code refactoring : split into modules #6

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Char-Al wants to merge 10 commits into SimCab-CHU:main from Char-Al:main

.editorconfig

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+    root = true
+    [*]
+    charset = utf-8
+    end_of_line = lf
+    insert_final_newline = true
+    trim_trailing_whitespace = true
+    indent_size = 4
+    indent_style = space
+    [*.{md,yml,yaml,html,css,scss,js}]
+    indent_size = 2
+    # These files are edited and tested upstream in nf-core/modules
+    [/modules/nf-core/**]
+    charset = unset
+    end_of_line = unset
+    insert_final_newline = unset
+    trim_trailing_whitespace = unset
+    indent_style = unset
+    [/subworkflows/nf-core/**]
+    charset = unset
+    end_of_line = unset
+    insert_final_newline = unset
+    trim_trailing_whitespace = unset
+    indent_style = unset
+    # ignore python and markdown
+    [*.{py,md}]
+    indent_style = unset

.gitattributes

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+    *.config linguist-language=nextflow
+    *.nf.test linguist-language=nextflow
+    modules/nf-core/** linguist-generated
+    subworkflows/nf-core/** linguist-generated

.gitignore

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-    # Prerequisites
-    *.d
-    # Object files
-    *.o
-    *.ko
-    *.obj
-    *.elf
-    # Linker output
-    *.ilk
-    *.map
-    *.exp
-    # Precompiled Headers
-    *.gch
-    *.pch
-    # Libraries
-    *.lib
-    *.a
-    *.la
-    *.lo
-    # Shared objects (inc. Windows DLLs)
-    *.dll
-    *.so
-    *.so.*
-    *.dylib
-    # Executables
-    *.exe
-    *.out
-    *.app
-    *.i*86
-    *.x86_64
-    *.hex
-    # Debug files
-    *.dSYM/
-    *.su
-    *.idb
-    *.pdb
-    # Kernel Module Compile Results
-    *.mod*
-    *.cmd
-    .tmp_versions/
-    modules.order
-    Module.symvers
-    Mkfile.old
-    dkms.conf
+    .nextflow*
+    work/
+    data/
+    results/
+    .DS_Store
+    testing/
+    testing*
+    *.pyc
+    null/
+    FETCH_HEAD

