369 lines
12 KiB
Plaintext
369 lines
12 KiB
Plaintext
#!/usr/bin/env nextflow
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import groovy.json.JsonBuilder
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nextflow.enable.dsl = 2
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include { fastq_ingress; xam_ingress } from './lib/ingress'
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include { getParams; configure_igv } from './lib/common'
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include { prepare_reference } from './lib/reference'
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include { transcriptome_analysis } from './subworkflows/transcriptome'
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include { differential_expression } from './subworkflows/differential_expression'
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OPTIONAL_FILE = file("$projectDir/data/OPTIONAL_FILE")
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process getVersions {
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label "wf_transcriptomes"
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publishDir "${params.out_dir}", mode: 'copy', pattern: "versions.txt"
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cpus 1
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memory "2 GB"
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output:
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path "versions.txt"
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script:
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"""
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minimap2 --version | sed 's/^/minimap2,/' >> versions.txt
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samtools --version | head -n 1 | sed 's/ /,/' >> versions.txt
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gffread --version | sed 's/^/gffread,/' >> versions.txt || true
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Rscript -e 'pkgs <- c("bambu", "DESeq2", "DEXSeq"); for (pkg in pkgs) {cat(pkg, as.character(packageVersion(pkg)), sep = ","); cat("\\n")}' >> versions.txt
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"""
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}
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process makeReport {
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label "wf_common"
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publishDir "${params.out_dir}", mode: 'copy', pattern: "wf-transcriptomes-report.html"
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cpus 1
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memory 8.GB
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input:
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tuple val(metadata), path(stats, stageAs: "stats_*")
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path "versions/*"
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path "params.json"
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path cohort_dir, stageAs: "cohort"
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path sample_dirs, stageAs: "samples/*"
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path sqanti_dirs, stageAs: "sqanti/*"
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path de_files
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val wf_version
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output:
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path "wf-transcriptomes-report.html", emit: report
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script:
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String metadata_json = new JsonBuilder(metadata).toPrettyString().replaceAll("'", "'\\\\''")
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def report_stats = (stats instanceof java.util.Collection ? stats : (stats ? [stats] : []))
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.findAll { it.name != OPTIONAL_FILE.name }
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String stats_args = report_stats ? "--stats ${report_stats.join(' ')}" : ""
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String de_args = de_files.name == OPTIONAL_FILE.name ? "" : "--de_dir de_analysis"
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"""
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echo '${metadata_json}' > metadata.json
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workflow-glue report wf-transcriptomes-report.html \
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--metadata metadata.json \
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${stats_args} \
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--cohort_dir cohort \
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--samples_dir samples \
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--sqanti_dir sqanti \
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${de_args} \
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--versions versions \
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--params params.json \
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--wf_version ${wf_version}
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"""
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}
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process publishResults {
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label "wf_common"
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memory 2.GB
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cpus 1
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publishDir (
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params.out_dir,
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mode: "copy",
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saveAs: { dirname ? "$dirname/$fname" : fname }
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)
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input:
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tuple path(fname), val(dirname)
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output:
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path fname
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script:
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"""
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"""
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}
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def coerceBooleanParam(value) {
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if (value == null || value instanceof Boolean) {
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return value
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}
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if (value instanceof CharSequence) {
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switch (value.toString().trim().toLowerCase()) {
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case "true":
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case "1":
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case "yes":
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return true
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case "false":
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case "0":
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case "no":
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return false
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}
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}
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return value
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}
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[
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"help",
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"version",
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"igv",
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"direct_rna",
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"de_analysis",
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"analyse_unclassified",
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"analyse_fail",
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"skip_sqanti",
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"sqanti_skip_orf",
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"disable_ping",
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"monochrome_logs",
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"validate_params",
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"show_hidden_params",
