Merge branch 'nf-core-add-pep-support' into add-pep-support

assets/samplesheet_schema.yaml

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

bin/detect_reads.py

@@ -1,117 +0,0 @@
-#!/usr/bin/env python
-import argparse
-import csv
-import logging
-import sys
-from enum import Enum
-from typing import List, NoReturn, Optional
-
-
-class ColumnNames(str, Enum):
-    SAMPLE = "sample"
-    FASTQ_1 = "fastq_1"
-    FASTQ_2 = "fastq_2"
-    FASTA = "fasta"
-    SINGLE_END = "single_end"
-
-
-def parse_args(args: Optional[List[str]] = None) -> argparse.Namespace:
-    """
-    Reformatting is based on detecting whether the reads are paired or single end.
-    Script appends appropriate column to samplesheet.csv file.
-    """
-    parser = argparse.ArgumentParser(
-        description="Reformat nf-core/taxprofiler samplesheet file.",
-        epilog="Example usage: python detect_reads.py <FILE_IN> <FILE_OUT>",
-    )
-    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_file_rows = []
-
-        with open(input_file_path, "r", newline="") as input_file:
-            csv_reader = csv.DictReader(input_file, delimiter=",")
-            self.headers = csv_reader.fieldnames
-            self.headers.append("single_end")
-
-            for samplesheet_row in csv_reader:
-
-                if self._is_paired_end_short_read(samplesheet_row):
-                    samplesheet_row[ColumnNames.SINGLE_END] = "0"
-                    new_file_rows.append(samplesheet_row.values())
-
-                elif self._is_single_end_short_long_read(samplesheet_row):
-                    samplesheet_row[ColumnNames.SINGLE_END] = "1"
-                    new_file_rows.append(samplesheet_row.values())
-
-                elif self._is_single_end_long_read(samplesheet_row):
-                    samplesheet_row[ColumnNames.SINGLE_END] = "1"
-                    new_file_rows.append(samplesheet_row.values())
-
-                elif self._is_error_row(samplesheet_row):
-                    logging.error(
-                        "FastQ and FastA files cannot be specified together in the same library!",
-                        "Line",
-                        ",".join(samplesheet_row.values()),
-                    )
-                else:
-                    logging.error(
-                        "Invalid combination of columns provided!", "Line", ",".join(samplesheet_row.values())
-                    )
-
-        ReadsModifier.save_reformatted_samplesheet([self.headers] + new_file_rows, output_file_path)
-
-    def _get_row_values(self, samplesheet_row: dict):
-        """
-        This method extracts data from the columns for given row of samplesheet table.
-        """
-        return (
-            samplesheet_row.get(ColumnNames.SAMPLE),
-            samplesheet_row.get(ColumnNames.FASTQ_1),
-            samplesheet_row.get(ColumnNames.FASTQ_2),
-            samplesheet_row.get(ColumnNames.FASTA),
-        )
-
-    def _is_paired_end_short_read(self, samplesheet_row: dict) -> 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: dict) -> 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: dict) -> 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: dict) -> bool:
-        sample, fastq_1, fastq_2, fasta = self._get_row_values(samplesheet_row)
-        return fasta and (fastq_1 or fastq_2)
-
-    @classmethod
-    def save_reformatted_samplesheet(cls, 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())

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" },

modules/local/samplesheet_check.nf

@@ -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
-    """
-}

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 +11,32 @@ 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 { check_missing_and_singleend_autodetect(it) }
         .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 +44,20 @@ 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 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
 }
 
 // Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
@@ -69,11 +87,12 @@ 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 = [:]