mirror of
https://github.com/MillironX/taxprofiler.git
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Remove detect_reads.py and replace remaining checks with nextflow code instead
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parent
1584d6fc51
commit
43a8aa4405
5 changed files with 27 additions and 169 deletions
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@ -53,3 +53,5 @@ properties:
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- fasta
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- fasta
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required:
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required:
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- samples
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- samples
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- run_accession
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- instrument_platform
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@ -1,125 +0,0 @@
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#!/usr/bin/env python
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import argparse
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import csv
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import sys
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from typing import List, NoReturn
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def parse_args(args=None) -> argparse.Namespace:
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"""
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Reformatting is based on detecting whether the reads are paired or single end.
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Script appends appropriate column to samplesheet.csv file.
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"""
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Description = "Reformat nf-core/taxprofiler samplesheet file."
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Epilog = "Example usage: python detect_reads.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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class ReadsModifier:
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def __init__(self):
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self.headers = None
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self.sample_index = None
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self.fastq_1_index = None
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self.fastq_2_index = None
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self.fasta_index = None
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def detect_reads_and_reformat(self, input_file_path: str, output_file_path: str) -> NoReturn:
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NEW_COLUMN_NAME = "single_end"
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new_file_rows = []
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with open(input_file_path, "r") as input_file:
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csv_reader = csv.reader(input_file, delimiter=",")
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self.headers = next(csv_reader)
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self.headers.append(NEW_COLUMN_NAME)
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self._infer_column_indexes()
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for samplesheet_row in csv_reader:
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if self._is_paired_end_short_read(samplesheet_row):
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new_file_rows.append([*samplesheet_row, "0"])
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elif self._is_single_end_short_long_read(samplesheet_row):
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new_file_rows.append([*samplesheet_row, "1"])
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elif self._is_single_end_long_read(samplesheet_row):
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new_file_rows.append([*samplesheet_row, "1"])
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elif self._is_error_row(samplesheet_row):
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self.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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",".join(samplesheet_row),
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)
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else:
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self.print_error("Invalid combination of columns provided!", "Line", ",".join(samplesheet_row))
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self.save_reformatted_samplesheet([self.headers] + new_file_rows, output_file_path)
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def _get_row_values(self, samplesheet_row):
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"""
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This method extracts data from the columns for given row of samplesheet table, based on
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previously infered column indexes.
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"""
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sample = samplesheet_row[self.sample_index]
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fastq_1 = samplesheet_row[self.fastq_1_index] if self.fastq_1_index else None
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fastq_2 = samplesheet_row[self.fastq_2_index] if self.fastq_2_index else None
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fasta = samplesheet_row[self.fasta_index] if self.fasta_index else None
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return sample, fastq_1, fastq_2, fasta
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def _infer_column_indexes(self):
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"""
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This method infers indexes of necessary columns from samplesheet table
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"""
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self.sample_index = self.headers.index("sample")
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self.fastq_1_index = self.headers.index("fastq_1") if "fastq_1" in self.headers else None
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self.fastq_2_index = self.headers.index("fastq_2") if "fastq_2" in self.headers else None
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self.fasta_index = self.headers.index("fasta") if "fasta" in self.headers else None
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def _is_paired_end_short_read(self, samplesheet_row: List) -> bool:
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sample, fastq_1, fastq_2, _ = self._get_row_values(samplesheet_row)
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return sample and fastq_1 and fastq_2
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def _is_single_end_short_long_read(self, samplesheet_row: List) -> bool:
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sample, fastq_1, fastq_2, _ = self._get_row_values(samplesheet_row)
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return sample and fastq_1 and not fastq_2
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def _is_single_end_long_read(self, samplesheet_row: List) -> bool:
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sample, fastq_1, fastq_2, fasta = self._get_row_values(samplesheet_row)
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return sample and fasta and not fastq_1 and not fastq_2
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def _is_error_row(self, samplesheet_row: List) -> bool:
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sample, fastq_1, fastq_2, fasta = self._get_row_values(samplesheet_row)
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return fasta and (fastq_1 or fastq_2)
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@staticmethod
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def print_error(error: str, context: str = "Line", context_str: 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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@staticmethod
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def save_reformatted_samplesheet(new_file_rows: List[List], output_file_path: str) -> NoReturn:
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"""
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Write new samplesheet.
