mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-13 05:53:09 +00:00
Template update for nf-core/tools version 2.7.2
This commit is contained in:
parent
36f3b5723b
commit
ab591e01ff
12 changed files with 75 additions and 81 deletions
4
.github/workflows/fix-linting.yml
vendored
4
.github/workflows/fix-linting.yml
vendored
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@ -34,9 +34,9 @@ jobs:
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id: prettier_status
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run: |
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if prettier --check ${GITHUB_WORKSPACE}; then
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echo "name=result::pass" >> $GITHUB_OUTPUT
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echo "result=pass" >> $GITHUB_OUTPUT
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else
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echo "name=result::fail" >> $GITHUB_OUTPUT
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echo "result=fail" >> $GITHUB_OUTPUT
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fi
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- name: Run 'prettier --write'
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2
.github/workflows/linting_comment.yml
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2
.github/workflows/linting_comment.yml
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@ -18,7 +18,7 @@ jobs:
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- name: Get PR number
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id: pr_number
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run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
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run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
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- name: Post PR comment
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uses: marocchino/sticky-pull-request-comment@v2
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@ -72,7 +72,7 @@ class WorkflowMain {
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NfcoreTemplate.checkConfigProvided(workflow, log)
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// Check that conda channels are set-up correctly
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if (params.enable_conda) {
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if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
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Utils.checkCondaChannels(log)
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}
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@ -7,17 +7,17 @@
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"nf-core": {
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"custom/dumpsoftwareversions": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"fastqc": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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}
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}
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@ -2,7 +2,7 @@ process SAMPLESHEET_CHECK {
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tag "$samplesheet"
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label 'process_single'
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conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
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conda "conda-forge::python=3.8.3"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/python:3.8.3' :
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'quay.io/biocontainers/python:3.8.3' }"
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@ -2,7 +2,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
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label 'process_single'
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// Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
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conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
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conda "bioconda::multiqc=1.13"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
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'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
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87
modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
generated
Normal file → Executable file
87
modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
generated
Normal file → Executable file
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@ -1,5 +1,9 @@
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#!/usr/bin/env python
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"""Provide functions to merge multiple versions.yml files."""
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import platform
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from textwrap import dedent
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@ -7,6 +11,7 @@ import yaml
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def _make_versions_html(versions):
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"""Generate a tabular HTML output of all versions for MultiQC."""
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html = [
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dedent(
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"""\\
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@ -45,47 +50,53 @@ def _make_versions_html(versions):
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return "\\n".join(html)
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versions_this_module = {}
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versions_this_module["${task.process}"] = {
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"python": platform.python_version(),
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"yaml": yaml.__version__,
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}
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def main():
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"""Load all version files and generate merged output."""
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versions_this_module = {}
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versions_this_module["${task.process}"] = {
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"python": platform.python_version(),
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"yaml": yaml.__version__,
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}
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with open("$versions") as f:
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versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
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with open("$versions") as f:
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versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
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# aggregate versions by the module name (derived from fully-qualified process name)
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versions_by_module = {}
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for process, process_versions in versions_by_process.items():
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module = process.split(":")[-1]
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try:
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if versions_by_module[module] != process_versions:
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raise AssertionError(
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"We assume that software versions are the same between all modules. "
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"If you see this error-message it means you discovered an edge-case "
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"and should open an issue in nf-core/tools. "
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)
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except KeyError:
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versions_by_module[module] = process_versions
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# aggregate versions by the module name (derived from fully-qualified process name)
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versions_by_module = {}
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for process, process_versions in versions_by_process.items():
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module = process.split(":")[-1]
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try:
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if versions_by_module[module] != process_versions:
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raise AssertionError(
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"We assume that software versions are the same between all modules. "
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"If you see this error-message it means you discovered an edge-case "
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"and should open an issue in nf-core/tools. "
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)
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except KeyError:
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versions_by_module[module] = process_versions
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versions_by_module["Workflow"] = {
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"Nextflow": "$workflow.nextflow.version",
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"$workflow.manifest.name": "$workflow.manifest.version",
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}
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versions_by_module["Workflow"] = {
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"Nextflow": "$workflow.nextflow.version",
