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Merge pull request #79 from fulaibaowang/ae_skip-instead-of-run-and-documentation
Ae skip instead of run and documentation
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‎README.md‎

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@@ -62,9 +62,6 @@ nextflow run nf-core/drop \
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--outdir <OUTDIR> \
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--genome hg19 \
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--gene_annotation <path/to/gene/annotation/yaml> \
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--ae_run true \
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--as_run true \
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--mae_run true \
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--ucsc_fasta <path/to/fasta>
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```
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‎assets/schema_input.json‎

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"pattern": "^\\S+$",
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"errorMessage": "DNA ID must be provided and cannot contain spaces",
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"meta": ["dna_id"],
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"description": "Unique identifier for the DNA sample. Must not contain spaces."
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"description": "Identifier for the DNA sample. Must not contain spaces."
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},
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"DNA_VCF_FILE": {
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"type": "string",
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"type": "string",
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"format": "file-path",
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"exists": true,
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"pattern": "^\\S+\\.tsv\\.gz$",
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"errorMessage": "The gene counts file has to exist, cannot contain spaces and must have extension '.tsv.gz'",
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"pattern": "^\\S+\\.tsv(\\.gz)?$",
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"errorMessage": "The gene counts file has to exist, cannot contain spaces and must have extension '.tsv' or '.tsv.gz'",
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"description": "Path to the gene counts file. Must exist and cannot contain spaces."
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},
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"GENE_ANNOTATION": {

‎conf/test.config‎

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ncbi_fai = "https://github.com/gagneurlab/drop_demo_data/raw/refs/heads/main/Data/chr21_ncbi.fa.fai"
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// Aberrant expression
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ae_run = true
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ae_groups = 'outrider,outrider_external'
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ae_genes_to_test = 'https://github.com/gagneurlab/drop_demo_data/raw/refs/heads/main/Data/genes_to_test.yaml'
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ae_fpkm_cutoff = 1
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ae_yield_size = 2000000
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// Aberrant splicing
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as_run = true
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as_groups = 'fraser,fraser_external'
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as_recount = true
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as_long_read = false
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as_delta_psi_cutoff = 0.05
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// MAE
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mae_run = true
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mae_groups = 'mae'
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mae_gatk_header_check = false
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mae_padj_cutoff = 0.5

‎docs/output.md‎

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<summary>Output files</summary>
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- `multiqc/`
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- `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
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- `multiqc_report.html`: a merged report for all subworkflows.
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- `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
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- `multiqc_plots/`: directory containing static images from the report in various formats.
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‎docs/usage.md‎

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## Introduction
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nf-core/drop allows controlling which subworkflows to run via parameters (`--ae_run` (Aberrant Expression), `--as_run` (Aberrant Splicing), `--mae_run` (Mono-Allelic Expression)). By default, each subworkflow is set to false. We describe different global and module-specific parameters in the [parameter documentation](https://nf-co.re/drop/parameters).
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nf-core/drop allows controlling which subworkflows to run. By default, all subworkflows will run. You can skip subsworkflow via parameters (`--ae_skip` (Aberrant Expression), `--as_skip` (Aberrant Splicing), `--mae_skip` (Mono-Allelic Expression)). We describe different global and module-specific parameters in the [parameter documentation](https://nf-co.re/drop/parameters).
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## Samplesheet input
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An [example samplesheet](../assets/samplesheet.tsv) has been provided with the pipeline.
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| Column | Description |
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| ------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| `RNA_ID` | Unique identifier for the RNA sample. |
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| `RNA_BAM_FILE` | Path to the RNA BAM file. |
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| `RNA_BAI_FILE` | Path to the RNA BAM index file. It will be automatically generated from the BAM files if not given. |
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| `DNA_ID` | Identifier for the DNA sample. It shall be the sample header in the VCF file. |
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| `DNA_VCF_FILE` | Path to the DNA VCF file. |
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| `DNA_TBI_FILE` | Path to the DNA VCF index file. It will be automatically generated from the VCF files if not given. |
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| `DROP_GROUP` | See [above](#drop_group). |
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| `PAIRED_END` | Indicates if the input is paired-end or single-end. Default: `true` (paired-end). Refer to the documentation of [HTSeq](https://htseq.readthedocs.io/en/latest/). |
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| `COUNT_MODE` | Count mode. Default: `IntersectionStrict`. Options: `union`, `IntersectionStrict`, `IntersectionNotEmpty`. Refer to the documentation of [HTSeq](https://htseq.readthedocs.io/en/latest/). |
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| `COUNT_OVERLAPS` | Indicates if overlaps should be counted. Default: `true`. Refer to the documentation of [HTSeq](https://htseq.readthedocs.io/en/latest/). |
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| `STRAND` | Samples within each `DROP_GROUP` should either be stranded (`yes`, `reverse`, or a combination of `yes` and `reverse`) or unstranded (only `no`), and this can vary between different `DROP_GROUP`s. |
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| `HPO_TERMS` | Comma-separated list of HPO terms associated with the sample. |
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| `GENE_COUNTS_FILE` | Path to the gene counts file (`.tsv` or `.tsv.gz`). See details also [above](#aberrant-expression). |
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| `GENE_ANNOTATION` | Gene annotation in YAML format, e.g. [assets/gene_annotation.yaml](../assets/gene_annotation.yaml). |
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| `GENOME` | See details [above](#mae). Default: `ucsc`. Options: `ncbi`, `ucsc`. |
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| `SPLICE_COUNTS_DIR` | Path to the splice counts directory. See details [above](#aberrant-splicing). |
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| `SEX` | Sex of the sample. Samples of `m`, `male`, `f`, `femal` are analysed for sex bias aberrant expression report. |
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## Running the pipeline
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The typical command for running the pipeline is as follows:
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```bash
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nextflow run nf-core/drop --input ./samplesheet.tsv --outdir ./results --genome hg19 --gene_annotation ./gene_annotation.yaml -profile docker --ae_run true
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nextflow run nf-core/drop --input ./samplesheet.tsv --outdir ./results --genome hg19 --gene_annotation ./gene_annotation.yaml -profile docker
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```
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This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.

