnotation: # path to sample annotation (see documenation on how to create it) + + geneAnnotation: + gtf: null + # multiple annotations with custom names are possible + # : + # v37: /path/to/gencode29.gtf.gz # example + + genomeAssembly: hg19 # either hg19/hs37d5 or hg38/GRCh38 + exportCounts: + # specify which gene annotations to include and which + # groups to exclude when exporting counts + geneAnnotations: + - gtf + excludeGroups: + - null + genome: # path to genome sequence in fasta format. + # You can define multiple reference genomes in yaml format, ncbi: path_to_ncbi, ucsc: path_to_ucsc + # the keywords that define the path should be in the GENOME column of the SA table + + exportCounts: + # specify which gene annotations to include and which + # groups to exclude when exporting counts + geneAnnotations: + - gtf + excludeGroups: + - null + + aberrantExpression: + run: true + groups: + - outrider + fpkmCutoff: 1 + implementation: autoencoder + padjCutoff: 0.05 + zScoreCutoff: 0 + genesToTest: null + maxTestedDimensionProportion: 3 + yieldSize: 2000000 + + aberrantSplicing: + run: false + groups: + - outrider + recount: false + longRead: false + keepNonStandardChrs: true + filter: true + minExpressionInOneSample: 20 + quantileMinExpression: 10 + minDeltaPsi: 0.05 + implementation: PCA + padjCutoff: 0.1 + maxTestedDimensionProportion: 6 + genesToTest: null + FRASER_version: "FRASER2" + deltaPsiCutoff : 0.1 + quantileForFiltering: 0.75 + + mae: + run: false + groups: + - outrider + gatkIgnoreHeaderCheck: true + padjCutoff: .05 + allelicRatioCutoff: 0.8 + addAF: true + maxAF: .001 + maxVarFreqCohort: .05 + # VCF-BAM matching + qcVcf: null + qcGroups: mae + dnaRnaMatchCutoff: 0.85 + + rnaVariantCalling: + run: false + groups: + - batch_0 + highQualityVCFs: + - Data/Mills_and_1000G_gold_standard.indels.hg19.sites.chrPrefix.vcf.gz + - Data/1000G_phase1.snps.high_confidence.hg19.sites.chrPrefix.vcf.gz + dbSNP: Data/00-All.vcf.gz + repeat_mask: Data/hg19_repeatMasker_sorted.chrPrefix.bed + createSingleVCF: true + addAF: true + maxAF: 0.001 + maxVarFreqCohort: 0.05 + hcArgs: "" + minAlt: 3 + yieldSize: 100000 + + tools: + gatkCmd: gatk + bcftoolsCmd: bcftools + samtoolsCmd: samtools + """ + ) + + +def update_config(yaml_object, genome, gtf): + gtf_name = Path(gtf).name + gtf_without_ext = Path(gtf).stem + genome_name = Path(genome).name + + yaml_object["genome"] = genome_name + yaml_object["root"] = "output" + yaml_object["htmlOutputPath"] = "output/html" + yaml_object["sampleAnnotation"] = "sample_annotation.tsv" + yaml_object["geneAnnotation"][gtf_without_ext] = gtf_name + yaml_object["geneAnnotation"].pop("gtf", None) + + ## Export counts + yaml_object["exportCounts"]["geneAnnotations"] = [gtf_without_ext] + + ## Expression module + yaml_object["aberrantExpression"]["groups"] = ["outrider"] + + ## Splicing module + + ## MAE module + return yaml_object + + +def write_yaml(out_path, yaml_object): + with open(out_path, "w") as outfile: + yaml.dump(yaml_object, outfile, sort_keys=False) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser( + formatter_class=argparse.MetavarTypeHelpFormatter, + description="""Generate config file for DROP.""", + ) + + parser.add_argument( + "--genome_fasta", + type=str, + help="Specify genome fasta base name", + ) + + parser.add_argument( + "--gtf", + type=str, + help="Specify