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Remove detect_reads.py and replace remaining checks with nextflow code instead

This commit is contained in:
James Fellows Yates 2022-09-27 15:32:51 +02:00
parent 1584d6fc51
commit 43a8aa4405
5 changed files with 27 additions and 169 deletions

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@ -53,3 +53,5 @@ properties:
- fasta - fasta
required: required:
- samples - samples
- run_accession
- instrument_platform

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@ -1,125 +0,0 @@
#!/usr/bin/env python
import argparse
import csv
import sys
from typing import List, NoReturn
def parse_args(args=None) -> argparse.Namespace:
"""
Reformatting is based on detecting whether the reads are paired or single end.
Script appends appropriate column to samplesheet.csv file.
"""
Description = "Reformat nf-core/taxprofiler samplesheet file."
Epilog = "Example usage: python detect_reads.py <FILE_IN> <FILE_OUT>"
parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
parser.add_argument("FILE_IN", help="Input samplesheet file.")
parser.add_argument("FILE_OUT", help="Output file.")
return parser.parse_args(args)
class ReadsModifier:
def __init__(self):
self.headers = None
self.sample_index = None
self.fastq_1_index = None
self.fastq_2_index = None
self.fasta_index = None
def detect_reads_and_reformat(self, input_file_path: str, output_file_path: str) -> NoReturn:
NEW_COLUMN_NAME = "single_end"
new_file_rows = []
with open(input_file_path, "r") as input_file:
csv_reader = csv.reader(input_file, delimiter=",")
self.headers = next(csv_reader)
self.headers.append(NEW_COLUMN_NAME)
self._infer_column_indexes()
for samplesheet_row in csv_reader:
if self._is_paired_end_short_read(samplesheet_row):
new_file_rows.append([*samplesheet_row, "0"])
elif self._is_single_end_short_long_read(samplesheet_row):
new_file_rows.append([*samplesheet_row, "1"])
elif self._is_single_end_long_read(samplesheet_row):
new_file_rows.append([*samplesheet_row, "1"])
elif self._is_error_row(samplesheet_row):
self.print_error(
"FastQ and FastA files cannot be specified together in the same library!",
"Line",
",".join(samplesheet_row),
)
else:
self.print_error("Invalid combination of columns provided!", "Line", ",".join(samplesheet_row))
self.save_reformatted_samplesheet([self.headers] + new_file_rows, output_file_path)
def _get_row_values(self, samplesheet_row):
"""
This method extracts data from the columns for given row of samplesheet table, based on
previously infered column indexes.
"""
sample = samplesheet_row[self.sample_index]
fastq_1 = samplesheet_row[self.fastq_1_index] if self.fastq_1_index else None
fastq_2 = samplesheet_row[self.fastq_2_index] if self.fastq_2_index else None
fasta = samplesheet_row[self.fasta_index] if self.fasta_index else None
return sample, fastq_1, fastq_2, fasta
def _infer_column_indexes(self):
"""
This method infers indexes of necessary columns from samplesheet table
"""
self.sample_index = self.headers.index("sample")
self.fastq_1_index = self.headers.index("fastq_1") if "fastq_1" in self.headers else None
self.fastq_2_index = self.headers.index("fastq_2") if "fastq_2" in self.headers else None
self.fasta_index = self.headers.index("fasta") if "fasta" in self.headers else None
def _is_paired_end_short_read(self, samplesheet_row: List) -> bool:
sample, fastq_1, fastq_2, _ = self._get_row_values(samplesheet_row)
return sample and fastq_1 and fastq_2
def _is_single_end_short_long_read(self, samplesheet_row: List) -> bool:
sample, fastq_1, fastq_2, _ = self._get_row_values(samplesheet_row)
return sample and fastq_1 and not fastq_2
def _is_single_end_long_read(self, samplesheet_row: List) -> bool:
sample, fastq_1, fastq_2, fasta = self._get_row_values(samplesheet_row)
return sample and fasta and not fastq_1 and not fastq_2
def _is_error_row(self, samplesheet_row: List) -> bool:
sample, fastq_1, fastq_2, fasta = self._get_row_values(samplesheet_row)
return fasta and (fastq_1 or fastq_2)
@staticmethod
def print_error(error: str, context: str = "Line", context_str: str = ""):
error_str = "ERROR: Please check samplesheet -> {}".format(error)
if context != "" and context_str != "":
error_str = "ERROR: Please check samplesheet -> {}\n{}: '{}'".format(
error, context.strip(), context_str.strip()
)
print(error_str)
sys.exit(1)
@staticmethod
def save_reformatted_samplesheet(new_file_rows: List[List], output_file_path: str) -> NoReturn:
"""
Write new samplesheet.
"""
with open(output_file_path, "w") as output_file:
csv.writer(output_file).writerows(new_file_rows)
def main(args=None):
args = parse_args(args)
ReadsModifier().detect_reads_and_reformat(args.FILE_IN, args.FILE_OUT)
if __name__ == "__main__":
sys.exit(main())

