121 lines
4.6 KiB
Plaintext
121 lines
4.6 KiB
Plaintext
nextflow.enable.dsl = 2
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OPTIONAL_FILE = file("$projectDir/data/OPTIONAL_FILE")
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process bambuDiscover {
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label "wf_transcriptomes"
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cpus {
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int requested = (params.threads ?: 4) as int
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int sampleCount = aliases instanceof Collection ? aliases.size() : 1
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sampleCount > 1 ? requested : 1
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}
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memory "60 GB"
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input:
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tuple val(meta), val(aliases), path(bams, stageAs: "bams/??.bam"), path(bais, stageAs: "bams/??.bam.bai"), path(sample_sheet)
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path annotation, stageAs: "annotation/*"
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tuple path(reference, stageAs: "reference/reference.fa"), path(ref_fai, stageAs: "reference/reference.fai")
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output:
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tuple val(meta), path("discover"), emit: dir
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script:
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def bam_list = bams instanceof Collection ? bams : [bams]
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def alias_list = aliases instanceof Collection ? aliases : [aliases]
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String bams_arg = "--bams '${bam_list.join(",")}'"
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String aliases_arg = "--aliases '${alias_list.join(",")}'"
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String sample_sheet_arg = sample_sheet.name == OPTIONAL_FILE.name ? "" : "--sample_sheet '${sample_sheet}'"
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String ndr_arg = params.ndr != null ? "--ndr ${params.ndr}" : ""
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"""
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supeRglue bambu discover \
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${bams_arg} \
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${aliases_arg} \
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${sample_sheet_arg} \
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--annotation "${annotation}" \
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--genome "${reference}" \
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--transcriptome_mode "${params.transcriptome_mode}" \
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--threads ${task.cpus} \
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${ndr_arg} \
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--out_dir discover
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"""
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}
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process bambuQuant {
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label "wf_transcriptomes"
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cpus {
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int requested = (params.threads ?: 4) as int
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boolean isJoint = meta instanceof Map && meta.alias == 'cohort'
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isJoint ? requested : 1
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}
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memory { ["8.GB", "16.GB", "48.GB"][task.attempt - 1] }
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maxRetries 2
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errorStrategy 'retry'
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input:
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tuple val(meta), val(chunk_id), val(annotation_tx_count), path(chunk_rds), path(discovered_annotation)
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tuple path(reference, stageAs: "reference/reference.fa"), path(ref_fai, stageAs: "reference/reference.fai")
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output:
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tuple val(meta), val(chunk_id), path("${chunk_id}"), emit: dir
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script:
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"""
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supeRglue bambu quant \
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--chunk_rds "${chunk_rds}" \
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--discovered_annotation_rds "${discovered_annotation}" \
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--genome "${reference}" \
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--threads ${task.cpus} \
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--out_dir "${chunk_id}"
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"""
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}
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process bambuEmpty {
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label "wf_transcriptomes"
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cpus 1
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memory "4 GB"
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input:
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tuple val(meta), val(aliases)
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output:
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tuple val(meta), path("${meta.alias}"), emit: dir
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tuple val(meta), path("${meta.alias}/transcripts.gtf"), emit: gtf
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tuple val(meta), path("${meta.alias}/transcript_counts.tsv"), emit: transcript_counts
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tuple val(meta), path("${meta.alias}/gene_counts.tsv"), emit: gene_counts
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tuple val(meta), path("${meta.alias}/bambu_transcripts.rds"), emit: transcript_rds
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tuple val(meta), path("${meta.alias}/bambu_genes.rds"), emit: gene_rds
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tuple val(meta), path("${meta.alias}/transcript_metadata.tsv"), emit: transcript_metadata
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script:
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def alias_list = aliases instanceof Collection ? aliases : [aliases]
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String aliases_arg = "--aliases '${alias_list.join(",")}'"
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"""
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supeRglue bambu empty \
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${aliases_arg} \
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--transcriptome_mode "${params.transcriptome_mode}" \
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--out_dir "${meta.alias}"
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"""
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}
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process collateBambuQuant {
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label "wf_transcriptomes"
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cpus 1
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memory "16 GB"
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input:
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tuple val(meta), path(chunk_dirs, stageAs: "chunks/*")
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output:
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tuple val(meta), path("${meta.alias}"), emit: dir
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tuple val(meta), path("${meta.alias}/transcripts.gtf"), emit: gtf
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tuple val(meta), path("${meta.alias}/transcript_counts.tsv"), emit: transcript_counts
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tuple val(meta), path("${meta.alias}/gene_counts.tsv"), emit: gene_counts
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tuple val(meta), path("${meta.alias}/bambu_transcripts.rds"), emit: transcript_rds
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tuple val(meta), path("${meta.alias}/bambu_genes.rds"), emit: gene_rds
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tuple val(meta), path("${meta.alias}/transcript_metadata.tsv"), emit: transcript_metadata
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script:
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def chunk_dir_list = chunk_dirs instanceof Collection ? chunk_dirs : [chunk_dirs]
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String chunk_dirs_arg = "--chunk_dirs '${chunk_dir_list.join(",")}'"
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String ndr_arg = params.ndr != null ? "--ndr ${params.ndr}" : ""
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"""
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supeRglue bambu collate \
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${chunk_dirs_arg} \
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--transcriptome_mode "${params.transcriptome_mode}" \
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${ndr_arg} \
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--out_dir "${meta.alias}"
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"""
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}
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