mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-21 21:16:05 +00:00
Revert PEP validation back to python samplesheet check
This commit is contained in:
parent
13c4f44ca6
commit
4b68e95770
18 changed files with 275 additions and 328 deletions
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@ -77,8 +77,6 @@ On release, automated continuous integration tests run the pipeline on a full-si
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nextflow run nf-core/taxprofiler --input samplesheet.csv --databases database.csv --outdir <OUTDIR> --run_<TOOL1> --run_<TOOL1> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
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```
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Note pipeline supports both CSV and PEP input sample sheets. Find out more [here](http://pep.databio.org/en/2.1.0/specification/).
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## Documentation
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The nf-core/taxprofiler pipeline comes with documentation about the pipeline [usage](https://nf-co.re/taxprofiler/usage), [parameters](https://nf-co.re/taxprofiler/parameters) and [output](https://nf-co.re/taxprofiler/output).
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@ -1,55 +0,0 @@
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description: A schema for validation of samplesheet.csv for taxprofiler pipeline.
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imports:
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- https://schema.databio.org/pep/2.1.0.yaml
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properties:
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samples:
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type: array
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items:
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type: object
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properties:
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sample:
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type: string
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description: "Sample identifier."
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pattern: "^\\S*$"
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run_accession:
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type: string
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description: "Run accession number."
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instrument_platform:
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type: string
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description: "Name of the platform that sequenced the samples."
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enum:
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[
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"ABI_SOLID",
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"BGISEQ",
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"CAPILLARY",
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"COMPLETE_GENOMICS",
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"DNBSEQ",
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"HELICOS",
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"ILLUMINA",
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"ION_TORRENT",
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"LS454",
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"OXFORD_NANOPORE",
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"PACBIO_SMRT",
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]
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fastq1:
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type: ["string", "null"]
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description: "Optional FASTQ file for read 1 of paired-end sequenced libraries."
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pattern: "^[\\S]+.(fq\\.gz|fastq\\.gz)$"
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fastq2:
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type: ["string", "null"]
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description: "Optional FASTQ file for read 2 of paired-end sequenced libraries."
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pattern: "^[\\S]+.(fq\\.gz|fastq\\.gz)$"
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fasta:
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type: ["string", "null"]
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description: "Optional FASTA file."
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pattern: "^[\\S]+.(fa\\.gz|fasta\\.gz)$"
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required:
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- sample
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- run_accession
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- instrument_platform
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files:
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- fastq1
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- fastq2
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- fasta
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required:
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- samples
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236
bin/check_samplesheet.py
Executable file
236
bin/check_samplesheet.py
Executable file
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@ -0,0 +1,236 @@
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#!/usr/bin/env python
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from distutils import extension
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import os
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import sys
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import errno
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import argparse
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def parse_args(args=None):
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Description = "Reformat nf-core/taxprofiler samplesheet file and check its contents."
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Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>"
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parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
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parser.add_argument("FILE_IN", help="Input samplesheet file.")
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parser.add_argument("FILE_OUT", help="Output file.")
