refactor: Switch to SRA direct download for samples
This commit is contained in:
parent
9f70b504e2
commit
3e411cc688
2 changed files with 12 additions and 7 deletions
|
@ -12,12 +12,12 @@
|
|||
"pattern": "^\\S+$",
|
||||
"errorMessage": "Sample name must be provided and cannot contain spaces"
|
||||
},
|
||||
"fastq_1": {
|
||||
"sra": {
|
||||
"type": "string",
|
||||
"pattern": "^\\S+\\.f(ast)?q\\.gz$",
|
||||
"errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
|
||||
"pattern": "^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM])|(syn))(\\d+)$",
|
||||
"errorMessage": "Please provide a valid SRA, ENA, DDBJ or GEO identifier"
|
||||
}
|
||||
},
|
||||
"required": ["sample", "fastq_1"]
|
||||
"required": ["sample", "sra"]
|
||||
}
|
||||
}
|
||||
|
|
11
main.nf
11
main.nf
|
@ -1,9 +1,10 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
include { validateParameters } from 'plugin/nf-validation'
|
||||
include { validateParameters; fromSamplesheet } from 'plugin/nf-validation'
|
||||
|
||||
include { CLIQUESNV } from './modules/cliquesnv'
|
||||
include { EFETCH } from './modules/efetch'
|
||||
include { FASTERQ_DUMP } from './modules/fasterq_dump'
|
||||
include { HAPLINK_HAPLOTYPES as HAPLINK_ML_HAPLOTYPES } from './modules/haplink/haplotypes'
|
||||
include { HAPLINK_HAPLOTYPES as HAPLINK_RAW_HAPLOTYPES } from './modules/haplink/haplotypes'
|
||||
include { HAPLINK_SEQUENCES } from './modules/haplink/sequences'
|
||||
|
@ -20,8 +21,12 @@ workflow {
|
|||
validateParameters()
|
||||
|
||||
Channel
|
||||
.fromPath("*.fastq.gz")
|
||||
.map { file -> tuple(file.simpleName, file) }
|
||||
.fromSamplesheet("input")
|
||||
.set { ch_sras }
|
||||
|
||||
FASTERQ_DUMP( ch_sras )
|
||||
FASTERQ_DUMP
|
||||
.out
|
||||
.set { ch_input }
|
||||
|
||||
EFETCH("${params.reference}")
|
||||
|
|
Loading…
Reference in a new issue