Merge pull request #133 from rafalstepien/add-pep-support

Add working version of PEP-nf-core integration

README.md

@@ -75,6 +75,8 @@ On release, automated continuous integration tests run the pipeline on a full-si
    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>
    ```
 
+Note pipeline supports both CSV and PEP input sample sheets. Find out more [here](http://pep.databio.org/en/2.1.0/specification/).
+
 ## Documentation
 
 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).

assets/samplesheet_schema.yaml

@@ -0,0 +1,55 @@
+description: A schema for validation of samplesheet.csv for taxprofiler pipeline.
+imports:
+  - https://schema.databio.org/pep/2.1.0.yaml
+properties:
+  samples:
+    type: array
+    items:
+      type: object
+      properties:
+        sample:
+          type: string
+          description: "Sample identifier."
+          pattern: "^\\S*$"
+        run_accession:
+          type: string
+          description: "Run accession number."
+        instrument_platform:
+          type: string
+          description: "Name of the platform that sequenced the samples."
+          enum:
+            [
+              "ABI_SOLID",
+              "BGISEQ",
+              "CAPILLARY",
+              "COMPLETE_GENOMICS",
+              "DNBSEQ",
+              "HELICOS",
+              "ILLUMINA",
+              "ION_TORRENT",
+              "LS454",
+              "OXFORD_NANOPORE",
+              "PACBIO_SMRT",
+            ]
+        fastq1:
+          type: ["string", "null"]
+          description: "Optional FASTQ file for read 1 of paired-end sequenced libraries."
+          pattern: "^[\\S]+.(fq\\.gz|fastq\\.gz)$"
+        fastq2:
+          type: ["string", "null"]
+          description: "Optional FASTQ file for read 2 of paired-end sequenced libraries."
+          pattern: "^[\\S]+.(fq\\.gz|fastq\\.gz)$"
+        fasta:
+          type: ["string", "null"]
+          description: "Optional FASTA file."
+          pattern: "^[\\S]+.(fa\\.gz|fasta\\.gz)$"
+      required:
+        - sample
+        - run_accession
+        - instrument_platform
+      files:
+        - fastq1
+        - fastq2
+        - fasta
+required:
+  - samples