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return parser.parse_args(args)
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def make_dir(path):
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if len(path) > 0:
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try:
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os.makedirs(path)
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except OSError as exception:
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if exception.errno != errno.EEXIST:
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raise exception
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def print_error(error, context="Line", context_str=""):
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error_str = "ERROR: Please check samplesheet -> {}".format(error)
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if context != "" and context_str != "":
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error_str = "ERROR: Please check samplesheet -> {}\n{}: '{}'".format(
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error, context.strip(), context_str.strip()
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)
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print(error_str)
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sys.exit(1)
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def check_samplesheet(file_in, file_out):
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"""
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This function checks that the samplesheet follows the following structure:
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sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
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2611,ERR5766174,ILLUMINA,,,ERX5474930_ERR5766174_1.fa.gz
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2612,ERR5766176,ILLUMINA,ERX5474932_ERR5766176_1.fastq.gz,ERX5474932_ERR5766176_2.fastq.gz,
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2612,ERR5766174,ILLUMINA,ERX5474936_ERR5766180_1.fastq.gz,,
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2613,ERR5766181,ILLUMINA,ERX5474937_ERR5766181_1.fastq.gz,ERX5474937_ERR5766181_2.fastq.gz,
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"""
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FQ_EXTENSIONS = (".fq.gz", ".fastq.gz")
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FA_EXTENSIONS = (
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".fa",
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".fa.gz",
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".fasta",
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".fasta.gz",
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".fna",
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".fna.gz",
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".fas",
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".fas.gz",
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)
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INSTRUMENT_PLATFORMS = [
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"ABI_SOLID",
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"BGISEQ",
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"CAPILLARY",
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"COMPLETE_GENOMICS",
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"DNBSEQ",
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"HELICOS",
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"ILLUMINA",
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"ION_TORRENT",
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"LS454",
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"OXFORD_NANOPORE",
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"PACBIO_SMRT",
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]
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sample_mapping_dict = {}
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with open(file_in, "r") as fin:
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## Check header
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MIN_COLS = 4
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HEADER = [
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"sample",
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"run_accession",
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"instrument_platform",
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"fastq_1",
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"fastq_2",
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"fasta",
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]
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header = [x.strip('"') for x in fin.readline().strip().split(",")]
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## Check for missing mandatory columns
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missing_columns = list(set(HEADER) - set(header))
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if len(missing_columns) > 0:
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print(
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"ERROR: Missing required column header -> {}. Note some columns can otherwise be empty. See pipeline documentation (https://nf-co.re/taxprofiler/usage).".format(
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",".join(missing_columns)
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)
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)
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sys.exit(1)
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## Find locations of mandatory columns
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header_locs = {}
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for i in HEADER:
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header_locs[i] = header.index(i)
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## Check sample entries
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for line in fin:
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## Pull out only relevant columns for downstream checking
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line_parsed = [x.strip().strip('"') for x in line.strip().split(",")]
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lspl = [line_parsed[i] for i in header_locs.values()]
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# Check valid number of columns per row
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if len(lspl) < len(HEADER):
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print_error(
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"Invalid number of columns (minimum = {})!".format(len(HEADER)),
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"Line",
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line,
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)
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num_cols = len([x for x in lspl if x])
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if num_cols < MIN_COLS:
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print_error(
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"Invalid number of populated columns (minimum = {})!".format(MIN_COLS),
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"Line",
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line,
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)
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## Check sample name entries
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(
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sample,
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run_accession,
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instrument_platform,
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fastq_1,
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fastq_2,
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fasta,
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) = lspl[: len(HEADER)]
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sample = sample.replace(" ", "_")
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if not sample:
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print_error("Sample entry has not been specified!", "Line", line)
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## Check FastQ file extension
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for fastq in [fastq_1, fastq_2]:
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if fastq:
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if fastq.find(" ") != -1:
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print_error("FastQ file contains spaces!", "Line", line)
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if not fastq.endswith(FQ_EXTENSIONS):
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print_error(
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f"FastQ file does not have extension {' or '.join(list(FQ_EXTENSIONS))} !",
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"Line",
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line,
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)
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if fasta:
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if fasta.find(" ") != -1:
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print_error("FastA file contains spaces!", "Line", line)
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if not fasta.endswith(FA_EXTENSIONS):
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print_error(
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f"FastA file does not have extension {' or '.join(list(FA_EXTENSIONS))}!",
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"Line",
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line,
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)
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sample_info = []
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# Check run_accession
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if not run_accession:
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print_error("Run accession has not been specified!", "Line", line)
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else:
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sample_info.append(run_accession)
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# Check instrument_platform
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if not instrument_platform:
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print_error("Instrument platform has not been specified!", "Line", line)
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else:
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if instrument_platform not in INSTRUMENT_PLATFORMS:
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print_error(
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f"Instrument platform {instrument_platform} is not supported!",
