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Added ToulligQC in raw read QC step#287

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yuukiiwa merged 6 commits intonf-core:add_template_to_dev_firstfrom
Salome-Brunon:Salome-Brunon-add_toulligqc
May 15, 2025
Merged

Added ToulligQC in raw read QC step#287
yuukiiwa merged 6 commits intonf-core:add_template_to_dev_firstfrom
Salome-Brunon:Salome-Brunon-add_toulligqc

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@Salome-Brunon Salome-Brunon commented Nov 22, 2024

Added ToulligQC to pipeline for raw read QC step.
ToulligQC was importing from the nf-core module library.

@yuukiiwa yuukiiwa changed the base branch from dev to add_template_to_dev_first May 15, 2025 11:22
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github-actions bot commented May 15, 2025 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 33ed088

+| ✅ 177 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗ 119 tests had warnings |!
-| ❌   1 tests failed       |-
Details

❌ Test failures:

  • schema_params - Param skip_toulligqc from nextflow config not found in nextflow_schema.json

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.1.0
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "

    \n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-nanoseq_logo_dark.png">\n <img alt="nf-core/nanoseq" src="docs/images/nf-core-nanoseq_logo_light.png">\n \n

    \n\nGitHub Actions CI Status\nGitHub Actions Linting StatusAWS CICite with Zenodo\nnf-test\n\nNextflow\nrun with conda\nrun with docker\nrun with singularity\nLaunch on Seqera Platform\n\nGet help on SlackFollow on TwitterFollow on MastodonWatch on YouTube\n\n## Introduction\n\nnf-core/nanoseq is a bioinformatics pipeline that ...\n\n TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n\n\n Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. \n Fill in short bullet-pointed list of the default steps in the pipeline 1. Read QC (FastQC)2. Present QC for raw reads (MultiQC)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.\n\n Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\nsamplesheet.csv:\n\ncsv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n\n\nNow, you can run the pipeline using:\n\n update the following command to include all required parameters for a minimal example \n\nbash\nnextflow run nf-core/nanoseq \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <OUTDIR>\n\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.\n\nFor more details and further functionality, please refer to the usage documentation and the parameter documentation.\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\noutput documentation.\n\n## Credits\n\nnf-core/nanoseq was originally written by Chelsea Sawyer, Yuk Kei Wan.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n If applicable, make list of people who have also contributed \n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the contributing guidelines.\n\nFor further information or help, don't hesitate to get in touch on the Slack #nanoseq channel (you can join with this invite).\n\n## Citations\n\n Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. \n If you use nf-core/nanoseq for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX \n\n Add bibliography of tools and data used in your pipeline \n\nAn extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.\n\nYou can cite the nf-core publication as follows:\n\n> The nf-core framework for community-curated bioinformatics pipelines.\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.\n",
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • schema_lint - Schema $id should be https://raw.githubusercontent.com/nf-core/nanoseq/main/nextflow_schema.json or https://raw.githubusercontent.com/nf-core/nanoseq/master/nextflow_schema.json.
    Found https://raw.githubusercontent.com/nf-core/nanoseq//nextflow_schema.json
  • schema_description - Ungrouped param in schema: protocol
  • schema_description - Ungrouped param in schema: genome
  • schema_description - Ungrouped param in schema: fasta
  • schema_description - Ungrouped param in schema: gtf
  • schema_description - Ungrouped param in schema: input_path
  • schema_description - Ungrouped param in schema: input_path_file_type
  • schema_description - Ungrouped param in schema: bedmethyl_out
  • schema_description - Ungrouped param in schema: flowcell
  • schema_description - Ungrouped param in schema: kit
  • schema_description - Ungrouped param in schema: barcode_kit
  • schema_description - Ungrouped param in schema: barcode_both_ends
  • schema_description - Ungrouped param in schema: trim_barcodes
  • schema_description - Ungrouped param in schema: dorado_model
  • schema_description - Ungrouped param in schema: doraro_modification
  • schema_description - Ungrouped param in schema: dorado_device
  • schema_description - Ungrouped param in schema: qcat_min_score
  • schema_description - Ungrouped param in schema: qcat_detect_middle
  • schema_description - Ungrouped param in schema: skip_basecalling
  • schema_description - Ungrouped param in schema: skip_demultiplexing
  • schema_description - Ungrouped param in schema: nanolyse_fasta
  • schema_description - Ungrouped param in schema: run_nanolyse
  • schema_description - Ungrouped param in schema: aligner
  • schema_description - Ungrouped param in schema: stranded
  • schema_description - Ungrouped param in schema: save_align_intermeds
  • schema_description - Ungrouped param in schema: skip_alignment
  • schema_description - Ungrouped param in schema: call_variants
  • schema_description - Ungrouped param in schema: variant_caller
  • schema_description - Ungrouped param in schema: structural_variant_caller
  • schema_description - Ungrouped param in schema: split_mnps
