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Merge pull request #926 from nf-core/dsl2-indexing
DSL2: single-genome indexing
2 parents 75c95d4 + 996d101 commit 098b0b7

26 files changed

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‎bin/check_samplesheet.py‎

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‎conf/base.config‎

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// See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
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withLabel:process_single {
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cpus = { check_max( 1 , 'cpus' ) }
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memory = { check_max( 6.GB * task.attempt, 'memory' ) }
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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time = { check_max( 4.h * task.attempt, 'time' ) }
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}
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withLabel:process_low {
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cpus = { check_max( 2 * task.attempt, 'cpus' ) }
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memory = { check_max( 12.GB * task.attempt, 'memory' ) }
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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time = { check_max( 4.h * task.attempt, 'time' ) }
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}
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withLabel:process_medium {
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cpus = { check_max( 6 * task.attempt, 'cpus' ) }
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memory = { check_max( 36.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 8.h * task.attempt, 'time' ) }
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}
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withLabel:process_high {
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cpus = { check_max( 12 * task.attempt, 'cpus' ) }
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memory = { check_max( 72.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 12.GB * task.attempt, 'memory' ) }
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time = { check_max( 16.h * task.attempt, 'time' ) }
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}
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withLabel:process_long {

‎conf/modules.config‎

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]
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}
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withName: SAMTOOLS_FAIDX {
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publishDir = [
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path: { "${params.outdir}/reference/${meta.id}/" },
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mode: params.publish_dir_mode,
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pattern: '*.fai',
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enabled: params.save_reference
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]
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}
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withName: PICARD_CREATESEQUENCEDICTIONARY {
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publishDir = [
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path: { "${params.outdir}/reference/${meta.id}/" },
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mode: params.publish_dir_mode,
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pattern: '*.dict',
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enabled: params.save_reference
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]
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}
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withName: BOWTIE2_BUILD {
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publishDir = [
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path: { "${params.outdir}/reference/${meta.id}/" },
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mode: params.publish_dir_mode,
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pattern: 'bowtie2/',
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enabled: params.save_reference
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]
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}
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withName: BWA_INDEX {
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publishDir = [
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path: { "${params.outdir}/reference/${meta.id}/" },
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mode: params.publish_dir_mode,
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pattern: 'bwa/',
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enabled: params.save_reference
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]
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}
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}

‎conf/test.config‎

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// Input data
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// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
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// TODO nf-core: Give any required params for the test so that command line flags are not needed
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
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input = 'https://github.com/nf-core/test-datasets/raw/eager/testdata/Mammoth/samplesheet.tsv'
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// Genome references
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genome = 'R64-1-1'
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fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
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}

‎docs/usage.md‎

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An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
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## Reference input
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nf-core/eager supports two methods of supplying a reference FASTA via `--fasta`.
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The first is a direct path to a single FASTA file with optional prebuilt indicies via `--fasta_fai`, `--fasta_dict`, etc., and the second is via a reference sheet.
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Providing a reference sheet to `--fasta` allows users to simultaenously map their input reads (separately) to _multiple_ reference genomes. The reference sheet must be in the format of, and the file extension to be either `csv` or `tsv`.
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This reference file is also used to specfiy paths to optional user-built reference indicies (namely, `.fai`, `.dict`, and a directory pointing to a directory containing the indicies for the given mapper).
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Note that passing the reference sheet to `--fasta` to the pipeline will _override_ the corredonding user-build indicies parameters (`--fasta_fai`, `--fasta_dict`).
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If using a reference sheet, this must be in format (if in `csv`), and must have a header consisting of:
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```txt
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reference_name,fasta,fai,dict,mapper_index,circular_target,mitochondrion
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```
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Only `reference_name`, and `fasta` are required.
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Files for `fai`, `dict`, `mapper_index` will be generated by the pipeline for you if not specified.
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`circular_target` and `mitochondiron` are only needed if circular mapper and MtNucRatio modules are selected.
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A filled-in example is like so, where a user-supplied `.dict` file nor circular generator not MtNucRatio is required:
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```txt
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reference_name,fasta,fai,dict,mapper_index,circular_target,mitochondrion
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tannerella_forsythia,~/data/reference/tannerella_forstythia.fasta,~/data/reference/tannerella_forstythia.fasta.fai,,~/data/reference/tannerella_forstythia.dict,~/data/reference/,,
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```
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## Running the pipeline
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The typical command for running the pipeline is as follows:

‎modules.json‎

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"https://github.com/nf-core/modules.git": {
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"modules": {
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"nf-core": {
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"bowtie2/build": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"patch": "modules/nf-core/bowtie2/build/bowtie2-build.diff"
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},
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"bwa/index": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"patch": "modules/nf-core/bwa/index/bwa-index.diff"
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},
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"custom/dumpsoftwareversions": {
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"branch": "master",
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"git_sha": "8022c68e7403eecbd8ba9c49496f69f8c49d50f0"
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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},
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"gunzip": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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},
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"picard/createsequencedictionary": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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},
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"samtools/faidx": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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}
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}
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}

‎modules/local/samplesheet_check.nf‎

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process SAMPLESHEET_CHECK {
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tag "$samplesheet"
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label 'process_single'
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conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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path '*.csv' , emit: csv
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script: // This script is bundled with the pipeline, in nf-core/eager/bin/
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"""
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check_samplesheet.py \\

‎modules/nf-core/bowtie2/build/bowtie2-build.diff‎

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‎modules/nf-core/bowtie2/build/main.nf‎

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‎modules/nf-core/bowtie2/build/meta.yml‎

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