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f"List of supported platforms {', '.join(INSTRUMENT_PLATFORMS)}",
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"Line",
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line,
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)
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sample_info.append(instrument_platform)
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## Auto-detect paired-end/single-end
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if sample and fastq_1 and fastq_2: ## Paired-end short reads
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sample_info.extend(["0", fastq_1, fastq_2, fasta])
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elif sample and fastq_1 and not fastq_2: ## Single-end short/long fastq reads
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sample_info.extend(["1", fastq_1, fastq_2, fasta])
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elif sample and fasta and not fastq_1 and not fastq_2: ## Single-end long reads
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sample_info.extend(["1", fastq_1, fastq_2, fasta])
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elif fasta and (fastq_1 or fastq_2):
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print_error(
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"FastQ and FastA files cannot be specified together in the same library!",
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"Line",
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line,
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)
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else:
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print_error("Invalid combination of columns provided!", "Line", line)
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## Create sample mapping dictionary = { sample: [ run_accession, instrument_platform, single_end, fastq_1, fastq_2 , fasta ] }
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if sample not in sample_mapping_dict:
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sample_mapping_dict[sample] = [sample_info]
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else:
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if sample_info in sample_mapping_dict[sample]:
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print_error("Samplesheet contains duplicate rows!", "Line", line)
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else:
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sample_mapping_dict[sample].append(sample_info)
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## Write validated samplesheet with appropriate columns
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HEADER_OUT = [
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"sample",
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"run_accession",
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"instrument_platform",
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"single_end",
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"fastq_1",
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"fastq_2",
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"fasta",
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]
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if len(sample_mapping_dict) > 0:
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out_dir = os.path.dirname(file_out)
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make_dir(out_dir)
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with open(file_out, "w") as fout:
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fout.write(",".join(HEADER_OUT) + "\n")
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for sample in sorted(sample_mapping_dict.keys()):
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for idx, val in enumerate(sample_mapping_dict[sample]):
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fout.write(f"{sample},{','.join(val)}\n")
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else:
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print_error("No entries to process!", "Samplesheet: {}".format(file_in))
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def main(args=None):
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args = parse_args(args)
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check_samplesheet(args.FILE_IN, args.FILE_OUT)
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if __name__ == "__main__":
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sys.exit(main())
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@ -495,12 +495,4 @@ process {
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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}
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withName: 'EIDO_VALIDATE' {
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ext.args = '--st-index sample'
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}
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withName: 'EIDO_CONVERT' {
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ext.args = '--st-index sample'
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}
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}
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@ -60,10 +60,4 @@ process {
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withName: MEGAN_RMA2INFO_KRONA {
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maxForks = 1
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}
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withName: 'EIDO_VALIDATE' {
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ext.args = '--st-index sample'
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}
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withName: 'EIDO_CONVERT' {
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ext.args = '--st-index sample'
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}
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}
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@ -63,10 +63,4 @@ process {
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withName: MEGAN_RMA2INFO_KRONA {
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maxForks = 1
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}
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withName: 'EIDO_VALIDATE' {
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ext.args = '--st-index sample'
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}
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withName: 'EIDO_CONVERT' {
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ext.args = '--st-index sample'
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}
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}
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@ -1,45 +0,0 @@
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params {
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config_profile_name = 'Test PEP profile'
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config_profile_description = 'Minimal test dataset to check pipeline function with PEP file as an input.'
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// Limit resources so that this can run on GitHub Actions
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max_cpus = 2
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max_memory = '6.GB'
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max_time = '6.h'
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// Input data
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml'
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databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
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perform_shortread_qc = true
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perform_longread_qc = true
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perform_shortread_complexityfilter = true
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perform_shortread_hostremoval = true
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perform_longread_hostremoval = true
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perform_runmerging = true
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hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
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run_kaiju = true
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run_kraken2 = true
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run_bracken = true
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run_malt = true
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run_metaphlan3 = true
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run_centrifuge = true
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run_diamond = true
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run_motus = false
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run_krona = true
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krona_taxonomy_directory = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
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malt_save_reads = true
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kraken2_save_reads = true
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centrifuge_save_reads = true
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diamond_save_reads = true
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}
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process {
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withName: MALT_RUN {
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maxForks = 1
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ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
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}
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withName: MEGAN_RMA2INFO {
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maxForks = 1
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}
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}
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@ -22,10 +22,6 @@ This samplesheet is then specified on the command line as follows:
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--input '[path to samplesheet file]' --databases '[path to database sheet file]'
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```
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Note pipeline supports both CSV and PEP input sample sheets. Find out more [here](http://pep.databio.org/en/2.1.0/specification/).
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When using PEP as an input, the `samplesheet.csv` must be placed in the same folder
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as `config.yaml` file. A path to `samplesheet.csv` within the config must be absolute.