bin/check_samplesheet.py

@@ -1,236 +0,0 @@
-#!/usr/bin/env python
-
-from distutils import extension
-import os
-import sys
-import errno
-import argparse
-
-
-def parse_args(args=None):
-    Description = "Reformat nf-core/taxprofiler samplesheet file and check its contents."
-
-    Epilog = "Example usage: python check_samplesheet.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)
-
-
-def make_dir(path):
-    if len(path) > 0:
-        try:
-            os.makedirs(path)
-        except OSError as exception:
-            if exception.errno != errno.EEXIST:
-                raise exception
-
-
-def print_error(error, context="Line", context_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)
-
-
-def check_samplesheet(file_in, file_out):
-    """
-    This function checks that the samplesheet follows the following structure:
-
-    sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
-    2611,ERR5766174,ILLUMINA,,,ERX5474930_ERR5766174_1.fa.gz
-    2612,ERR5766176,ILLUMINA,ERX5474932_ERR5766176_1.fastq.gz,ERX5474932_ERR5766176_2.fastq.gz,
-    2612,ERR5766174,ILLUMINA,ERX5474936_ERR5766180_1.fastq.gz,,
-    2613,ERR5766181,ILLUMINA,ERX5474937_ERR5766181_1.fastq.gz,ERX5474937_ERR5766181_2.fastq.gz,
-    """
-
-    FQ_EXTENSIONS = (".fq.gz", ".fastq.gz")
-    FA_EXTENSIONS = (
-        ".fa",
-        ".fa.gz",
-        ".fasta",
-        ".fasta.gz",
-        ".fna",
-        ".fna.gz",
-        ".fas",
-        ".fas.gz",
-    )
-    INSTRUMENT_PLATFORMS = [
-        "ABI_SOLID",
-        "BGISEQ",
-        "CAPILLARY",
-        "COMPLETE_GENOMICS",
-        "DNBSEQ",
-        "HELICOS",
-        "ILLUMINA",
-        "ION_TORRENT",
-        "LS454",
-        "OXFORD_NANOPORE",
-        "PACBIO_SMRT",
-    ]
-
-    sample_mapping_dict = {}
-    with open(file_in, "r") as fin:
-
-        ## Check header
-        MIN_COLS = 4
-        HEADER = [
-            "sample",
-            "run_accession",
-            "instrument_platform",
-            "fastq_1",
-            "fastq_2",
-            "fasta",
-        ]
-        header = [x.strip('"') for x in fin.readline().strip().split(",")]
-
-        ## Check for missing mandatory columns
-        missing_columns = list(set(HEADER) - set(header))
-        if len(missing_columns) > 0:
-            print(
-                "ERROR: Missing required column header -> {}. Note some columns can otherwise be empty. See pipeline documentation (https://nf-co.re/taxprofiler/usage).".format(
-                    ",".join(missing_columns)
-                )
-            )
-            sys.exit(1)
-
-        ## Find locations of mandatory columns
-        header_locs = {}
-        for i in HEADER:
-            header_locs[i] = header.index(i)
-
-        ## Check sample entries
-        for line in fin:
-
-            ## Pull out only relevant columns for downstream checking
-            line_parsed = [x.strip().strip('"') for x in line.strip().split(",")]
-            lspl = [line_parsed[i] for i in header_locs.values()]
-
-            # Check valid number of columns per row
-            if len(lspl) < len(HEADER):
-                print_error(
-                    "Invalid number of columns (minimum = {})!".format(len(HEADER)),
-                    "Line",
-                    line,
-                )
-            num_cols = len([x for x in lspl if x])
-            if num_cols < MIN_COLS:
-                print_error(
-                    "Invalid number of populated columns (minimum = {})!".format(MIN_COLS),
-                    "Line",
-                    line,
-                )
-
-            ## Check sample name entries
-
-            (
-                sample,
-                run_accession,
-                instrument_platform,
-                fastq_1,
-                fastq_2,
-                fasta,
-            ) = lspl[: len(HEADER)]
-            sample = sample.replace(" ", "_")
-            if not sample:
-                print_error("Sample entry has not been specified!", "Line", line)
-
-            ## Check FastQ file extension
-            for fastq in [fastq_1, fastq_2]:
-                if fastq:
-                    if fastq.find(" ") != -1:
-                        print_error("FastQ file contains spaces!", "Line", line)
-                    if not fastq.endswith(FQ_EXTENSIONS):
-                        print_error(
-                            f"FastQ file does not have extension {' or '.join(list(FQ_EXTENSIONS))} !",
-                            "Line",
-                            line,
-                        )
-            if fasta:
-                if fasta.find(" ") != -1:
-                    print_error("FastA file contains spaces!", "Line", line)
-                if not fasta.endswith(FA_EXTENSIONS):
-                    print_error(
-                        f"FastA file does not have extension {' or '.join(list(FA_EXTENSIONS))}!",
-                        "Line",
-                        line,
-                    )
-            sample_info = []
-
-            # Check run_accession
-            if not run_accession:
-                print_error("Run accession has not been specified!", "Line", line)
-            else:
-                sample_info.append(run_accession)
-
-            # Check instrument_platform
-            if not instrument_platform:
-                print_error("Instrument platform has not been specified!", "Line", line)
-            else:
-                if instrument_platform not in INSTRUMENT_PLATFORMS:
-                    print_error(
-                        f"Instrument platform {instrument_platform} is not supported!",
-                        f"List of supported platforms {', '.join(INSTRUMENT_PLATFORMS)}",
-                        "Line",
-                        line,
-                    )
-                sample_info.append(instrument_platform)
-
-            ## Auto-detect paired-end/single-end
-            if sample and fastq_1 and fastq_2:  ## Paired-end short reads
-                sample_info.extend(["0", fastq_1, fastq_2, fasta])
-            elif sample and fastq_1 and not fastq_2:  ## Single-end short/long fastq reads
-                sample_info.extend(["1", fastq_1, fastq_2, fasta])
-            elif sample and fasta and not fastq_1 and not fastq_2:  ## Single-end long reads
-                sample_info.extend(["1", fastq_1, fastq_2, fasta])
-            elif fasta and (fastq_1 or fastq_2):
-                print_error(
-                    "FastQ and FastA files cannot be specified together in the same library!",
-                    "Line",
-                    line,
-                )
-            else:
-                print_error("Invalid combination of columns provided!", "Line", line)
-
-            ## Create sample mapping dictionary = { sample: [ run_accession, instrument_platform, single_end, fastq_1, fastq_2 , fasta ] }
-            if sample not in sample_mapping_dict:
-                sample_mapping_dict[sample] = [sample_info]
-            else:
-                if sample_info in sample_mapping_dict[sample]:
-                    print_error("Samplesheet contains duplicate rows!", "Line", line)
-                else:
-                    sample_mapping_dict[sample].append(sample_info)
-
-    ## Write validated samplesheet with appropriate columns
-    HEADER_OUT = [
-        "sample",
-        "run_accession",
-        "instrument_platform",
-        "single_end",
-        "fastq_1",
-        "fastq_2",
-        "fasta",
-    ]
-    if len(sample_mapping_dict) > 0:
-        out_dir = os.path.dirname(file_out)
-        make_dir(out_dir)
-        with open(file_out, "w") as fout:
-            fout.write(",".join(HEADER_OUT) + "\n")
-            for sample in sorted(sample_mapping_dict.keys()):
-                for idx, val in enumerate(sample_mapping_dict[sample]):
-                    fout.write(f"{sample},{','.join(val)}\n")
-    else:
-        print_error("No entries to process!", "Samplesheet: {}".format(file_in))
-
-
-def main(args=None):
-    args = parse_args(args)
-    check_samplesheet(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" },
@@ -450,4 +442,12 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+
+    withName: 'EIDO_VALIDATE' {
+        ext.args = '--st-index sample'
+    }
+
+    withName: 'EIDO_CONVERT' {
+        ext.args = '--st-index sample'
+    }
 }

