Fixed linting tests

#!/usr/bin/env python

from __future__ import print_function

import os

results = {}

version_files = [x for x in os.listdir(".") if x.endswith(".version.txt")]

for version_file in version_files:

    software = version_file.replace(".version.txt", "")

    if software == "pipeline":

        software = "nf-core/cutandrun"

    with open(version_file) as fin:

        version = fin.read().strip()

    results[software] = version

# Dump to YAML

print(

    """

id: 'software_versions'

section_name: 'nf-core/cutandrun Software Versions'

section_href: 'https://github.com/nf-core/cutandrun'

plot_type: 'html'

description: 'are collected at run time from the software output.'

data: |

    <dl class="dl-horizontal">

"""

)

for k, v in sorted(results.items()):

    print("        <dt>{}</dt><dd><samp>{}</samp></dd>".format(k, v))

print("    </dl>")

# Write out as tsv file:

with open("software_versions.tsv", "w") as f:

    for k, v in sorted(results.items()):

        f.write("{}\t{}\n".format(k, v))

// Import generic module functions

include { initOptions; saveFiles } from './common/functions'

params.options = [:]

options        = initOptions(params.options)

process GET_SOFTWARE_VERSIONS {

    publishDir "${params.outdir}",

        mode: params.publish_dir_mode,

        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) }

    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)

    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

        container "https://depot.galaxyproject.org/singularity/python:3.8.3"

    } else {

        container "quay.io/biocontainers/python:3.8.3"

    }

    input:

    path versions

    output:

    path "software_versions.tsv"     , emit: tsv

    path 'software_versions_mqc.yaml', emit: yaml

    script: // This script is bundled with the pipeline, in nf-core/cutandrun/bin/

    """

    echo $workflow.manifest.version > pipeline.version.txt

    echo $workflow.nextflow.version > nextflow.version.txt

    scrape_software_versions.py &> software_versions_mqc.yaml

    """

}

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