│ :city_sunset: GitHub Actions CI Status :city_sunset: GitHub Actions Linting Status :city_sunset: AWS CI :city_sunset: Cite with Zenodo :city_sunset: nf-test :city_sunset: Nextflow :city_sunset: run with conda :city_sunset: run with docker :city_sunset: run with singularity :city_sunset: Launch on Seqera Plat │
│ <img alt="nf-core/multiplesequencealign" src="docs/images/nf-core-multiplesequencealign_logo_light.png">\n  \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n## Introduction\n\nnf-core/multiplesequencealign 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 \n\n1. Read QC             │
│ (FastQC)\n2. 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/multiplesequencealign \\\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/multiplesequencealign was originally written by Luisa Santus, Jose Espinosa Carrasco.\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 #multiplesequencealign 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/multiplesequencealign 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",