Merge branch 'nf-core:dev' into update_usage

.github/workflows/fix-linting.yml

@@ -34,9 +34,9 @@ jobs:
         id: prettier_status
         run: |
           if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "name=result::pass" >> $GITHUB_OUTPUT
+            echo "result=pass" >> $GITHUB_OUTPUT
           else
-            echo "name=result::fail" >> $GITHUB_OUTPUT
+            echo "result=fail" >> $GITHUB_OUTPUT
           fi
 
       - name: Run 'prettier --write'

.github/workflows/linting_comment.yml

@@ -18,7 +18,7 @@ jobs:
 
       - name: Get PR number
         id: pr_number
-        run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
+        run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
         uses: marocchino/sticky-pull-request-comment@v2

README.md

@@ -77,8 +77,6 @@ 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

@@ -1,55 +0,0 @@
-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

@@ -0,0 +1,233 @@
+#!/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.gz",
+        ".fasta.gz",
+        ".fna.gz",
+        ".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(",")]
+
+            # Check valid number of columns per row
+            if len(line_parsed) < len(HEADER):
+                print_error(
+                    "Invalid number of columns (minimum = {})!".format(len(HEADER)),
+                    "Line",
+                    line,
+                )
+            num_cols = len([x for x in line_parsed if x])
+            if num_cols < MIN_COLS:
+                print_error(
+                    "Invalid number of populated columns (minimum = {})!".format(MIN_COLS),
+                    "Line",
+                    line,
+                )
+
+            lspl = [line_parsed[i] for i in header_locs.values()]
+
+            ## 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

@@ -552,12 +552,4 @@ 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

@@ -60,10 +60,4 @@ 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_krakenuniq.config

@@ -63,10 +63,4 @@ 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

@@ -1,45 +0,0 @@
-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_bracken                           = 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
-        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
-    }
-    withName: MEGAN_RMA2INFO {
-        maxForks = 1
-    }
-}

docs/usage.md

@@ -12,7 +12,7 @@
 
 nf-core/taxprofiler can accept as input raw or preprocessed single- or paired-end short-read (e.g. Illumina) FASTQ files, long-read FASTQ files (e.g. Oxford Nanopore), or FASTA sequences (available for a subset of profilers).
 
-> ⚠️ Input FASTQ files _must_ be gzipped, while FASTA files may optionally be uncompressed (although this is not recommended)
+> ⚠️ Input FASTQ and FASTA files _must_ be gzipped
 
 You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 6 columns, and a header row as shown in the examples below. Furthermother, nf-core/taxprofiler also requires a second comma-separated file of 3 columns with a header row as in the examples below.
 
@@ -22,10 +22,6 @@ 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:
@@ -271,9 +267,6 @@ 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
 - `docker`
   - A generic configuration profile to be used with [Docker](https://docker.com/)
 - `singularity`

lib/WorkflowMain.groovy

@@ -72,7 +72,7 @@ class WorkflowMain {
         NfcoreTemplate.checkConfigProvided(workflow, log)
 
         // Check that conda channels are set-up correctly
-        if (params.enable_conda) {
+        if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
             Utils.checkCondaChannels(log)
         }
 
@@ -81,7 +81,7 @@ class WorkflowMain {
 
         // Check input has been provided
         if (!params.input) {
-            log.error "Please provide an input samplesheet or PEP to the pipeline e.g. '--input samplesheet.csv'"
+            log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"
             System.exit(1)
         }
     }

modules.json

@@ -52,7 +52,7 @@
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "diamond/blastx": {
@@ -60,16 +60,6 @@
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
                         "installed_by": ["modules"]
                     },
-                    "eido/convert": {
-                        "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed_by": ["modules"]
-                    },
-                    "eido/validate": {
-                        "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed_by": ["modules"]
-                    },
                     "falco": {
                         "branch": "master",
                         "git_sha": "fc959214036403ad83efe7a41d43d0606c445cda",
@@ -83,7 +73,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "filtlong": {
@@ -128,7 +118,7 @@
                     },
                     "krakenuniq/preloadedkrakenuniq": {
                         "branch": "master",
-                        "git_sha": "05649975c6611c6e007537a7984e186e12ae03af",
+                        "git_sha": "a6eb17f65b3ee5761c25c075a6166c9f76733cee",
                         "installed_by": ["modules"]
                     },
                     "krona/ktimporttaxonomy": {
@@ -183,7 +173,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "porechop/porechop": {

modules/local/samplesheet_check.nf

@@ -0,0 +1,27 @@
+process SAMPLESHEET_CHECK {
+    tag "$samplesheet"
+
+    conda "conda-forge::python=3.8.3"
+    container "${ 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/custom/dumpsoftwareversions/main.nf

@@ -2,7 +2,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
+    conda "bioconda::multiqc=1.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
         'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"

modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py

@@ -1,11 +1,17 @@
 #!/usr/bin/env python
 
-import yaml
+
+"""Provide functions to merge multiple versions.yml files."""
+
+
 import platform
 from textwrap import dedent
 
