nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    sanjaysgk/ipg Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/

// Global default params, used in configs
params {

    // Input options
    input                      = null

    // References
    genome                     = null
    igenomes_base              = 's3://ngi-igenomes/igenomes/'
    igenomes_ignore            = false

    // Pipeline step control (sarek-style)
    // 'db_construct' = full pipeline from FASTQ (default)
    // 'ms_search'    = MS search + rescoring + integration (requires --ms_input)
    // 'post_ms'      = post-MS search analysis only (requires --post_ms_input)
    // 'immunoinformatics' = HLA binding, clustering, quantification (future)
    step                       = 'db_construct'

    // Post-MS analysis parameters (only used when step == 'post_ms')
    post_ms_input              = null    // samplesheet CSV for post-MS step
    uniprot_fasta              = null    // UniProt FASTA for origins
    transcriptome_fasta        = null    // transcriptome.fa from DB construction
    prefix_tracking            = null    // .tracking file from gffcompare

    // MS search parameters (only used when step == 'ms_search')
    ms_input                   = null    // samplesheet CSV for MS data
    search_fasta               = null    // cryptic FASTA database for search (from db_construct)
    // Canonical proteome. Provide a local FASTA via --canonical_fasta (wins), else
    // DOWNLOAD_UNIPROT_PROTEOME fetches canonical_proteome_url (default = UniProt human
    // reference proteome UP000005640) and caches it. Gzipped or plain both work (zcat -f).
    // Set db_search_mode = 'cryptic_only' to disable canonical entirely.
    canonical_fasta            = null    // local canonical proteome FASTA; takes precedence over the download
    canonical_proteome_url     = 'https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000005640/UP000005640_9606.fasta.gz'
    db_search_mode             = 'appended'  // 'appended' (canonical+cryptic in one DB, class-separated FDR), 'separate' (independent searches, reconciled downstream), or 'cryptic_only' (no canonical)
    ms_engines                 = 'msfragger'  // comma-separated: msfragger,comet,sage,peaks
    msfragger_jar              = null    // path to MSFragger JAR; leave null to use bioconda wrapper
    msfragger_license          = null    // MSFragger academic license key (required with bioconda wrapper; pass to --msfragger_license)
    msfragger_mem              = 8       // GB for MSFragger JVM heap
    msfragger_split            = 1       // >1: MSFragger split-database search into N chunks (for large no-enzyme cryptic DBs that OOM the fragment index); needs the real MSFragger (--msfragger_jar or --msfragger_license)
    instrument                 = null    // orbitrap or timsTOF (auto-detect if null)
    mod_type                   = 'mod'   // mod, nomod, TMT10, TMT16, mhcii, lowres
    peptide_length             = '9'     // immunopeptide length or range like '8-11'
    peaks_psm_csv              = null    // PEAKS Studio db.psms.csv export; required when 'peaks' in --ms_engines
    peaks_min_match_fraction   = 0.98    // min fraction of PEAKS rows that must resolve to scan numbers
    skip_ms2rescore            = false   // bypass MS2Rescore step
    ms2rescore_engine          = 'mokapot'  // MS2Rescore rescoring engine: mokapot or percolator
    ms2rescore_write_report    = false   // write the MS2Rescore HTML QC report (DeepLC scatter can fail on sparse predictions)
    mokapot_train_fdr          = 0.1     // mokapot model-training FDR (internal calibration only, NOT final FDR); raise (e.g. 0.5) for small/low-ID databases
    mokapot_test_fdr           = 0.1     // mokapot score-calibration FDR (internal only); raise for small/low-ID databases where mokapot cannot calibrate at 0.01
    integrate_fdr              = 0.01    // FINAL FDR threshold applied in INTEGRATE_ENGINES (per-class); this is the reported FDR
    canonical_protein_prefixes = 'sp|,tr|'  // accession prefixes marking canonical proteins (sugar for canonical_id_regex); peptides mapping only to non-canonical proteins are 'cryptic'/'other'
    canonical_id_regex         = null       // regex marking canonical accessions; overrides canonical_protein_prefixes when set (null = compile the prefixes)
    cryptic_id_regex           = null       // regex marking cryptic ORF accessions; null = default ORF suffix '_f<frame>p<orf>_<copy>' that db_construct appends
    gene_regex                 = null       // regex (capture group 1) extracting gene from a FASTA header; null = 'GN=(\\S+)'
    species_regex              = null       // regex (capture group 1) extracting species from a FASTA header; null = 'OS=...'
    filter_other               = false      // drop 'other' proteins (contaminants/iRT matching neither pattern) pre-FDR; default false = annotate only
    skip_integrate_engines     = false   // bypass INTEGRATE_ENGINES (implied when skip_ms2rescore is true)
    run_protein_group_fdr      = false    // protein/ORF-group FDR (PickedGroupFDR) on the mokapot output
    protein_group_fdr          = 0.01     // protein-group FDR threshold for PickedGroupFDR (--protein_group_fdr_threshold)
    protein_group_fdr_class    = 'global' // PickedGroupFDR scope: 'global' (overall list) | 'cryptic' (class-specific)
    run_pepquery               = false   // PepQuery2 spectrum-level validation of the cryptic peptide subset
    cryptic_min_spec_pearson   = null    // min MS2PIP spectral correlation for a cryptic peptide to pass (null = annotate only)
    cryptic_max_rt_diff        = null    // max DeepLC RT error for a cryptic peptide to pass (null = annotate only)
    run_annotate_origin        = false   // backtrack cryptic peptides to RNAseq source ORF/transcript/gene
    origin_orf_fasta           = null    // 3-frame ORF FASTA (TRIPLE_TRANSLATE output) for origin annotation
    origin_gtf                 = null    // gffcompare .combined.gtf (gene/locus/class/tss/coords) for origin annotation
    origin_tmap                = null    // gffcompare .tmap (FPKM/TPM/len) for origin annotation
    annotate_with_ensembl      = true    // rich region/frame/biotype calls via the origins(full) Ensembl pass (default); false = local annotate_origin only
    origin_transcriptome       = null    // reference transcriptome FASTA (origins -n); else DB_CONSTRUCT.transcriptome_fasta
    origin_tracking            = null    // gffcompare .tracking (origins -r); else TRANSCRIPT_ASSEMBLY.tracking
    run_cryptic_report         = false   // generate the cryptic-discovery HTML report + summary