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@ -12,14 +12,6 @@
process { process {
withName: SAMPLESHEET_CHECK {
publishDir = [
path: { "${params.outdir}/pipeline_info" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: DATABASE_CHECK { withName: DATABASE_CHECK {
publishDir = [ publishDir = [
path: { "${params.outdir}/pipeline_info" }, path: { "${params.outdir}/pipeline_info" },

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@ -1,27 +0,0 @@
process SAMPLESHEET_CHECK {
tag "$samplesheet"
conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/python:3.8.3' :
'quay.io/biocontainers/python:3.8.3' }"
input:
path samplesheet
output:
path '*.csv' , emit: csv
path "versions.yml", emit: versions
script: // detect_reads.py script is bundled with the pipeline, in nf-core/taxprofiler/bin/
"""
python3 $projectDir/bin/detect_reads.py \\
$samplesheet \\
samplesheet_validated.csv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
}

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@ -2,7 +2,6 @@
// Check input samplesheet and get read channels // Check input samplesheet and get read channels
// //
include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check'
include { EIDO_VALIDATE } from '../../modules/nf-core/modules/eido/validate/main' include { EIDO_VALIDATE } from '../../modules/nf-core/modules/eido/validate/main'
include { EIDO_CONVERT } from '../../modules/nf-core/modules/eido/convert/main' include { EIDO_CONVERT } from '../../modules/nf-core/modules/eido/convert/main'
@ -12,26 +11,43 @@ workflow INPUT_CHECK {
pep_input_base_dir pep_input_base_dir
main: main:
ch_versions = Channel.empty()
EIDO_VALIDATE ( samplesheet_or_pep_config, file("$projectDir/assets/samplesheet_schema.yaml"), pep_input_base_dir ) EIDO_VALIDATE ( samplesheet_or_pep_config, file("$projectDir/assets/samplesheet_schema.yaml"), pep_input_base_dir )
converted_samplesheet = EIDO_CONVERT ( samplesheet_or_pep_config, "csv", pep_input_base_dir ) ch_versions = ch_versions.mix(EIDO_VALIDATE.out.versions)
parsed_samplesheet = SAMPLESHEET_CHECK ( converted_samplesheet.samplesheet_converted )
.csv 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
.splitCsv ( header:true, sep:',' ) .splitCsv ( header:true, sep:',' )
.map{
// Checks not supported by EIDO(?)
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']}" }
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: ${it['sample']}" }
single_end = it['fastq_2'] == "" ? true : false
it['single_end'] = single_end
[ it ]
}
.flatten()
.branch { .branch {
fasta: it['fasta'] != '' fasta: it['fasta'] != ''
nanopore: it['instrument_platform'] == 'OXFORD_NANOPORE' nanopore: it['instrument_platform'] == 'OXFORD_NANOPORE'
fastq: true fastq: true
} }
parsed_samplesheet.fastq ch_parsed_samplesheet.fastq
.map { create_fastq_channel(it) } .map { create_fastq_channel(it) }
.set { fastq } .set { fastq }
parsed_samplesheet.nanopore ch_parsed_samplesheet.nanopore
.map { create_fastq_channel(it) } .map { create_fastq_channel(it) }
.set { nanopore } .set { nanopore }
parsed_samplesheet.fasta ch_parsed_samplesheet.fasta
.map { create_fasta_channel(it) } .map { create_fasta_channel(it) }
.set { fasta } .set { fasta }
@ -39,7 +55,7 @@ workflow INPUT_CHECK {
fastq = fastq ?: [] // channel: [ val(meta), [ reads ] ] fastq = fastq ?: [] // channel: [ val(meta), [ reads ] ]
nanopore = nanopore ?: [] // channel: [ val(meta), [ reads ] ] nanopore = nanopore ?: [] // channel: [ val(meta), [ reads ] ]
fasta = fasta ?: [] // channel: [ val(meta), fasta ] fasta = fasta ?: [] // channel: [ val(meta), fasta ]
versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ] versions = ch_versions // channel: [ versions.yml ]
} }
// Function to get list of [ meta, [ fastq_1, fastq_2 ] ] // Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
@ -69,7 +85,7 @@ def create_fastq_channel(LinkedHashMap row) {
if (!file(row.fastq_2).exists()) { if (!file(row.fastq_2).exists()) {
exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}" 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) ] ]
} }
} }