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### Multiple runs of the same sample
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The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate different runs FASTQ files of the same sample before performing profiling, when `--perform_runmerging` is supplied. Below is an example for the same sample sequenced across 3 lanes:
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|
@ -312,9 +308,6 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
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- `test`
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- A profile with a complete configuration for automated testing
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- Includes links to test data so needs no other parameters
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- `test_pep`
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- A profile with a complete configuration for running a pipeline with PEP as input
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- Includes links to test data so needs no other parameters
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- `docker`
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- A generic configuration profile to be used with [Docker](https://docker.com/)
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- `singularity`
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|
|
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@ -81,7 +81,7 @@ class WorkflowMain {
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// Check input has been provided
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if (!params.input) {
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log.error "Please provide an input samplesheet or PEP to the pipeline e.g. '--input samplesheet.csv'"
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log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"
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System.exit(1)
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}
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}
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|
|
10
modules.json
10
modules.json
|
@ -55,16 +55,6 @@
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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},
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"eido/convert": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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},
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"eido/validate": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"installed_by": ["modules"]
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},
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"falco": {
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"branch": "master",
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"git_sha": "fc959214036403ad83efe7a41d43d0606c445cda",
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|
|
27
modules/local/samplesheet_check.nf
Normal file
27
modules/local/samplesheet_check.nf
Normal file
|
@ -0,0 +1,27 @@
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process SAMPLESHEET_CHECK {
|
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tag "$samplesheet"
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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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'https://depot.galaxyproject.org/singularity/python:3.8.3' :
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||||
'quay.io/biocontainers/python:3.8.3' }"
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input:
|
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path samplesheet
|
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|
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output:
|
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path '*.csv' , emit: csv
|
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path "versions.yml", emit: versions
|
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|
||||
script: // This script is bundled with the pipeline, in nf-core/taxprofiler/bin/
|
||||
"""
|
||||
check_samplesheet.py \\
|
||||
$samplesheet \\
|
||||
samplesheet.valid.csv
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
python: \$(python --version | sed 's/Python //g')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
38
modules/nf-core/eido/convert/main.nf
generated
38
modules/nf-core/eido/convert/main.nf
generated
|
@ -1,38 +0,0 @@
|
|||
process EIDO_CONVERT {
|
||||
tag "$samplesheet"
|
||||
label 'process_single'
|
||||
|
||||
conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://containers.biocontainers.pro/s3/SingImgsRepo/eido/0.1.9_cv1/eido_0.1.9_cv1.sif' :
|
||||
'biocontainers/eido:0.1.9_cv1' }"
|
||||
|
||||
input:
|
||||
path samplesheet
|
||||
val format
|
||||
path pep_input_base_dir
|
||||
|
||||
output:
|
||||
path "versions.yml" , emit: versions
|
||||
path "${prefix}.${format}" , emit: samplesheet_converted
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.prefix ?: "samplesheet_converted"
|
||||
"""
|
||||
eido \\
|
||||
convert \\
|
||||
-f $format \\
|
||||
$samplesheet \\
|
||||
$args \\
|
||||
-p samples=${prefix}.${format}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
eido: \$(echo \$(eido --version 2>&1) | sed 's/^.*eido //;s/ .*//' ))
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
39
modules/nf-core/eido/convert/meta.yml
generated
39
modules/nf-core/eido/convert/meta.yml
generated
|
@ -1,39 +0,0 @@
|
|||
name: "eido_convert"
|
||||
description: Convert any PEP project or Nextflow samplesheet to any format
|
||||
keywords:
|
||||
- eido
|
||||
- convert
|
||||
- PEP
|
||||
- format
|
||||
- samplesheet
|
||||
tools:
|
||||
- "eido":
|
||||
description: "Convert any PEP project or Nextflow samplesheet to any format"
|
||||
homepage: "http://eido.databio.org/en/latest/"
|
||||
documentation: "http://eido.databio.org/en/latest/"
|
||||
doi: "10.1093/gigascience/giab077"
|
||||
licence: "BSD-2-Clause"
|
||||
|
||||
input:
|
||||
- samplesheet:
|
||||
type: file
|
||||
description: Nextflow samplesheet or PEP project
|
||||
pattern: "*.{yaml,yml,csv}"
|
||||
- format:
|
||||
type: value
|
||||
description: Extension of an output file
|
||||
- pep_input_base_dir:
|
||||
type: file
|
||||
description: Optional path to the directory where files specified in a PEP config file are stored. Any paths specified in the config will need to be relative to this base directory.