gtf file name", + ) + + parser.add_argument( + "--output", + type=str, + help="Specify output file", + ) + + args = parser.parse_args() + + yaml_object = read_config() + master_config = update_config(yaml_object=yaml_object, genome=args.genome_fasta, gtf=args.gtf) + write_yaml(out_path=args.output, yaml_object=master_config) diff --git a/bin/generate_gene_counts.py b/bin/drop_counts.py similarity index 100% rename from bin/generate_gene_counts.py rename to bin/drop_counts.py diff --git a/bin/generate_drop_sample_annot.py b/bin/drop_sample_annot.py similarity index 78% rename from bin/generate_drop_sample_annot.py rename to bin/drop_sample_annot.py index ea909792..2fa4d22b 100755 --- a/bin/generate_drop_sample_annot.py +++ b/bin/drop_sample_annot.py @@ -25,9 +25,8 @@ class SampleAnnotation: "GENOME", ] - def __init__(self, cnts_file, out_file, gtf_file, ref_cnts_file=False): + def __init__(self, cnts_file, out_file, gtf_file): """Create SampleAnnotation given the parameters""" - self.ref_cnts_file = ref_cnts_file self.cnts_file = cnts_file self.out_file = out_file self.gtf_file = gtf_file @@ -42,13 +41,6 @@ def parse_header(self): sample_cnt_file = {sample: os.path.basename(self.cnts_file) for sample in samples} - if self.ref_cnts_file: - with open(self.ref_cnts_file) as file_object: - ref_samples = file_object.readline().split()[1:] - - samples += ref_samples - sample_cnt_file.update({ref_sample: os.path.basename(self.ref_cnts_file) for ref_sample in ref_samples}) - return samples, sample_cnt_file def write_table(self): @@ -81,12 +73,6 @@ def write_table(self): required=True, ) - parser.add_argument( - "--ref_count_file", - type=str, - help="A tsv file of gene counts. Used as background", - ) - parser.add_argument( "--output", type=str, @@ -103,4 +89,4 @@ def write_table(self): args = parser.parse_args() - SampleAnnotation(args.count_file, args.output, args.gtf, args.ref_count_file).write_table() + SampleAnnotation(args.count_file, args.output, args.gtf).write_table() diff --git a/conf/modules.config b/conf/modules.config index e6dfef40..66844af8 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -307,7 +307,24 @@ process { // process { - withName: '.*ANALYSE_TRANSCRIPTS:GENERATE_COUNTS_DROP' { + withName: '.*ANALYSE_TRANSCRIPTS:DROP_COUNTS' { + publishDir = [ + path: { "${params.outdir}/analyse_transcripts" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + ] + } + + withName: '.*ANALYSE_TRANSCRIPTS:DROP_ANNOTATION' { + ext.when = {!params.drop_annot_file} + publishDir = [ + path: { "${params.outdir}/analyse_transcripts" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + ] + } + + withName: '.*ANALYSE_TRANSCRIPTS:DROP_CONFIG_RUN_AE' { publishDir = [ path: { "${params.outdir}/analyse_transcripts" }, mode: params.publish_dir_mode, diff --git a/modules/local/drop_config_runAE.nf b/modules/local/drop_config_runAE.nf new file mode 100644 index 00000000..6fb52536 --- /dev/null +++ b/modules/local/drop_config_runAE.nf @@ -0,0 +1,57 @@ +process DROP_CONFIG_RUN_AE { + tag "DROP_CONFIG_RUN_AE" + label 'process_high' + + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + exit 1, "Local DROP module does not support Conda. Please use Docker / Singularity / Podman instead." + } + + container "docker.io/clinicalgenomics/drop:1.3.3" + + input: + tuple val(meta), path(fasta), path(fai) + path gtf + path sample_annotation + path gene_counts + + output: + path('config.yaml'), emit: config_drop + path('output') , emit: drop_ae_out + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + """ + TMPDIR=\$PWD + + drop init + + $baseDir/bin/drop_config.py \\ + --genome_fasta $fasta \\ + --gtf $gtf \\ + --output config.yaml + + snakemake aberrantExpression --cores ${task.cpus} --rerun-triggers mtime + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + drop_config: v1.0 + drop: v\$(echo \$(drop --version) | sed -n 's/drop, version //p') + END_VERSIONS + """ + + stub: + """ + touch config.yaml + mkdir output + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + drop_config: v1.0 + drop: v\$(echo \$(drop --version) | sed -n 's/drop, version //p') + END_VERSIONS + """ +} diff --git a/modules/local/generate_gene_counts4drop.nf b/modules/local/drop_counts.nf similarity index 77% rename from modules/local/generate_gene_counts4drop.nf rename to modules/local/drop_counts.nf index d0320352..bfae3075 100644 --- a/modules/local/generate_gene_counts4drop.nf +++ b/modules/local/drop_counts.nf @@ -1,11 +1,11 @@ -process GENERATE_COUNTS_DROP { +process DROP_COUNTS { tag "DROP_counts" label 'process_low' - conda "bioconda::pydamage=0.70" + conda "bioconda::drop=1.3.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' : - 'biocontainers/pydamage:0.70--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/drop:1.3.3--pyhdfd78af_0' : + 'biocontainers/drop:1.3.3--pyhdfd78af_0' }" input: path(counts) @@ -25,7 +25,7 @@ process GENERATE_COUNTS_DROP { def strandedness = samples ? "--strandedness ${samples.strandedness}" : "" def input_samples = samples ? "${samples.id}" : "" """ - $baseDir/bin/generate_gene_counts.py \\ + $baseDir/bin/drop_counts.py \\ --star ${counts} \\ --sample $input_samples \\ $strandedness \\ @@ -35,7 +35,7 @@ process GENERATE_COUNTS_DROP { cat <<-END_VERSIONS > versions.yml "${task.process}": - generate_gene_counts: v1.0 + drop_counts: v1.0 END_VERSIONS """ @@ -45,7 +45,7 @@ process GENERATE_COUNTS_DROP { cat <<-END_VERSIONS > versions.yml "${task.process}": - generate_gene_counts: v1.0 + drop_counts: v1.0 END_VERSIONS """ } diff --git a/modules/local/generate_sample_annot.nf b/modules/local/drop_sample_annot.nf similarity index 63% rename from modules/local/generate_sample_annot.nf rename to modules/local/drop_sample_annot.nf index ad20d238..0701909a 100644 --- a/modules/local/generate_sample_annot.nf +++ b/modules/local/drop_sample_annot.nf @@ -1,16 +1,15 @@ -process GENERATE_ANNOTATION_DROP { +process DROP_ANNOTATION { tag "DROP_annot" label 'process_low' - conda "bioconda::pydamage=0.70" + conda "bioconda::drop=1.3.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' : - 'biocontainers/pydamage:0.70--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/drop:1.3.3--pyhdfd78af_0' : + 'biocontainers/drop:1.3.3--pyhdfd78af_0' }" input: path(processed_gene_counts) path(gtf) - path(reference_count_file) output: path('sample_annotation.tsv'), emit: sample_annotation_drop @@ -20,19 +19,17 @@ process GENERATE_ANNOTATION_DROP { task.ext.when == null || task.ext.when script: - def ref_counts = reference_count_file ? "--ref_count_file $reference_count_file" : "" def gtf_name = gtf ? gtf.getBaseName() : "" """ - generate_drop_sample_annot.py \\ + drop_sample_annot.py \\ --count_file $processed_gene_counts \\ --gtf $gtf_name \\ - $ref_counts \\ --output sample_annotation.