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Merge pull request #1648 from nf-core/refactor-sra-fastq
refactor: rename and update subworkflow
This commit is contained in:
Harshil Patel
GitHub
commit
be0f022053
9 changed files with 106 additions and 86 deletions
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@ -1,34 +0,0 @@
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//
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// Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
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//
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params.prefetch_options = [:]
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params.fasterqdump_options = [:]
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include { SRATOOLS_PREFETCH } from '../../../modules/sratools/prefetch/main' addParams( options: params.prefetch_options )
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include { SRATOOLS_FASTERQDUMP } from '../../../modules/sratools/fasterqdump/main' addParams( options: params.fasterqdump_options )
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workflow SRA_FASTQ {
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take:
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sra_ids // channel: [ val(meta), val(id) ]
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main:
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ch_versions = Channel.empty()
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//
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// Prefetch sequencing reads in SRA format.
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//
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SRATOOLS_PREFETCH ( sra_ids )
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ch_versions = ch_versions.mix( SRATOOLS_PREFETCH.out.versions.first() )
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//
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// Convert the SRA format into one or more compressed FASTQ files.
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//
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SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra )
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ch_versions = ch_versions.mix( SRATOOLS_FASTERQDUMP.out.versions.first() )
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emit:
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reads = SRATOOLS_FASTERQDUMP.out.reads // channel: [ val(meta), [ reads ] ]
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versions = ch_versions // channel: [ versions.yml ]
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}
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38
subworkflows/nf-core/srafastq/main.nf
Normal file
38
subworkflows/nf-core/srafastq/main.nf
Normal file
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@ -0,0 +1,38 @@
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include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../modules/custom/sratoolsncbisettings/main'
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include { SRATOOLS_PREFETCH } from '../../../modules/sratools/prefetch/main'
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include { SRATOOLS_FASTERQDUMP } from '../../../modules/sratools/fasterqdump/main'
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/**
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* Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
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*/
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workflow SRAFASTQ {
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take:
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sra_ids // channel: [ val(meta), val(id) ]
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main:
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ch_versions = Channel.empty()
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//
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// Detect existing NCBI user settings or create new ones.
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//
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CUSTOM_SRATOOLSNCBISETTINGS()
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def settings = CUSTOM_SRATOOLSNCBISETTINGS.out.ncbi_settings
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ch_versions = ch_versions.mix( CUSTOM_SRATOOLSNCBISETTINGS.out.versions )
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//
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// Prefetch sequencing reads in SRA format.
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//
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SRATOOLS_PREFETCH ( sra_ids, settings )
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ch_versions = ch_versions.mix( SRATOOLS_PREFETCH.out.versions.first() )
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//
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// Convert the SRA format into one or more compressed FASTQ files.
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//
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SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra, settings )
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ch_versions = ch_versions.mix( SRATOOLS_FASTERQDUMP.out.versions.first() )
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emit:
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reads = SRATOOLS_FASTERQDUMP.out.reads // channel: [ val(meta), [ reads ] ]
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versions = ch_versions // channel: [ versions.yml ]
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}
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@ -1,11 +1,14 @@
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name: sra_fastq
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description: Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
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keywords:
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- SRA
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- NCBI
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- sequencing
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- FASTQ
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- prefetch
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- dump
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- fasterq-dump
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modules:
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- custom/sratoolsncbisettings
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- sratools/prefetch
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- sratools/fasterqdump
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input:
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@ -17,7 +20,7 @@ input:
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- id:
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type: string
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description: >
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SRA identifier.
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SRA run identifier.