    // De novo lane (Phase 1a — InstaNovo + classify; runs in parallel to the DB-search engines)
    run_denovo                 = false        // enable the de novo sequencing discovery lane
    denovo_engines             = 'instanovo'  // comma-separated de novo engines (Phase 1a: instanovo)
    denovo_min_logprob         = -0.5         // drop de novo predictions below this raw log-probability
    denovo_min_length          = 7            // drop de novo peptides shorter than this

    // Immunoinformatics parameters (used after ms_search; modules are individually gated)
    run_netmhcpan              = false   // run MHC class I binding prediction
    run_netmhciipan            = false   // run MHC class II binding prediction
    run_gibbscluster           = false   // run GibbsCluster motif discovery
    run_flashlfq               = false   // run FlashLFQ quantification
    run_blastp_host            = false   // run blastp-short against host/contaminant DB
    hla                        = null    // comma-separated HLA alleles (e.g. 'HLA-A01:01,HLA-B07:02')
    netmhcpan_path             = null    // path to netMHCpan-4.1 binary (academic license)
    netmhciipan_path           = null    // path to netMHCIIpan-4.3 binary (academic license)
    gibbscluster_path          = null    // path to GibbsCluster-2.0e_SA.pl (academic license)
    gibbs_clusters             = 'auto'  // 'auto' → [2-5]; or explicit integer/range string
    blast_db                   = null    // path prefix to pre-built blastp DB (e.g. /path/human)
    host_species               = 'HUMAN' // upper-case host species tag for species-column check

    // Cryptic peptide pipeline reference bundle
    // Provide explicit paths OR set --genome GRCh38 to auto-resolve from config.
    // Derivable indices (fai, dict, star_index) are built by PREPARE_GENOME if null.
    fasta                      = null
    fasta_fai                  = null
    fasta_dict                 = null
    star_index                 = null
    gtf                        = null
    rseqc_bed                  = null
    dbsnp                      = null
    dbsnp_tbi                  = null
    known_indels               = null
    known_indels_tbi           = null
    mills                      = null
    mills_tbi                  = null
    germline_resource          = null
    germline_resource_tbi      = null

    // Variant annotation (vcf_annotate_all) — published leaf branch, optional
    tools                      = null          // CSV: 'vep,snpeff,alphamissense'; null = skip annotation
    vep_cache                  = null          // path or null (auto-download)
    vep_genome                 = 'GRCh38'
    vep_species                = 'homo_sapiens'
    vep_cache_version          = 113
    snpeff_cache               = null          // path or null (auto-download)
    snpeff_db                  = 'GRCh38.105'
    alphamissense_tsv          = null          // path or null (opt-in VEP plugin)

    // Save built/downloaded reference files to outdir/reference so they can
    // be reused in future runs without re-downloading or re-building.
    save_reference             = false