‎main.nf‎

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ec_exclude_groups,
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// Aberrant expression parameters
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params.ae_run,
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params.ae_skip,
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ae_groups,
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ae_genes_to_test,
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// Aberrant splicing parameters
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params.as_run,
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params.as_skip,
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as_groups,
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params.as_fraser_version,
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as_genes_to_test,
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// Mono Allelic Expression parameters
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params.mae_run,
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params.mae_skip,
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mae_groups,
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mae_qc_groups
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)

‎nextflow.config‎

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ec_exclude_groups = null
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// Aberrant expression
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ae_run = false
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ae_skip = false
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ae_groups = ""
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ae_min_ids = 1
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ae_fpkm_cutoff = 1
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ae_genes_to_test = null
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// Aberrant splicing
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as_run = false
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as_skip = false
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as_groups = ""
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as_min_ids = 1
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as_recount = false
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as_genes_to_test = null
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// Mono-allelic expression
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mae_run = false
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mae_skip = false
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mae_groups = null
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mae_gatk_header_check = false
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mae_padj_cutoff = 0.05

‎nextflow_schema.json‎

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"fa_icon": "fas fa-file-export",
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"description": "Aberrant expression options.",
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"properties": {
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"ae_run": {
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"ae_skip": {
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"type": "boolean",
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"description": "Run aberrant expression analysis.",
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"description": "Skip aberrant expression analysis.",
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"fa_icon": "fas fa-file-export"
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},
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"ae_groups": {
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"fa_icon": "fas fa-file-export",
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"description": "Aberrant splicing options.",
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"properties": {
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"as_run": {
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"as_skip": {
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"type": "boolean",
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"description": "Run aberrant splicing analysis.",
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"description": "Skip aberrant splicing analysis.",
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"fa_icon": "fas fa-file-export"
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},
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"as_groups": {
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"fa_icon": "fas fa-file-export",
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"description": "Mono-allelic expression options.",
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"properties": {
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"mae_run": {
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"mae_skip": {
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"type": "boolean",
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"description": "Run mono-allelic expression analysis.",
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"description": "Skip mono-allelic expression analysis.",
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"fa_icon": "fas fa-file-export"
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},
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"mae_groups": {

‎ro-crate-metadata.json‎

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‎subworkflows/local/utils_nfcore_drop_pipeline/main.nf‎

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def validateInputParameters() {
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genomeExistsError()
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if (params.ae_run && params.gene_annotation == null) {
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if ((!params.ae_skip) && params.gene_annotation == null) {
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error("Please provide a gene annotation file using the --gene_annotation parameter when running the aberrant expression analysis.")
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}
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}

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