conf/test.config

@@ -57,4 +57,10 @@ process {
     withName: MEGAN_RMA2INFO_KRONA {
         maxForks = 1
     }
+    withName: 'EIDO_VALIDATE' {
+        ext.args = '--st-index sample'
+    }
+    withName: 'EIDO_CONVERT' {
+        ext.args = '--st-index sample'
+    }
 }

conf/test_pep.config

@@ -0,0 +1,43 @@
+params {
+    config_profile_name        = 'Test PEP profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function with PEP file as an input.'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input data
+    input                                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml'
+    databases                             = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
+    perform_shortread_qc                  = true
+    perform_longread_qc                   = true
+    perform_shortread_complexityfilter    = true
+    perform_shortread_hostremoval         = true
+    perform_longread_hostremoval          = true
+    perform_runmerging                    = true
+    hostremoval_reference                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
+    run_kaiju                             = true
+    run_kraken2                           = true
+    run_malt                              = true
+    run_metaphlan3                        = true
+    run_centrifuge                        = true
+    run_diamond                           = true
+    run_motus                             = false
+    run_krona                             = true
+    krona_taxonomy_directory              = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
+    malt_save_reads                       = true
+    kraken2_save_reads                    = true
+    centrifuge_save_reads                 = true
+    diamond_save_reads                    = true
+}
+
+
+process {
+    withName: MALT_RUN {
+        maxForks = 1
+    }
+    withName: MEGAN_RMA2INFO {
+        maxForks = 1
+    }
+}