|
||||
|
||||
output:
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- samplesheet_converted:
|
||||
type: file
|
||||
description: PEP project or samplesheet converted to csv file
|
||||
|
||||
authors:
|
||||
- "@rafalstepien"
|
33
modules/nf-core/eido/validate/main.nf
generated
33
modules/nf-core/eido/validate/main.nf
generated
|
@ -1,33 +0,0 @@
|
|||
process EIDO_VALIDATE {
|
||||
tag "$samplesheet"
|
||||
label 'process_single'
|
||||
|
||||
conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://containers.biocontainers.pro/s3/SingImgsRepo/eido/0.1.9_cv2/eido_0.1.9_cv2.sif' :
|
||||
'biocontainers/eido:0.1.9_cv2' }"
|
||||
|
||||
input:
|
||||
path samplesheet
|
||||
path schema
|
||||
path pep_input_base_dir
|
||||
|
||||
output:
|
||||
path "versions.yml" , emit: versions
|
||||
path "*.log" , emit: log
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "validation"
|
||||
"""
|
||||
eido validate $args $samplesheet -s $schema -e > ${prefix}.log
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
eido: \$(echo \$(eido --version 2>&1) | sed 's/^.*eido //;s/ .*//' ))
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
41
modules/nf-core/eido/validate/meta.yml
generated
41
modules/nf-core/eido/validate/meta.yml
generated
|
@ -1,41 +0,0 @@
|
|||
name: "eido_validate"
|
||||
description: Validate samplesheet or PEP config against a schema
|
||||
keywords:
|
||||
- eido
|
||||
- validate
|
||||
- schema
|
||||
- format
|
||||
- pep
|
||||
tools:
|
||||
- "validate":
|
||||
description: "Validate samplesheet or PEP config against a schema."
|
||||
homepage: "http://eido.databio.org/en/latest/"
|
||||
documentation: "http://eido.databio.org/en/latest/"
|
||||
doi: "10.1093/gigascience/giab077"
|
||||
licence: "BSD-2-Clause"
|
||||
|
||||
input:
|
||||
- samplesheet:
|
||||
type: file
|
||||
description: Samplesheet or PEP file to be validated
|
||||
pattern: "*.{yaml,yml,csv}"
|
||||
- schema:
|
||||
type: file
|
||||
description: Schema that the samplesheet will be validated against
|
||||
pattern: "*.{yaml,yml}"
|
||||
- pep_input_base_dir:
|
||||
type: file
|
||||
description: Optional path to the directory where files specified in a PEP config file are stored. Any paths specified in the config will need to be relative to this base directory.
|
||||
|
||||
output:
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- log:
|
||||
type: file
|
||||
description: File containing validation log.
|
||||
pattern: "*.log"
|
||||
|
||||
authors:
|
||||
- "@rafalstepien"
|
|
@ -252,7 +252,6 @@ profiles {
|
|||
test_nothing { includeConfig 'conf/test_nothing.config' }
|
||||
test_motus { includeConfig 'conf/test_motus.config' }
|
||||
test_krakenuniq { includeConfig 'conf/test_krakenuniq.config' }
|
||||
test_pep { includeConfig 'conf/test_pep.config' }
|
||||
}
|
||||
|
||||
|
||||
|
|
|
@ -2,41 +2,31 @@
|
|||
// Check input samplesheet and get read channels
|
||||
//
|
||||
|
||||
include { EIDO_VALIDATE } from '../../modules/nf-core/eido/validate/main'
|
||||
include { EIDO_CONVERT } from '../../modules/nf-core/eido/convert/main'
|
||||
include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check'
|
||||
|
||||
workflow INPUT_CHECK {
|
||||
take:
|
||||
samplesheet_or_pep_config // file: /path/to/samplesheet.csv or /path/to/pep/config.yaml
|
||||
pep_input_base_dir
|
||||
samplesheet // file: /path/to/samplesheet.csv
|
||||
|
||||
main:
|
||||
ch_versions = Channel.empty()
|
||||
|
||||
EIDO_VALIDATE ( samplesheet_or_pep_config, file("$projectDir/assets/samplesheet_schema.yaml"), pep_input_base_dir )
|
||||
ch_versions = ch_versions.mix(EIDO_VALIDATE.out.versions)