.nf-core.yml

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+    bump_version: null
+    lint:
+      files_exist:
+      - .github/ISSUE_TEMPLATE/bug_report.yml
+      - .github/ISSUE_TEMPLATE/feature_request.yml
+      - .github/PULL_REQUEST_TEMPLATE.md
+      - .github/CONTRIBUTING.md
+      - .github/.dockstore.yml
+      - .github/workflows/branch.yml
+      - .github/workflows/ci.yml
+      - .github/workflows/linting_comment.yml
+      - .github/workflows/linting.yml
+      - assets/email_template.html
+      - assets/sendmail_template.txt
+      - assets/email_template.txt
+      - .github/ISSUE_TEMPLATE/bug_report.yml
+      - .github/ISSUE_TEMPLATE/feature_request.yml
+      - .github/PULL_REQUEST_TEMPLATE.md
+      - .github/CONTRIBUTING.md
+      - .github/.dockstore.yml
+      - .github/workflows/branch.yml
+      - .github/workflows/ci.yml
+      - .github/workflows/linting_comment.yml
+      - .github/workflows/linting.yml
+      - assets/email_template.html
+      - assets/sendmail_template.txt
+      - assets/email_template.txt
+      - CODE_OF_CONDUCT.md
+      - assets/nf-core-mobict_logo_light.png
+      - docs/images/nf-core-mobict_logo_light.png
+      - docs/images/nf-core-mobict_logo_dark.png
+      - .github/ISSUE_TEMPLATE/config.yml
+      - .github/workflows/awstest.yml
+      - .github/workflows/awsfulltest.yml
+      files_unchanged:
+      - .github/ISSUE_TEMPLATE/bug_report.yml
+      - .github/ISSUE_TEMPLATE/config.yml
+      - .github/ISSUE_TEMPLATE/feature_request.yml
+      - .github/PULL_REQUEST_TEMPLATE.md
+      - .github/workflows/branch.yml
+      - .github/workflows/linting_comment.yml
+      - .github/workflows/linting.yml
+      - .github/CONTRIBUTING.md
+      - .github/.dockstore.yml
+      - .github/CONTRIBUTING.md
+      - .prettierignore
+      - .prettierignore
+      - .prettierignore
+      - .github/ISSUE_TEMPLATE/bug_report.yml
+      - .github/ISSUE_TEMPLATE/config.yml
+      - .github/ISSUE_TEMPLATE/feature_request.yml
+      - .github/PULL_REQUEST_TEMPLATE.md
+      - .github/workflows/branch.yml
+      - .github/workflows/linting_comment.yml
+      - .github/workflows/linting.yml
+      - .github/CONTRIBUTING.md
+      - .github/.dockstore.yml
+      - .github/CONTRIBUTING.md
+      - .prettierignore
+      - .prettierignore
+      - .prettierignore
+      - CODE_OF_CONDUCT.md
+      - assets/nf-core-mobict_logo_light.png
+      - docs/images/nf-core-mobict_logo_light.png
+      - docs/images/nf-core-mobict_logo_dark.png
+      - .github/ISSUE_TEMPLATE/bug_report.yml
+      multiqc_config:
+      - report_comment
+      nextflow_config:
+      - manifest.name
+      - manifest.homePage
+      - validation.help.beforeText
+      - validation.help.afterText
+      - validation.summary.beforeText
+      - validation.summary.afterText
+      readme:
+      - nextflow_badge
+      - nextflow_badge
+      - nextflow_badge
+    nf_core_version: 3.0.2
+    org_path: null
+    repository_type: pipeline
+    template:
+      author: Simon Cabello-Aguilar
+      description: ctDNA Analysis pipeline
+      force: true
+      is_nfcore: false
+      name: mobiCT
+      org: mobidic
+      outdir: .
+      skip_features:
+      - github
+      - ci
+      - github_badges
+      - gitpod
+      - codespaces
+      - fastqc
+      - email
+      - adaptivecard
+      - slackreport
+      - seqera_platform
+      version: 1.0.0dev
+    update: null

.pre-commit-config.yaml

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+    repos:
+      - repo: https://github.com/pre-commit/mirrors-prettier
+        rev: "v3.1.0"
+        hooks:
+          - id: prettier
+            additional_dependencies:
+              - prettier@3.2.5
+      - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+        rev: "3.0.3"
+        hooks:
+          - id: editorconfig-checker
+            alias: ec

.prettierignore

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+    .nextflow*
+    work/
+    data/
+    results/
+    .DS_Store
+    testing/
+    testing*
+    *.pyc
+    bin/

.prettierrc.yml

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		printWidth: 120

CHANGELOG.md

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+    # mobidic/mobict: Changelog
+    The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
+    and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+    ## v1.0.0dev - [date]
+    Initial release of mobidic/mobict, created with the [nf-core](https://nf-co.re/) template.
+    ### `Added`
+    ### `Fixed`
+    ### `Dependencies`
+    ### `Deprecated`

CITATIONS.md

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+    # mobidic/mobict: Citations
+    ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
+    > Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.
+    ## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)
+    > Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
+    ## Pipeline tools
+    - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+    > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+    ## Software packaging/containerisation tools
+    - [Anaconda](https://anaconda.com)
+      > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
+    - [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
+      > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
+    - [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
+      > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
+    - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
+      > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
+    - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
+      > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

LICENSE

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+    MIT License
+    Copyright (c) Simon Cabello-Aguilar
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    The above copyright notice and this permission notice shall be included in all
+    copies or substantial portions of the Software.
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+    SOFTWARE.

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