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].each { name ->
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params[name] = coerceBooleanParam(params[name])
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}
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[
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"keep_unaligned",
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"return_fastq",
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"per_read_stats",
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"allow_multiple_basecall_models",
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].each { name ->
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if (params.wf?.containsKey(name)) {
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params.wf[name] = coerceBooleanParam(params.wf[name])
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}
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}
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workflow pipeline {
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take:
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reads
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sample_sheet
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ref_genome
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ref_annotation
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main:
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software_versions = getVersions()
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workflow_params = getParams()
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transcriptome = transcriptome_analysis(reads, ref_genome, ref_annotation, sample_sheet)
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if (params.de_analysis) {
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de_results = differential_expression(
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transcriptome.joint_transcript_rds,
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transcriptome.joint_gene_rds,
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sample_sheet
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)
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de_dir = de_results.dir
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} else {
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de_dir = Channel.of(OPTIONAL_FILE)
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}
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report_input = reads
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.collect(flat: false)
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.map { rows ->
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def metadata = rows.collect { meta, xam, xai, stats ->
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meta + [has_stats: stats as boolean]
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}
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def stats_rows = rows.findAll { meta, xam, xai, stats -> stats != null }
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[
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metadata,
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stats_rows ? stats_rows.collect { meta, xam, xai, stats -> stats } : [OPTIONAL_FILE]
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]
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}
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sample_dirs_for_report = transcriptome.sample_dirs
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.map { meta, sample_dir -> sample_dir }
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.collect()
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sqanti_dirs_for_report = transcriptome.joint_sqanti_dir
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.concat(transcriptome.sample_sqanti_dirs.map { meta, sqanti_dir -> sqanti_dir })
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.ifEmpty(OPTIONAL_FILE)
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.collect()
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// meta.src_xam is non-null if BAMs are "passed through"
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generated_alignment_outputs = reads
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.filter { meta, bam, bai, stats -> meta.src_xam == null }
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.flatMap { meta, bam, bai, stats ->
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def outdir = "cohort/alignments/${meta.alias}"
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[
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[bam, outdir],
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[bai, outdir],
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[stats.resolve("bamstats.flagstat.tsv"), outdir],
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]
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}
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report = makeReport(
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report_input,
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software_versions,
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workflow_params,
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transcriptome.joint_dir,
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sample_dirs_for_report,
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sqanti_dirs_for_report,
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de_dir,
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workflow.manifest.version
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)
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results = Channel.empty()
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.concat(report.report.map { [it, null] })
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.concat(workflow_params.map { [it, null] })
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.concat(transcriptome.annotation_reference_summary.map { [it, "cohort/reference"] })
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.concat(transcriptome.unstranded_annotation.map { [it, "cohort/reference"] })
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.concat(transcriptome.joint_gtf.map { [it, "cohort"] })
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.concat(transcriptome.joint_fasta.map { [it, "cohort"] })
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.concat(transcriptome.joint_transcript_counts.map { [it, "cohort"] })
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.concat(transcriptome.joint_gene_counts.map { [it, "cohort"] })
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.concat(transcriptome.joint_transcript_rds.map { [it, "cohort"] })
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.concat(transcriptome.joint_gene_rds.map { [it, "cohort"] })
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.concat(transcriptome.joint_metadata.map { [it, "cohort"] })
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.concat(transcriptome.sample_gtf.map { meta, gtf -> [gtf, "samples/${meta.alias}"] })
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.concat(transcriptome.sample_fastas.map { meta, fasta -> [fasta, "samples/${meta.alias}"] })
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.concat(transcriptome.sample_transcript_counts.map { meta, counts -> [counts, "samples/${meta.alias}"] })
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.concat(transcriptome.sample_gene_counts.map { meta, counts -> [counts, "samples/${meta.alias}"] })
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.concat(transcriptome.sample_transcript_rds.map { meta, rds -> [rds, "samples/${meta.alias}"] })
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.concat(transcriptome.sample_gene_rds.map { meta, rds -> [rds, "samples/${meta.alias}"] })
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.concat(transcriptome.sample_metadata.map { meta, metadata -> [metadata, "samples/${meta.alias}"] })
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.concat(generated_alignment_outputs)
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.concat(transcriptome.joint_sqanti_dir.map { [it, "cohort"] })
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.concat(transcriptome.sample_sqanti_dirs.map { meta, sqanti_dir -> [sqanti_dir, "samples/${meta.alias}"] })
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reference_basename = file(params.ref_genome).getName()
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if (params.igv) {
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//todo ???