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": - generate_drop_sample_annot: v1.0 + drop_sample_annot: v1.0 END_VERSIONS """ @@ -42,7 +39,7 @@ process GENERATE_ANNOTATION_DROP { cat <<-END_VERSIONS > versions.yml "${task.process}": - generate_drop_sample_annot: v1.0 + drop_sample_annot: v1.0 END_VERSIONS """ } diff --git a/nextflow.config b/nextflow.config index f18426d5..5da9065c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -36,6 +36,7 @@ params { variant_caller = 'bcftools' bcftools_caller_mode = 'multiallelic' run_drop_ae = true + drop_annot_file = null // MultiQC options multiqc_config = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 4dd24a34..5ed9ca85 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -262,6 +262,14 @@ "description": "Should DROP Aberrant Expression module be run?", "fa_icon": "fas fa-toggle-off" }, + "drop_annot_file": { + "type": "string", + "default": "None", + "description": "Path to a tsv file containing sample annotation for DROP. If it is not provided, it will be generated.", + "fa_icon": "fas fa-file", + "format": "file-path", + "mimetype": "tsv" + }, "reference_count_file": { "type": "string", "default": "None", diff --git a/subworkflows/local/analyse_transcripts.nf b/subworkflows/local/analyse_transcripts.nf index c6a3183e..f4f6f1e0 100644 --- a/subworkflows/local/analyse_transcripts.nf +++ b/subworkflows/local/analyse_transcripts.nf @@ -2,10 +2,11 @@ // ANALYSE TRANSCRITPS // - include { STRINGTIE_STRINGTIE } from '../../modules/nf-core/stringtie/stringtie/main' - include { GFFCOMPARE } from '../../modules/nf-core/gffcompare/main' - include { GENERATE_COUNTS_DROP } from '../../modules/local/generate_gene_counts4drop' - include { GENERATE_ANNOTATION_DROP } from '../../modules/local/generate_sample_annot' + include { STRINGTIE_STRINGTIE } from '../../modules/nf-core/stringtie/stringtie/main' + include { GFFCOMPARE } from '../../modules/nf-core/gffcompare/main' + include { DROP_COUNTS } from '../../modules/local/drop_counts' + include { DROP_ANNOTATION } from '../../modules/local/drop_sample_annot' + include { DROP_CONFIG_RUN_AE } from '../../modules/local/drop_config_runAE' workflow ANALYSE_TRANSCRIPTS { take: @@ -14,40 +15,57 @@ workflow ANALYSE_TRANSCRIPTS { ch_fasta_fai_meta // channel (mandatory): [ val(meta), [ path(fasta), path(fai) ] gene_counts // channel [val(meta), path(tsv)] reference_count_file // channel [ path(tsv) ] + drop_annot_file // channel [ path(tsv) ] main: ch_versions = Channel.empty() + // DROP + // Generates count files for samples and merges them with reference count file + star_count = gene_counts.map{ meta, cnt_file -> cnt_file }.collect() + star_samp = gene_counts.map{ meta, cnt_file -> meta }.collect() + DROP_COUNTS(star_count, star_samp, ch_gtf, reference_count_file) + + // Generates sample annotation file if it hasn't been provided by user + DROP_ANNOTATION(DROP_COUNTS.out.processed_gene_counts, ch_gtf) + ch_samp_annot = drop_annot_file.mix(DROP_ANNOTATION.out.sample_annotation_drop) + + // Generates config file and runs Aberrant expression module + DROP_CONFIG_RUN_AE( + ch_fasta_fai_meta, + ch_gtf, + ch_samp_annot, + DROP_COUNTS.out.processed_gene_counts + ) + + // Stringtie STRINGTIE_STRINGTIE( ch_bam, ch_gtf ) - ch_versions = ch_versions.mix(STRINGTIE_STRINGTIE.out.versions.first()) - - // DROP - // Count file - star_count = gene_counts.map{ meta, cnt_file -> cnt_file }.collect() - star_samp = gene_counts.map{ meta, cnt_file -> meta }.collect() - GENERATE_COUNTS_DROP(star_count, star_samp, ch_gtf, reference_count_file) - ch_versions = ch_versions.mix(GENERATE_COUNTS_DROP.out.versions) - // Annotation file - GENERATE_ANNOTATION_DROP(GENERATE_COUNTS_DROP.out.processed_gene_counts, ch_gtf, reference_count_file) - ch_versions = ch_versions.mix(GENERATE_ANNOTATION_DROP.out.versions) + // Compare stringtie results to reference GFFCOMPARE( STRINGTIE_STRINGTIE.out.transcript_gtf, ch_fasta_fai_meta, ch_gtf.map{ gtf -> [ [id:gtf.simpleName], gtf ] } ) + + ch_versions = ch_versions.mix(DROP_COUNTS.out.versions) + ch_versions = ch_versions.mix(DROP_ANNOTATION.out.versions) + ch_versions = ch_versions.mix(DROP_CONFIG_RUN_AE.out.versions) + ch_versions = ch_versions.mix(STRINGTIE_STRINGTIE.out.versions.first()) ch_versions = ch_versions.mix(GFFCOMPARE.out.versions.first()) emit: - transcript_gtf = STRINGTIE_STRINGTIE.out.transcript_gtf // channel: [ val(meta), [ path(transctript_gtf)] ] - abundance = STRINGTIE_STRINGTIE.out.abundance // channel: [ val(meta), [ path(abundance) ] ] - coverage_gtf = STRINGTIE_STRINGTIE.out.coverage_gtf // channel: [ val(meta), [ path(coverage_gtf) ] ] - annotated_gtf = GFFCOMPARE.out.annotated_gtf // channel: [ val(meta), [ path(annotated_gtf) ] ] - stats_gtf = GFFCOMPARE.out.stats // channel: [ val(meta), [ path(stats) ] ] - processed_gene_counts = GENERATE_COUNTS_DROP.out.processed_gene_counts // channel: [ path(tsv) ] - annotation_drop = GENERATE_ANNOTATION_DROP.out.sample_annotation_drop // channel: [ path(tsv) ] - versions = ch_versions // channel: [ path(versions.yml) ] + transcript_gtf = STRINGTIE_STRINGTIE.out.transcript_gtf // channel: [ val(meta), [ path(transctript_gtf)] ] + abundance = STRINGTIE_STRINGTIE.out.abundance // channel: [ val(meta), [ path(abundance) ] ] + coverage_gtf = STRINGTIE_STRINGTIE.out.coverage_gtf // channel: [ val(meta), [ path(coverage_gtf) ] ] + annotated_gtf = GFFCOMPARE.out.annotated_gtf // channel: [ val(meta), [ path(annotated_gtf) ] ] + stats_gtf = GFFCOMPARE.out.stats // channel: [ val(meta), [ path(stats) ] ] + processed_gene_counts = DROP_COUNTS.out.processed_gene_counts // channel: [ path(tsv) ] + annotation_drop = ch_samp_annot // channel: [ path(tsv) ] + config_drop = DROP_CONFIG_RUN_AE.out.config_drop // channel: [ path(confg_file.yml) ] + drop_ae_out = DROP_CONFIG_RUN_AE.out.drop_ae_out + versions = ch_versions // channel: [ path(versions.yml) ] } diff --git 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params.transcript_fasta, params.gtf, + params.drop_annot_file, params.reference_count_file, params.subsample_bed, params.vep_filters, @@ -117,6 +118,8 @@ workflow TOMTE { : Channel.empty() ch_reference_count_file = params.reference_count_file ? Channel.fromPath(params.reference_count_file).collect() : Channel.empty() + ch_drop_annot_filee = params.drop_annot_file ? Channel.fromPath(params.drop_annot_file).collect() + : Channel.empty() PREPARE_REFERENCES( fasta, @@ -179,7 +182,8 @@ workflow TOMTE { ch_references.gtf, ch_references.fasta_fai_meta, ch_alignment.gene_counts, - ch_reference_count_file + ch_reference_count_file, + ch_drop_annot_filee ) ch_versions = ch_versions.mix(ANALYSE_TRANSCRIPTS.out.versions)