163 lines
4.3 KiB
Plaintext
163 lines
4.3 KiB
Plaintext
params {
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help = false
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version = false
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fastq = null
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bam = null
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sample = null
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sample_sheet = null
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out_dir = "output"
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igv = false
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ref_genome = null
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ref_annotation = null
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transcriptome_mode = "discover"
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direct_rna = false
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de_analysis = false
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condition_column = "condition"
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covariates = null
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reference_level = null
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analyse_unclassified = false
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analyse_fail = false
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mod_codes = null
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force_alignment = false
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ndr = null
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sqanti_skip_orf = true
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aws_image_prefix = null
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aws_queue = null
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disable_ping = false
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monochrome_logs = false
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validate_params = true
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show_hidden_params = false
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schema_ignore_params = 'show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wf,store_dir'
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wf {
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keep_unaligned = true
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return_fastq = true
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per_read_stats = false
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allow_multiple_basecall_models = false
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example_cmd = [
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"--bam 'wf-transcriptomes-demo/samples'",
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"--de_analysis",
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"--direct_rna",
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"--ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf'",
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"--ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa'",
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"--sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv'",
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]
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common_sha = "sha21d552f9910c575766e5d465fcb7b52fefda4b79"
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container_sha = "sha02e44f706d88fa29d8344b78479f187db7eec4ec"
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modkit_sha = "sha077c7ca8d7bf1cc9e3a4f3400d6e882c495156e4"
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sqanti_sha = "sha5bd775836492699e2537ebf846098eb117191d87"
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agent = null
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epi2me_instance = null
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epi2me_user = null
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}
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}
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manifest {
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name = 'epi2me-labs/wf-transcriptomes'
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author = 'Oxford Nanopore Technologies'
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homePage = 'https://github.com/epi2me-labs/wf-transcriptomes'
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description = 'Long-read transcript discovery, quantification, differential expression, QC and mod counting.'
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mainScript = 'main.nf'
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nextflowVersion = '>=23.04.2'
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version = 'v2.0.0'
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}
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process {
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withLabel:wf_common {
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container = "ontresearch/wf-common:${params.wf.common_sha}"
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}
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withLabel:wf_transcriptomes {
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container = "ontresearch/wf-transcriptomes-core:${params.wf.container_sha}"
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}
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withLabel:modkit {
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container = "ontresearch/modkit:${params.wf.modkit_sha}"
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}
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withLabel:wf_transcriptomes_sqanti {
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container = "ontresearch/wf-transcriptomes-sqanti:${params.wf.sqanti_sha}"
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}
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shell = ['/bin/bash', '-euo', 'pipefail']
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}
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profiles {
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standard {
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docker {
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enabled = true
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runOptions = "--user \$(id -u):\$(id -g) --group-add 100"
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}
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}
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singularity {
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singularity {
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enabled = true
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autoMounts = true
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}
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}
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conda {
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conda.enabled = true
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}
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awsbatch {
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process {
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executor = 'awsbatch'
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queue = "${params.aws_queue}"
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withLabel:wf_common {
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container = "${params.aws_image_prefix}-wf-common:${params.wf.common_sha}"
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memory = '8G'
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}
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withLabel:wf_transcriptomes {
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container = "${params.aws_image_prefix}-wf-transcriptomes-core:${params.wf.container_sha}"
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}
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withLabel:modkit {
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container = "${params.aws_image_prefix}-modkit:${params.wf.modkit_sha}"
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}
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withLabel:wf_transcriptomes_sqanti {
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container = "${params.aws_image_prefix}-wf-transcriptomes-sqanti:${params.wf.sqanti_sha}"
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}
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shell = ['/bin/bash', '-euo', 'pipefail']
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}
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}
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local {
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process.executor = 'local'
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}
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}
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epi2melabs {
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tags = "wf-transcriptomes,transcriptomics,rna"
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icon = "faDna"
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}
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timeline {
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enabled = true
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overwrite = true
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file = "${params.out_dir}/execution/timeline.html"
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}
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report {
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enabled = true
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overwrite = true
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file = "${params.out_dir}/execution/report.html"
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}
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trace {
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enabled = true
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overwrite = true
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file = "${params.out_dir}/execution/trace.txt"
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}
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env {
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PYTHONNOUSERSITE = 1
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JAVA_TOOL_OPTIONS = "-Xlog:disable -Xlog:all=warning:stderr"
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R_BIOC_VERSION = "3.21"
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BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS = "FALSE"
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}
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