    // Test-profile bundle location (only used by -profile test);
    // see scripts/build_test_bundle.sh
    test_bundle                = null

    // Whether to include alt-reference variant-derived peptides in the
    // final cryptic peptide DB (db_construct subworkflow). When false
    // (default) the DB contains only reference-assembly peptides — the
    // legacy Scull et al. 2021 / D122_Lung behaviour. When true, also
    // build the unmasked + indel branches from the Mutect2 tumour-only
    // calls and squish all three together. This is a pipeline-level flag
    // (one run = one intent). NOTE: variant calling itself is always
    // tumour-only Mutect2 — this flag does NOT switch to matched
    // tumour-normal mode (which is not supported by this pipeline; the
    // 'normal vs tumour' terminology in standard cancer pipelines refers
    // to matched calling, not what this flag controls). See docs/usage
    // for the full caveat.
    include_variant_peptides   = true
    strandedness_threshold     = 0.8     // strandedness='auto': min infer_experiment fraction to call forward/reverse; below this => unstranded

    // MultiQC options
    multiqc_config             = null
    multiqc_title              = null
    multiqc_logo               = null
    max_multiqc_email_size     = '25.MB'
    multiqc_methods_description = null

    // Boilerplate options
    outdir                       = null
    publish_dir_mode             = 'copy'
    email                        = null
    email_on_fail                = null
    plaintext_email              = false
    monochrome_logs              = false
    hook_url                     = null
    help                         = false
    help_full                    = false
    show_hidden                  = false
    version                      = false
    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options
    config_profile_name        = null
    config_profile_description = null

    custom_config_version      = 'master'
    custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
    config_profile_contact     = null
    config_profile_url         = null

    // Schema validation default options
    validate_params            = true
}

// Load base.config by default for all pipelines
includeConfig 'conf/base.config'

executor {
    // Per-task job names as ipg.<module>.<sample> (e.g. ipg.GATK4_MUTECT2.MB231_IFNpos)
    // instead of the long default nf-NFCORE_IPG_IPG_<subworkflow>_<module>_(tag).
    // Inert for the local executor; only takes effect on cluster executors (e.g. SLURM).
    jobName = { "ipg.${task.process.tokenize(':').last()}.${task.tag ?: task.index}" }
}

profiles {
    debug {
        dumpHashes              = true
        process.beforeScript    = 'echo $HOSTNAME'
        cleanup                 = false
        nextflow.enable.configProcessNamesValidation = true
    }
    conda {
        conda.enabled           = true
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        conda.channels          = ['conda-forge', 'bioconda']
        apptainer.enabled       = false
    }
    mamba {
        conda.enabled           = true
        conda.useMamba          = true
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    docker {
        docker.enabled          = true
        conda.enabled           = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
        docker.runOptions       = '-u $(id -u):$(id -g)'
    }
    arm {
        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
    }
    singularity {
        singularity.enabled     = true
        singularity.autoMounts  = true
        conda.enabled           = false
        docker.enabled          = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    podman {
        podman.enabled          = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    shifter {
        shifter.enabled         = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    charliecloud {
        charliecloud.enabled    = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        apptainer.enabled       = false
    }
    apptainer {
        apptainer.enabled       = true
        apptainer.autoMounts    = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
    }
    pixi {
        // Run every process directly from the local pixi env, no containers.
        // Requires `pixi run nextflow run ...` so STAR/GATK/samtools/etc are
        // resolved from the pixi-managed PATH. The pixi.toml at repo root
        // declares all required tools.
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false

        // MS2RESCORE lives in an isolated pixi feature env (pyopenms/eigen
        // conflicts with the main env). Switch into it for those processes.
        process {
            withName: 'MS2RESCORE.*' {
                beforeScript = "eval \"\$(pixi shell-hook -e ms2rescore --manifest-path ${projectDir}/pixi.toml)\""
            }
            // InstaNovo + torch live in the isolated `denovo` pixi env. DENOVO_CLASSIFY
            // is pure-stdlib python, so it stays in the default env.
            withName: 'INSTANOVO_PREDICT' {
                beforeScript = "eval \"\$(pixi shell-hook -e denovo --manifest-path ${projectDir}/pixi.toml)\""
            }
            // PickedGroupFDR (PyPI-only) lives in the isolated `picked` pixi env.
            withName: 'PICKED_GROUP_FDR' {
                beforeScript = "eval \"\$(pixi shell-hook -e picked --manifest-path ${projectDir}/pixi.toml)\""
            }
        }
    }
    wave {
        apptainer.ociAutoPull   = true
        singularity.ociAutoPull = true
        wave.enabled            = true
        wave.freeze             = true
        wave.strategy           = 'conda,container'
    }
    gitpod {
        executor.name           = 'local'
        executor.cpus           = 4
        executor.memory         = 8.GB
        process {
            resourceLimits = [
                memory: 8.GB,
                cpus  : 4,
                time  : 1.h
            ]
        }
    }
    test                   { includeConfig 'conf/test.config'                   }
    test_ms_search         { includeConfig 'conf/test_ms_search.config'         }
    test_ms_search_hepg2   { includeConfig 'conf/test_ms_search_hepg2.config'   }
    test_e2e_hepg2_chr22   { includeConfig 'conf/test_e2e_hepg2_chr22.config'  }
    test_full              { includeConfig 'conf/test_full.config'              }
    test_spike             { includeConfig 'conf/test_spike.config'             }
    test_spike_multirep    { includeConfig 'conf/test_spike_multirep.config'    }
    test_dbconstruct_rnavar { includeConfig 'conf/test_dbconstruct_rnavar.config' }
    monash    { includeConfig 'conf/monash.config'    }
}