+import yaml
+
 
 def _make_versions_html(versions):
+    """Generate a tabular HTML output of all versions for MultiQC."""
     html = [
         dedent(
             """\\
@@ -44,47 +50,53 @@ def _make_versions_html(versions):
     return "\\n".join(html)
 
 
-versions_this_module = {}
-versions_this_module["${task.process}"] = {
-    "python": platform.python_version(),
-    "yaml": yaml.__version__,
-}
+def main():
+    """Load all version files and generate merged output."""
+    versions_this_module = {}
+    versions_this_module["${task.process}"] = {
+        "python": platform.python_version(),
+        "yaml": yaml.__version__,
+    }
 
-with open("$versions") as f:
-    versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
+    with open("$versions") as f:
+        versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
 
-# aggregate versions by the module name (derived from fully-qualified process name)
-versions_by_module = {}
-for process, process_versions in versions_by_process.items():
-    module = process.split(":")[-1]
-    try:
-        if versions_by_module[module] != process_versions:
-            raise AssertionError(
-                "We assume that software versions are the same between all modules. "
-                "If you see this error-message it means you discovered an edge-case "
-                "and should open an issue in nf-core/tools. "
-            )
-    except KeyError:
-        versions_by_module[module] = process_versions
+    # aggregate versions by the module name (derived from fully-qualified process name)
+    versions_by_module = {}
+    for process, process_versions in versions_by_process.items():
+        module = process.split(":")[-1]
+        try:
+            if versions_by_module[module] != process_versions:
+                raise AssertionError(
+                    "We assume that software versions are the same between all modules. "
+                    "If you see this error-message it means you discovered an edge-case "
+                    "and should open an issue in nf-core/tools. "
+                )
+        except KeyError:
+            versions_by_module[module] = process_versions
 
-versions_by_module["Workflow"] = {
-    "Nextflow": "$workflow.nextflow.version",
-    "$workflow.manifest.name": "$workflow.manifest.version",
-}
+    versions_by_module["Workflow"] = {
+        "Nextflow": "$workflow.nextflow.version",
+        "$workflow.manifest.name": "$workflow.manifest.version",
+    }
 
-versions_mqc = {
-    "id": "software_versions",
-    "section_name": "${workflow.manifest.name} Software Versions",
-    "section_href": "https://github.com/${workflow.manifest.name}",
-    "plot_type": "html",
-    "description": "are collected at run time from the software output.",
-    "data": _make_versions_html(versions_by_module),
-}
+    versions_mqc = {
+        "id": "software_versions",
+        "section_name": "${workflow.manifest.name} Software Versions",
+        "section_href": "https://github.com/${workflow.manifest.name}",
+        "plot_type": "html",
+        "description": "are collected at run time from the software output.",
+        "data": _make_versions_html(versions_by_module),
+    }
 
-with open("software_versions.yml", "w") as f:
-    yaml.dump(versions_by_module, f, default_flow_style=False)
-with open("software_versions_mqc.yml", "w") as f:
-    yaml.dump(versions_mqc, f, default_flow_style=False)
+    with open("software_versions.yml", "w") as f:
+        yaml.dump(versions_by_module, f, default_flow_style=False)
+    with open("software_versions_mqc.yml", "w") as f:
+        yaml.dump(versions_mqc, f, default_flow_style=False)
 
-with open("versions.yml", "w") as f:
-    yaml.dump(versions_this_module, f, default_flow_style=False)
+    with open("versions.yml", "w") as f:
+        yaml.dump(versions_this_module, f, default_flow_style=False)
+
+
+if __name__ == "__main__":
+    main()

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

@@ -1,38 +0,0 @@
-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/eido/convert/meta.yml

@@ -1,39 +0,0 @@
-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/eido/validate/main.nf

@@ -1,33 +0,0 @@
-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/eido/validate/meta.yml

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

modules/nf-core/fastqc/main.nf

@@ -2,7 +2,7 @@ process FASTQC {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
+    conda "bioconda::fastqc=0.11.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
         'quay.io/biocontainers/fastqc:0.11.9--0' }"
@@ -20,30 +20,22 @@ process FASTQC {
 
     script:
     def args = task.ext.args ?: ''
-    // Add soft-links to original FastQs for consistent naming in pipeline
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if (meta.single_end) {
-        """
-        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
-        fastqc $args --threads $task.cpus ${prefix}.fastq.gz
+    // Make list of old name and new name pairs to use for renaming in the bash while loop
+    def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
+    def rename_to = old_new_pairs*.join(' ').join(' ')
+    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+    """
+    printf "%s %s\\n" $rename_to | while read old_name new_name; do
+        [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
+    done
+    fastqc $args --threads $task.cpus $renamed_files
 
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-        END_VERSIONS
-        """
-    } else {
-        """
-        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
-        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
-        fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-        END_VERSIONS
-        """
-    }
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+    END_VERSIONS
+    """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf

@@ -2,10 +2,10 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::krakenuniq=1.0.0" : null)
+    conda "bioconda::krakenuniq=1.0.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/krakenuniq:1.0.0--pl5321h19e8d03_0':
-        'quay.io/biocontainers/krakenuniq:1.0.0--pl5321h19e8d03_0' }"
+        'https://depot.galaxyproject.org/singularity/krakenuniq:1.0.2--pl5321h19e8d03_0':
+        'quay.io/biocontainers/krakenuniq:1.0.2--pl5321h19e8d03_0' }"
 
     input:
     tuple val(meta), path(fastqs)

modules/nf-core/multiqc/main.nf

@@ -1,7 +1,7 @@
 process MULTIQC {
     label 'process_single'
 
-    conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
+    conda "bioconda::multiqc=1.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
         'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"

nextflow.config

@@ -39,7 +39,6 @@ params {
     validate_params            = true
     show_hidden_params         = false
     schema_ignore_params       = 'genomes,fasta'
-    enable_conda               = false
 
 
     // Config options
@@ -182,7 +181,6 @@ try {
 profiles {
     debug { process.beforeScript = 'echo $HOSTNAME' }
     conda {
-        params.enable_conda    = true
         conda.enabled          = true
         docker.enabled         = false
         singularity.enabled    = false
@@ -191,7 +189,6 @@ profiles {
         charliecloud.enabled   = false
     }
     mamba {
-        params.enable_conda    = true
         conda.enabled          = true
         conda.useMamba         = true
         docker.enabled         = false
@@ -252,7 +249,6 @@ profiles {
     test_nothing            { includeConfig 'conf/test_nothing.config' }
     test_motus              { includeConfig 'conf/test_motus.config' }
     test_krakenuniq         { includeConfig 'conf/test_krakenuniq.config' }
-    test_pep                { includeConfig 'conf/test_pep.config' }
 }
 
 

nextflow_schema.json

@@ -696,12 +696,6 @@
                     "description": "Show all params when using `--help`",
                     "hidden": true,
                     "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
-                },
-                "enable_conda": {
-                    "type": "boolean",
-                    "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
-                    "hidden": true,
-                    "fa_icon": "fas fa-bacon"
                 }
             }
         },

subworkflows/local/input_check.nf

@@ -2,62 +2,36 @@
 // Check input samplesheet and get read channels
 //
 
-include { EIDO_VALIDATE } from '../../modules/nf-core/eido/validate/main'
-include { EIDO_CONVERT } from '../../modules/nf-core/eido/convert/main'
+include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check'
 
 workflow INPUT_CHECK {
     take:
-    samplesheet_or_pep_config // file: /path/to/samplesheet.csv or /path/to/pep/config.yaml
-    pep_input_base_dir
+    samplesheet // file: /path/to/samplesheet.csv
 
     main:
-    ch_versions = Channel.empty()
-
-    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
+    parsed_samplesheet = SAMPLESHEET_CHECK ( samplesheet )
+        .csv
         .splitCsv ( header:true, sep:',' )
-        .map { check_missing_and_singleend_autodetect(it) }
         .branch {
             fasta: it['fasta'] != ''
             nanopore: it['instrument_platform'] == 'OXFORD_NANOPORE'
             fastq: true
         }
 
-    ch_parsed_samplesheet.fastq
+    fastq = parsed_samplesheet.fastq
         .map { create_fastq_channel(it) }
-        .set { fastq }
 
-    ch_parsed_samplesheet.nanopore
+    nanopore = parsed_samplesheet.nanopore
         .map { create_fastq_channel(it) }
-        .set { nanopore }
 
-    ch_parsed_samplesheet.fasta
+    fasta = parsed_samplesheet.fasta
         .map { create_fasta_channel(it) }
-        .set { fasta }
 
     emit:
     fastq = fastq ?: []                       // channel: [ val(meta), [ reads ] ]
     nanopore = nanopore ?: []                 // channel: [ val(meta), [ reads ] ]
     fasta = fasta ?: []                       // channel: [ val(meta), fasta ]
-    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
+    versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]
 }
 
 // Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
@@ -87,12 +61,11 @@ 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

@@ -20,9 +20,8 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
 // Check mandatory parameters
 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"
+    exit 1, "Input samplesheet not specified"
 }
 
 if (params.databases) { ch_databases = file(params.databases, checkIfExists: true) } else { exit 1, 'Input database sheet not specified!' }
@@ -115,7 +114,7 @@ workflow TAXPROFILER {
         SUBWORKFLOW: Read in samplesheet, validate and stage input files
     */
     INPUT_CHECK (
-        ch_input, pep_input_base_dir
+        ch_input
     )
     ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
 
@@ -251,7 +250,7 @@ workflow TAXPROFILER {
     */
 
     CUSTOM_DUMPSOFTWAREVERSIONS (
-        ch_versions.unique{ it.text }.collectFile(name: 'collated_versions.yml')
+        ch_versions.unique().collectFile(name: 'collated_versions.yml')
     )