docs/usage.md

@@ -22,6 +22,10 @@ This samplesheet is then specified on the command line as follows:
 --input '[path to samplesheet file]' --databases '[path to database sheet file]'
 ```
 
+Note pipeline supports both CSV and PEP input sample sheets. Find out more [here](http://pep.databio.org/en/2.1.0/specification/).
+When using PEP as an input, the `samplesheet.csv` must be placed in the same folder
+as `config.yaml` file. A path to `samplesheet.csv` within the config must be absolute.
+
 ### Multiple runs of the same sample
 
 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:
@@ -277,6 +281,9 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
 - `test`
   - A profile with a complete configuration for automated testing
   - Includes links to test data so needs no other parameters
+- `test_pep`
+  - A profile with a complete configuration for running a pipeline with PEP as input
+  - Includes links to test data so needs no other parameters
 
 ### `-resume`
 

lib/WorkflowMain.groovy

@@ -75,7 +75,7 @@ class WorkflowMain {
 
         // Check input has been provided
         if (!params.input) {
-            log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"
+            log.error "Please provide an input samplesheet or PEP to the pipeline e.g. '--input samplesheet.csv'"
             System.exit(1)
         }
     }

modules.json

@@ -41,6 +41,14 @@
                     "branch": "master",
                     "git_sha": "3531824af826c16cd252bc5aa82ae169b244ebaa"
                 },
+                "eido/convert": {
+                    "branch": "master",
+                    "git_sha": "9764eef361ded86e9242075bda64c2662421386a"
+                },
+                "eido/validate": {
+                    "branch": "master",
+                    "git_sha": "38383cfaefc06cd35e25de99989a3e6ab9ed2980"
+                },
                 "fastp": {
                     "branch": "master",
                     "git_sha": "2c70c1c1951aaf884d2e8d8d9c871db79f7b35aa"

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: // 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
-    """
-}

modules/nf-core/modules/eido/convert/main.nf

@@ -0,0 +1,38 @@
+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
+    """
+}

modules/nf-core/modules/eido/convert/meta.yml

@@ -0,0 +1,39 @@
+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"

modules/nf-core/modules/eido/validate/main.nf

@@ -0,0 +1,33 @@
+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
+    """
+}

modules/nf-core/modules/eido/validate/meta.yml

@@ -0,0 +1,41 @@
+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"

nextflow.config

@@ -227,6 +227,7 @@ profiles {
     test_nopreprocessing    { includeConfig 'conf/test_nopreprocessing.config' }
     test_nothing            { includeConfig 'conf/test_nothing.config' }
     test_motus              { includeConfig 'conf/test_motus.config' }
+    test_pep                { includeConfig 'conf/test_pep.config' }
 }
 
 

nextflow_schema.json

@@ -10,13 +10,13 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["input", "databases", "outdir"],
+            "required": ["input", "outdir", "databases"],
             "properties": {
                 "input": {
                     "type": "string",
                     "format": "file-path",
                     "mimetype": "text/csv",
-                    "pattern": "^\\S+\\.csv$",
+                    "pattern": "^\\S+\\.(csv|yaml|yml)$",
                     "schema": "assets/schema_input.json",
                     "description": "Path to comma-separated file containing information about the samples and libraries/runs.",
                     "help_text": "You will need to create a design file with information about the samples and libraries/runs you want to running in your pipeline run. Use this parameter to specify its location. It has to be a comma-separated file with 6 columns, and a header row. See [usage docs](https://nf-co.re/taxprofiler/usage#samplesheet-input).",

subworkflows/local/input_check.nf

@@ -2,31 +2,41 @@
 // 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'
 
 workflow INPUT_CHECK {
     take:
-    samplesheet // file: /path/to/samplesheet.csv
+    samplesheet_or_pep_config // file: /path/to/samplesheet.csv or /path/to/pep/config.yaml
+    pep_input_base_dir
 
     main:
-    parsed_samplesheet = SAMPLESHEET_CHECK ( samplesheet )
+    ch_versions = Channel.empty()
-        .csv
+
+    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
         .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 }
 
@@ -34,7 +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 ] ]
@@ -64,11 +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 = [:]

workflows/taxprofiler.nf

@@ -17,7 +17,13 @@ def checkPathParamList = [ params.input, params.databases, params.hostremoval_re
 for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
 
 // Check mandatory parameters
-if (params.input    ) { ch_input     = file(params.input)     } else { exit 1, 'Input samplesheet not specified!' }
+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"
+}
+
 if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
 
 if (params.shortread_qc_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
@@ -98,7 +104,7 @@ workflow TAXPROFILER {
         SUBWORKFLOW: Read in samplesheet, validate and stage input files
     */
     INPUT_CHECK (
-        ch_input
+        ch_input, pep_input_base_dir
     )
     ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)