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"$workflow.manifest.name": "$workflow.manifest.version",
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}
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versions_mqc = {
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"id": "software_versions",
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"section_name": "${workflow.manifest.name} Software Versions",
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"section_href": "https://github.com/${workflow.manifest.name}",
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"plot_type": "html",
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"description": "are collected at run time from the software output.",
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"data": _make_versions_html(versions_by_module),
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}
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versions_mqc = {
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"id": "software_versions",
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"section_name": "${workflow.manifest.name} Software Versions",
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"section_href": "https://github.com/${workflow.manifest.name}",
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"plot_type": "html",
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"description": "are collected at run time from the software output.",
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"data": _make_versions_html(versions_by_module),
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}
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with open("software_versions.yml", "w") as f:
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yaml.dump(versions_by_module, f, default_flow_style=False)
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with open("software_versions_mqc.yml", "w") as f:
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yaml.dump(versions_mqc, f, default_flow_style=False)
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with open("software_versions.yml", "w") as f:
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yaml.dump(versions_by_module, f, default_flow_style=False)
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with open("software_versions_mqc.yml", "w") as f:
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yaml.dump(versions_mqc, f, default_flow_style=False)
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with open("versions.yml", "w") as f:
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yaml.dump(versions_this_module, f, default_flow_style=False)
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with open("versions.yml", "w") as f:
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yaml.dump(versions_this_module, f, default_flow_style=False)
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if __name__ == "__main__":
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main()
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38
modules/nf-core/fastqc/main.nf
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38
modules/nf-core/fastqc/main.nf
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@ -2,7 +2,7 @@ process FASTQC {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
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conda "bioconda::fastqc=0.11.9"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
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'quay.io/biocontainers/fastqc:0.11.9--0' }"
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script:
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def args = task.ext.args ?: ''
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// Add soft-links to original FastQs for consistent naming in pipeline
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def prefix = task.ext.prefix ?: "${meta.id}"
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if (meta.single_end) {
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"""
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[ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
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fastqc $args --threads $task.cpus ${prefix}.fastq.gz
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// Make list of old name and new name pairs to use for renaming in the bash while loop
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def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
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def rename_to = old_new_pairs*.join(' ').join(' ')
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def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
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"""
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printf "%s %s\\n" $rename_to | while read old_name new_name; do
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[ -f "\${new_name}" ] || ln -s \$old_name \$new_name
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done
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fastqc $args --threads $task.cpus $renamed_files
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
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END_VERSIONS
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"""
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} else {
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"""
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[ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
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[ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
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fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
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END_VERSIONS
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"""
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}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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2
modules/nf-core/multiqc/main.nf
generated
2
modules/nf-core/multiqc/main.nf
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process MULTIQC {
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label 'process_single'
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conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
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conda "bioconda::multiqc=1.13"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
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'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
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@ -39,7 +39,6 @@ params {
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validate_params = true
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show_hidden_params = false
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schema_ignore_params = 'genomes'
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enable_conda = false
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// Config options
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profiles {
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debug { process.beforeScript = 'echo $HOSTNAME' }
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conda {
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params.enable_conda = true
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conda.enabled = true
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docker.enabled = false
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singularity.enabled = false
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@ -90,7 +88,6 @@ profiles {
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charliecloud.enabled = false
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}
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mamba {
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params.enable_conda = true
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conda.enabled = true
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conda.useMamba = true
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docker.enabled = false
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@ -263,12 +263,6 @@
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"description": "Show all params when using `--help`",
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"hidden": true,
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"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."
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},
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"enable_conda": {
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"type": "boolean",
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"description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
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"hidden": true,
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"fa_icon": "fas fa-bacon"
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}
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}
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}
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@ -82,7 +82,7 @@ workflow TAXPROFILER {
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ch_versions = ch_versions.mix(FASTQC.out.versions.first())
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CUSTOM_DUMPSOFTWAREVERSIONS (
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ch_versions.unique{ it.text }.collectFile(name: 'collated_versions.yml')
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ch_versions.unique().collectFile(name: 'collated_versions.yml')
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)
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//
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