From 43a8aa4405e67e0616d63f71ef217ecb7b2e350b Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Tue, 27 Sep 2022 15:32:51 +0200 Subject: [PATCH] Remove detect_reads.py and replace remaining checks with nextflow code instead --- assets/samplesheet_schema.yaml | 2 + bin/detect_reads.py | 125 ----------------------------- conf/modules.config | 8 -- modules/local/samplesheet_check.nf | 27 ------- subworkflows/local/input_check.nf | 34 +++++--- 5 files changed, 27 insertions(+), 169 deletions(-) delete mode 100644 bin/detect_reads.py delete mode 100644 modules/local/samplesheet_check.nf diff --git a/assets/samplesheet_schema.yaml b/assets/samplesheet_schema.yaml index 88ff451..366ee93 100644 --- a/assets/samplesheet_schema.yaml +++ b/assets/samplesheet_schema.yaml @@ -53,3 +53,5 @@ properties: - fasta required: - samples + - run_accession + - instrument_platform diff --git a/bin/detect_reads.py b/bin/detect_reads.py deleted file mode 100644 index 8a1430e..0000000 --- a/bin/detect_reads.py +++ /dev/null @@ -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 " - - 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()) diff --git a/conf/modules.config b/conf/modules.config index 0efd251..73cc042 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -12,14 +12,6 @@ process { - withName: SAMPLESHEET_CHECK { - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - withName: DATABASE_CHECK { publishDir = [ path: { "${params.outdir}/pipeline_info" }, diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf deleted file mode 100644 index 91e0f04..0000000 --- a/modules/local/samplesheet_check.nf +++ /dev/null @@ -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 - """ -} diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf index 447eb15..d54d2ad 100644 --- a/subworkflows/local/input_check.nf +++ b/subworkflows/local/input_check.nf @@ -2,7 +2,6 @@ // 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_CONVERT } from '../../modules/nf-core/modules/eido/convert/main' @@ -12,26 +11,43 @@ workflow INPUT_CHECK { pep_input_base_dir main: + ch_versions = Channel.empty() + 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 ) - parsed_samplesheet = SAMPLESHEET_CHECK ( converted_samplesheet.samplesheet_converted ) - .csv + 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 .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: ${it['sample']}" } + + single_end = it['fastq_2'] == "" ? true : false + it['single_end'] = single_end + + [ it ] + } + .flatten() .branch { fasta: it['fasta'] != '' nanopore: it['instrument_platform'] == 'OXFORD_NANOPORE' fastq: true } - parsed_samplesheet.fastq + ch_parsed_samplesheet.fastq .map { create_fastq_channel(it) } .set { fastq } - parsed_samplesheet.nanopore + ch_parsed_samplesheet.nanopore .map { create_fastq_channel(it) } .set { nanopore } - parsed_samplesheet.fasta + ch_parsed_samplesheet.fasta .map { create_fasta_channel(it) } .set { fasta } @@ -39,7 +55,7 @@ workflow INPUT_CHECK { fastq = fastq ?: [] // channel: [ val(meta), [ reads ] ] nanopore = nanopore ?: [] // channel: [ val(meta), [ reads ] ] fasta = fasta ?: [] // channel: [ val(meta), fasta ] - versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ] + versions = ch_versions // channel: [ versions.yml ] } // Function to get list of [ meta, [ fastq_1, fastq_2 ] ] @@ -69,7 +85,7 @@ def create_fastq_channel(LinkedHashMap row) { if (!file(row.fastq_2).exists()) { exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${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) ] ] } }