// Load nf-core custom profiles from different Institutions
includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"

// sanjaysgk/ipg is not an official nf-core pipeline, so no pipeline-specific
// entry exists under nf-core/configs. Monash-specific settings live in
// conf/monash.config (added in Day 2).

// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry    = 'quay.io'
docker.registry       = 'quay.io'
podman.registry       = 'quay.io'
singularity.registry  = 'quay.io'
charliecloud.registry = 'quay.io'

// Load igenomes.config if required
includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'

// IPG-specific genome entries (GATK resources, GENCODE v44). Loaded after
// igenomes.config so entries here augment/override the iGenomes defaults.
includeConfig 'conf/genomes.config'

// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.

env {
    PYTHONNOUSERSITE = 1
    R_PROFILE_USER   = "/.Rprofile"
    R_ENVIRON_USER   = "/.Renviron"
    JULIA_DEPOT_PATH = "/usr/local/share/julia"
}

// Set bash options
process.shell = [
    "bash",
    "-C",         // No clobber - prevent output redirection from overwriting files.
    "-e",         // Exit if a tool returns a non-zero status/exit code
    "-u",         // Treat unset variables and parameters as an error
    "-o",         // Returns the status of the last command to exit..
    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
]

// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false

// Module-scoped binaries: a module's resources/usr/bin is added to PATH when that
// module runs. Used to co-locate single-module helper scripts with their module
// (e.g. split_fasta, merge_split_search). Scripts shared by 2+ modules stay in bin/.
nextflow.enable.moduleBinaries = true

timeline {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
}
report {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
}
trace {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
}
dag {
    enabled = true
    file    = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
}

manifest {
    name            = 'sanjaysgk/ipg'
    author          = """Sanjay SG Krishna, Kate Scull, Chen Li""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
    contributors    = [
        [
            name: 'Sanjay SG Krishna',
            affiliation: 'Monash University',
            email: '',
            github: 'https://github.com/sanjaysgk',
            contribution: ['author', 'maintainer'],
            orcid: ''
        ],
        [
            name: 'Kate Scull',
            affiliation: 'Monash University',
            email: '',
            github: '',
            contribution: ['author'],
            orcid: ''
        ],
        [
            name: 'Chen Li',
            affiliation: 'Monash University',
            email: '',
            github: '',
            contribution: ['author'],
            orcid: ''
        ],
    ]
    homePage        = 'https://github.com/sanjaysgk/ipg'
    description     = """Immunopeptidogenomics — cryptic peptide database construction from RNA-seq."""
    mainScript      = 'main.nf'
    defaultBranch   = 'main'
    // Minimum 24.10.0: the nf-core/samtools/sort module pinned in
    // modules.json uses bare-assigned `prefix` and `extension` Groovy
    // variables (no `def`) so the names leak into the process scope and
    // are visible in the `output:` block. The 24.04.x parser rejects
    // that pattern with a "Variable already defined" error during module
    // compilation. 24.10+ accepts it, 25.x is what we test against in
    // CI and pin in pixi.lock.
    nextflowVersion = '!>=24.10.0'
    version         = '1.0.0'
    doi             = '10.1016/j.mcpro.2021.100143'
}

// Nextflow plugins
plugins {
    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}

validation {
    defaultIgnoreParams = ["genomes"]
    monochromeLogs = params.monochrome_logs
    help {
        enabled = true
        command = "nextflow run sanjaysgk/ipg -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
        fullParameter = "help_full"
        showHiddenParameter = "show_hidden"
    }
}

// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'