|
||||
|
||||
EIDO_CONVERT ( samplesheet_or_pep_config, "csv", pep_input_base_dir )
|
||||
ch_versions = ch_versions.mix(EIDO_CONVERT.out.versions)
|
||||
|
||||
ch_parsed_samplesheet = EIDO_CONVERT.out.samplesheet_converted
|
||||
parsed_samplesheet = SAMPLESHEET_CHECK ( samplesheet )
|
||||
.csv
|
||||
.splitCsv ( header:true, sep:',' )
|
||||
.map { check_missing_and_singleend_autodetect(it) }
|
||||
.branch {
|
||||
fasta: it['fasta'] != ''
|
||||
nanopore: it['instrument_platform'] == 'OXFORD_NANOPORE'
|
||||
fastq: true
|
||||
}
|
||||
|
||||
ch_parsed_samplesheet.fastq
|
||||
parsed_samplesheet.fastq
|
||||
.map { create_fastq_channel(it) }
|
||||
.set { fastq }
|
||||
|
||||
ch_parsed_samplesheet.nanopore
|
||||
parsed_samplesheet.nanopore
|
||||
.map { create_fastq_channel(it) }
|
||||
.set { nanopore }
|
||||
|
||||
ch_parsed_samplesheet.fasta
|
||||
parsed_samplesheet.fasta
|
||||
.map { create_fasta_channel(it) }
|
||||
.set { fasta }
|
||||
|
||||
|
@ -44,20 +34,7 @@ workflow INPUT_CHECK {
|
|||
fastq = fastq ?: [] // channel: [ val(meta), [ reads ] ]
|
||||
nanopore = nanopore ?: [] // channel: [ val(meta), [ reads ] ]
|
||||
fasta = fasta ?: [] // channel: [ val(meta), fasta ]
|
||||
versions = ch_versions // channel: [ versions.yml ]
|
||||
}
|
||||
|
||||
// Function to validate input sheet and auto-detect R1/R2
|
||||
def check_missing_and_singleend_autodetect(LinkedHashMap row) {
|
||||
|
||||
// Checks not supported by EIDO(?)
|
||||
if ( ( row['fastq_1'] != "" || row['fastq_2'] != "" ) && row['fasta'] != "" ) { exit 1, "[nf-core/taxprofiler] ERROR: FastQ and FastA files cannot be specified together in the same library. Check input samplesheet! Check sample: ${row['sample']}" }
|
||||
if ( row['fastq_1'] == "" && row['fastq_2'] != "" ) { exit 1, "[nf-core/taxprofiler] ERROR: Input samplesheet has a missing fastq_1 when fastq_2 is specified. Check sample: ${row['sample']}" }
|
||||
|
||||
single_end = row['fastq_2'] == "" ? true : false
|
||||
row['single_end'] = single_end
|
||||
|
||||
return row
|
||||
versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]
|
||||
}
|
||||
|
||||
// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
|
||||
|
@ -87,12 +64,11 @@ def create_fastq_channel(LinkedHashMap row) {
|
|||
if (!file(row.fastq_2).exists()) {
|
||||
exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
|
||||
}
|
||||
fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
|
||||
fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
|
||||
}
|
||||
|
||||
}
|
||||
return fastq_meta
|
||||
|
||||
}// Function to get list of [ meta, fasta ]
|
||||
def create_fasta_channel(LinkedHashMap row) {
|
||||
def meta = [:]
|
||||
|
|
|
@ -20,9 +20,8 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
|
|||
// Check mandatory parameters
|
||||
if ( params.input ) {
|
||||
ch_input = file(params.input, checkIfExists: true)
|
||||
pep_input_base_dir = file(params.input).extension.matches("yaml|yml") ? file(file(params.input).getParent(), checkIfExists: true) : []
|
||||
} else {
|
||||
exit 1, "Input samplesheet, or PEP config and base directory not specified"
|
||||
exit 1, "Input samplesheet not specified"
|
||||
}
|
||||
|
||||
if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
|
||||
|
@ -115,7 +114,7 @@ workflow TAXPROFILER {
|
|||
SUBWORKFLOW: Read in samplesheet, validate and stage input files
|
||||
*/
|
||||
INPUT_CHECK (
|
||||
ch_input, pep_input_base_dir
|
||||
ch_input
|
||||
)
|
||||
ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
|
||||
|
||||
|
|
Loading…
Reference in a new issue