  • schema_description - Ungrouped param in schema: phase_vcf
  • schema_description - Ungrouped param in schema: skip_vc
  • schema_description - Ungrouped param in schema: skip_sv
  • schema_description - Ungrouped param in schema: deepvariant_gpu
  • schema_description - Ungrouped param in schema: skip_bigbed
  • schema_description - Ungrouped param in schema: skip_bigwig
  • schema_description - Ungrouped param in schema: quantification_method
  • schema_description - Ungrouped param in schema: skip_quantification
  • schema_description - Ungrouped param in schema: skip_differential_analysis
  • schema_description - Ungrouped param in schema: skip_modification_analysis
  • schema_description - Ungrouped param in schema: skip_xpore
  • schema_description - Ungrouped param in schema: skip_m6anet
  • schema_description - Ungrouped param in schema: skip_fusion_analysis
  • schema_description - Ungrouped param in schema: jaffal_ref_dir
  • schema_description - Ungrouped param in schema: skip_qc
  • schema_description - Ungrouped param in schema: skip_nanoplot
  • schema_description - Ungrouped param in schema: skip_fastqc
  • schema_description - Ungrouped param in schema: skip_multiqc
  • schema_description - Ungrouped param in schema: igenomes_base
  • schema_description - Ungrouped param in schema: igenomes_ignore
  • schema_description - Ungrouped param in schema: multiqc_config
  • schema_description - Ungrouped param in schema: multiqc_title
  • schema_description - Ungrouped param in schema: multiqc_logo
  • schema_description - Ungrouped param in schema: max_multiqc_email_size
  • schema_description - Ungrouped param in schema: multiqc_methods_description
  • schema_description - Ungrouped param in schema: publish_dir_mode
  • schema_description - Ungrouped param in schema: email
  • schema_description - Ungrouped param in schema: email_on_fail
  • schema_description - Ungrouped param in schema: plaintext_email
  • schema_description - Ungrouped param in schema: monochrome_logs
  • schema_description - Ungrouped param in schema: hook_url
  • schema_description - Ungrouped param in schema: pipelines_testdata_base_path
  • schema_description - Ungrouped param in schema: config_profile_name
  • schema_description - Ungrouped param in schema: config_profile_description
  • schema_description - Ungrouped param in schema: custom_config_version
  • schema_description - Ungrouped param in schema: custom_config_base
  • schema_description - Ungrouped param in schema: config_profile_contact
  • schema_description - Ungrouped param in schema: config_profile_url
  • local_component_structure - samplesheet_check.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - m6anet_inference.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - f5c_index_eventalign.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - get_nanolyse_fasta.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - xpore_dataprep.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - pepper_margin_deepvariant.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - fast5_to_pod5.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - dorado_aligner.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - dexseq.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - gtf2bed.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - modkit_pileup.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - blue-crab.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - dorado_basecaller.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bambu.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - nanopolish_index_eventalign.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - jaffal.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - xpore_diffmod.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bam_rename.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - multiqc.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - deseq2.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - get_chrom_sizes.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - get_jaffal_ref.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - get_test_data.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - m6anet_dataprep.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - medaka_variant.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - clair3.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - qcfastq_nanoplot_fastqc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - short_variant_calling.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - bedtools_ucsc_bigbed.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - bedtools_ucsc_bigwig.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - rna_fusions_jaffal.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - structural_variant_calling.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - differential_deseq2_dexseq.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - rna_modifications_xpore_m6anet.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - quantify_stringtie_featurecounts.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - align_minimap2.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - align_graphmap2.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.1
  • Run at 2025-05-15 11:30:51

yuukiiwa
yuukiiwa approved these changes May 15, 2025
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all test but linting pass. will fix schema in after merging

@yuukiiwa yuukiiwa merged commit e49e12a into nf-core:add_template_to_dev_first May 15, 2025
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@yuukiiwa yuukiiwa yuukiiwa approved these changes

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@Salome-Brunon @yuukiiwa