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"""
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with open(output_file_path, "w") as output_file:
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csv.writer(output_file).writerows(new_file_rows)
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def main(args=None):
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args = parse_args(args)
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ReadsModifier().detect_reads_and_reformat(args.FILE_IN, args.FILE_OUT)
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if __name__ == "__main__":
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sys.exit(main())
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@ -12,14 +12,6 @@
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process {
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process {
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withName: SAMPLESHEET_CHECK {
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publishDir = [
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path: { "${params.outdir}/pipeline_info" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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}
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withName: DATABASE_CHECK {
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withName: DATABASE_CHECK {
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/pipeline_info" },
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path: { "${params.outdir}/pipeline_info" },
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@ -1,27 +0,0 @@
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process SAMPLESHEET_CHECK {
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tag "$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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output:
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path '*.csv' , emit: csv
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path "versions.yml", emit: versions
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script: // detect_reads.py script is bundled with the pipeline, in nf-core/taxprofiler/bin/
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"""
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python3 $projectDir/bin/detect_reads.py \\
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$samplesheet \\
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samplesheet_validated.csv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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python: \$(python --version | sed 's/Python //g')
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END_VERSIONS
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"""
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}
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@ -2,7 +2,6 @@
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// Check input samplesheet and get read channels
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// Check input samplesheet and get read channels
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//
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//
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include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check'
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include { EIDO_VALIDATE } from '../../modules/nf-core/modules/eido/validate/main'
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include { EIDO_VALIDATE } from '../../modules/nf-core/modules/eido/validate/main'
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include { EIDO_CONVERT } from '../../modules/nf-core/modules/eido/convert/main'
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include { EIDO_CONVERT } from '../../modules/nf-core/modules/eido/convert/main'
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@ -12,26 +11,43 @@ workflow INPUT_CHECK {
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pep_input_base_dir
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pep_input_base_dir
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main:
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main:
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ch_versions = Channel.empty()
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EIDO_VALIDATE ( samplesheet_or_pep_config, file("$projectDir/assets/samplesheet_schema.yaml"), pep_input_base_dir )
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EIDO_VALIDATE ( samplesheet_or_pep_config, file("$projectDir/assets/samplesheet_schema.yaml"), pep_input_base_dir )
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converted_samplesheet = EIDO_CONVERT ( samplesheet_or_pep_config, "csv", pep_input_base_dir )
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ch_versions = ch_versions.mix(EIDO_VALIDATE.out.versions)
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parsed_samplesheet = SAMPLESHEET_CHECK ( converted_samplesheet.samplesheet_converted )
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.csv
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EIDO_CONVERT ( samplesheet_or_pep_config, "csv", pep_input_base_dir )
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ch_versions = ch_versions.mix(EIDO_CONVERT.out.versions)
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ch_parsed_samplesheet = EIDO_CONVERT.out.samplesheet_converted
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.splitCsv ( header:true, sep:',' )
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.splitCsv ( header:true, sep:',' )
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.map{
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// Checks not supported by EIDO(?)
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if ( ( it['fastq_1'] != "" || it['fastq_2'] != "" ) && it['fasta'] != "" ) { exit 1, "[nf-core/taxprofiler] ERROR: FastQ and FastA files cannot be specified together in the same library. Check input samplesheet! Check sample: ${it['sample']}" }
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if ( it['fastq_1'] == "" && it['fastq_2'] != "" ) { exit 1, "[nf-core/taxprofiler] ERROR: Input samplesheet has a missing fastq_1 when fastq_2 is specified. Check sample: ${it['sample']}" }
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single_end = it['fastq_2'] == "" ? true : false
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it['single_end'] = single_end
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[ it ]
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}
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.flatten()
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.branch {
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.branch {
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fasta: it['fasta'] != ''
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fasta: it['fasta'] != ''
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nanopore: it['instrument_platform'] == 'OXFORD_NANOPORE'
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nanopore: it['instrument_platform'] == 'OXFORD_NANOPORE'
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fastq: true
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fastq: true
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}
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}
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parsed_samplesheet.fastq
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ch_parsed_samplesheet.fastq
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.map { create_fastq_channel(it) }
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.map { create_fastq_channel(it) }
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.set { fastq }
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.set { fastq }
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parsed_samplesheet.nanopore
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ch_parsed_samplesheet.nanopore
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.map { create_fastq_channel(it) }
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.map { create_fastq_channel(it) }
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.set { nanopore }
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.set { nanopore }
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parsed_samplesheet.fasta
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ch_parsed_samplesheet.fasta
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.map { create_fasta_channel(it) }
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.map { create_fasta_channel(it) }
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.set { fasta }
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.set { fasta }
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@ -39,7 +55,7 @@ workflow INPUT_CHECK {
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fastq = fastq ?: [] // channel: [ val(meta), [ reads ] ]
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fastq = fastq ?: [] // channel: [ val(meta), [ reads ] ]
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nanopore = nanopore ?: [] // channel: [ val(meta), [ reads ] ]
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nanopore = nanopore ?: [] // channel: [ val(meta), [ reads ] ]
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fasta = fasta ?: [] // channel: [ val(meta), fasta ]
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fasta = fasta ?: [] // channel: [ val(meta), fasta ]
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versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]
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versions = ch_versions // channel: [ versions.yml ]
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}
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}
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// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
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// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
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@ -69,7 +85,7 @@ def create_fastq_channel(LinkedHashMap row) {
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if (!file(row.fastq_2).exists()) {
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if (!file(row.fastq_2).exists()) {
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exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
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exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
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}
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}
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fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
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fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
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}
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}
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}
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}
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