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# TODO Update when we decide on a standard for subworkflow docs
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output:
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- meta:
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@ -1,23 +0,0 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SRA_FASTQ } from '../../../../subworkflows/nf-core/sra_fastq/main.nf' addParams( [:] )
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workflow test_sra_fastq_single_end {
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input = [
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[ id:'test_single_end', single_end:true ], // meta map
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'SRR13255544'
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]
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SRA_FASTQ ( input )
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}
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workflow test_sra_fastq_paired_end {
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input = [
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[ id:'test_paired_end', single_end:false ], // meta map
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'SRR11140744'
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]
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SRA_FASTQ ( input )
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}
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@ -1,27 +0,0 @@
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- name: sra fastq single-end
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command: nextflow run ./tests/subworkflows/nf-core/sra_fastq -entry test_sra_fastq_single_end -c tests/config/nextflow.config
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tags:
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- subworkflows
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# - subworkflows/sra_fastq
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# Modules
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# - sratools
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# - sratools/prefetch
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# - sratools/fasterqdump
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files:
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- path: output/sratools/SRR13255544.fastq.gz
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md5sum: 1054c7b71884acdb5eed8a378f18be82
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- name: sra fastq paired-end
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command: nextflow run ./tests/subworkflows/nf-core/sra_fastq -entry test_sra_fastq_paired_end -c tests/config/nextflow.config
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tags:
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- subworkflows
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# - subworkflows/sra_fastq
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# Modules
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# - sratools
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# - sratools/prefetch
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# - sratools/fasterqdump
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files:
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- path: output/sratools/SRR11140744_1.fastq.gz
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md5sum: 193809c784a4ea132ab2a253fa4f55b6
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- path: output/sratools/SRR11140744_2.fastq.gz
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md5sum: 3e3b3af3413f50a1685fd7b3f1456d4e
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29
tests/subworkflows/nf-core/srafastq/main.nf
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29
tests/subworkflows/nf-core/srafastq/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SRAFASTQ } from '../../../../subworkflows/nf-core/srafastq/main.nf'
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workflow test_srafastq_single_end {
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input = Channel.of(
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[
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[ id:'test_single_end1', single_end:true ], // meta map
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'DRR000774'
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],
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[
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[ id:'test_single_end2', single_end:true ], // meta map
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'DRR000775'
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]
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)
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SRAFASTQ ( input )
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}
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workflow test_srafastq_paired_end {
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input = [
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[ id:'test_paired_end', single_end:false ], // meta map
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'SRR11140744'
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]
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SRAFASTQ ( input )
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}
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5
tests/subworkflows/nf-core/srafastq/nextflow.config
Normal file
5
tests/subworkflows/nf-core/srafastq/nextflow.config
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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}
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29
tests/subworkflows/nf-core/srafastq/test.yml
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29
tests/subworkflows/nf-core/srafastq/test.yml
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- name: srafastq single-end
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command: nextflow run ./tests/subworkflows/nf-core/srafastq -entry test_srafastq_single_end -c tests/config/nextflow.config -c tests/subworkflows/nf-core/srafastq/nextflow.config
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tags:
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- subworkflows
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# - subworkflows/srafastq
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# Modules
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# - sratools
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# - sratools/prefetch
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# - sratools/fasterqdump
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files:
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- path: output/sratools/DRR000774.fastq.gz
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md5sum: 19029a1132115b55277a0d79ee089b49
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- path: output/sratools/DRR000775.fastq.gz
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md5sum: 59ff24c86ecb260752668c059c2a1eaf
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- name: srafastq paired-end
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command: nextflow run ./tests/subworkflows/nf-core/srafastq -entry test_srafastq_paired_end -c tests/config/nextflow.config -c tests/subworkflows/nf-core/srafastq/nextflow.config
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tags:
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- subworkflows
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# - subworkflows/srafastq
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# Modules
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# - sratools
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# - sratools/prefetch
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# - sratools/fasterqdump
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files:
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- path: output/sratools/SRR11140744_1.fastq.gz
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md5sum: 193809c784a4ea132ab2a253fa4f55b6
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- path: output/sratools/SRR11140744_2.fastq.gz
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md5sum: 3e3b3af3413f50a1685fd7b3f1456d4e
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