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//results = results
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// .concat(transcriptome.reference.map { [it, "igv_reference"] })
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// .concat(transcriptome.reference_fai.map { [it, "igv_reference"] })
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// .concat(transcriptome.reference_gzi.map { [it, "igv_reference"] })
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results = Channel.empty()
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//igv_index_paths = transcriptome.reference_fai
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// .map { "igv_reference/${it.getName()}" }
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// .concat(transcriptome.reference_gzi.map { "igv_reference/${it.getName()}" })
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igv_index_paths = Channel.empty()
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igv_alignment_paths = reads
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.map { meta, bam, bai, stat -> [
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meta.src_xam ?: "cohort/alignments/${meta.alias}/reads.bam",
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meta.src_xai ?: "cohort/alignments/${meta.alias}/reads.bam.bai"
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] }
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.flatten()
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igv_files = Channel.of("igv_reference/${reference_basename}")
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.concat(igv_index_paths)
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.concat(igv_alignment_paths)
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.collectFile(name: "igv-files.txt", newLine: true, sort: false)
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igv_conf = configure_igv(
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igv_files,
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"",
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[displayMode: "SQUISHED", colorBy: "strand"],
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[:],
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false
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)
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results = results.concat(igv_conf.map { [it, null] })
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}
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if (params.de_analysis) {
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results = results.concat(de_dir.map { [it, null] })
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}
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emit:
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results = results
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}
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WorkflowMain.initialise(workflow, params, log)
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workflow {
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Pinguscript.ping_start(nextflow, workflow, params)
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if (params.containsKey("ref_transcriptome")) {
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throw new Exception("--ref_transcriptome has been removed. Use --transcriptome_mode fixed_annotation with --ref_genome and --ref_annotation.")
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}
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if (params.containsKey("transcriptome_source")) {
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throw new Exception("--transcriptome_source has been removed. Use --transcriptome_mode with either discover or fixed_annotation.")
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}
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if (!!params.fastq == !!params.bam) {
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throw new Exception("Provide exactly one of --fastq or --bam.")
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}
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if (!params.ref_genome) {
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throw new Exception("Provide --ref_genome.") //todo isnt this enforced in the schema?
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}
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if (!params.ref_annotation) {
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throw new Exception("Provide --ref_annotation.")
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}
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if (!(params.transcriptome_mode in ["discover", "fixed_annotation"])) {
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throw new Exception("--transcriptome_mode must be one of: discover, fixed_annotation.")
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}
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if (params.de_analysis && !params.sample_sheet) {
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throw new Exception("Provide --sample_sheet when running with --de_analysis.")
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}
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sample_sheet = params.sample_sheet ? file(params.sample_sheet, type: "file") : OPTIONAL_FILE
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ref_annotation = file(params.ref_annotation, type: "file")
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prepared_reference = prepare_reference(
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params.ref_genome, [
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"output_cache": false,
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"output_mmi": false,
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])
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ref_genome = prepared_reference.ref_tuple
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if (!ref_annotation.exists()) {
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throw new Exception("--ref_annotation does not exist.")
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}
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if (sample_sheet != OPTIONAL_FILE && !sample_sheet.exists()) {
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throw new Exception("--sample_sheet does not exist.")
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}
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def ingress_args = [
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"minimap2_memory": ["31GB", "62GB"],
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"minimap2_opts": params.direct_rna ? "-ax splice -uf -k14" : "-ax splice -uf",
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"alignment_threads": 12,
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"output_xam_fmt": "bam",
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"sample": params.sample,
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"sample_sheet": params.sample_sheet,
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"analyse_unclassified": params.analyse_unclassified,
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"analyse_fail": params.analyse_fail,
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"fastcat_extra_args": "",
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"required_sample_types": [],
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]
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if (params.fastq) {
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samples = fastq_ingress([
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"input": params.fastq,
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] + ingress_args, ref_genome)
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} else {
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samples = xam_ingress([
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"input": params.bam,
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] + ingress_args, ref_genome)
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}
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analysis_samples = samples
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.filter { meta, xam, xai, stats ->
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if (meta.n_seqs == 0) {
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log.warn("Sample ${meta.alias} has no reads - excluded from transcriptome analysis.")
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return false
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}
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true
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}
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.ifEmpty {
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throw new Exception("No samples with reads were available for transcriptome analysis.")
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}
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processed_samples = analysis_samples
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pipeline_run = pipeline(processed_samples, sample_sheet, ref_genome, ref_annotation)
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publishResults(pipeline_run.results)
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}
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workflow.onComplete {
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Pinguscript.ping_complete(nextflow, workflow, params)
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}
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workflow.onError {
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Pinguscript.ping_error(nextflow, workflow, params)
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}
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