catching up to master

.github/workflows/check_typos.yml

@@ -0,0 +1,22 @@
+on:
+    push:
+        branches:
+            - master
+    pull_request:
+        branches:
+            - master
+
+name: Check typos
+jobs:
+    codespell:
+        name: Discover typos with codespell
+        runs-on: ubuntu-latest
+        strategy:
+            fail-fast: false
+        steps:
+          - uses: actions/checkout@v3
+          - uses: codespell-project/actions-codespell@master
+            with:
+              check_filenames: true
+              skip: "*.yml,*.cff,*.js,*.lock"
+              ignore_words_list: RNAseq

3rd_Party_Licenses/Methyl-Seq_3rd_Party_Software.md

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+## The NASA GeneLab [Methyl-Seq](../Methyl-Seq) Processing Pipeline and workflow also makes use of the following 3rd party Open Source software:
+
+|3rd Party Software Name|License|License URL|Copyright Notice|
+|:----------------------|:------|:----------|:----------------------|
+|FastQC|[GNU GENERAL PUBLIC LICENSE Version 2, June 1991](Methyl-Seq_3rd_Party_Software_Licenses/FASTQC_LICENSE.pdf)|[https://github.com/s-andrews/FastQC/blob/master/LICENSE](https://github.com/s-andrews/FastQC/blob/master/LICENSE)|Copyright (C) 1989, 1991 Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.|
+|MultiQC|[GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007](Methyl-Seq_3rd_Party_Software_Licenses/MultiQC_LICENSE.pdf)|[https://github.com/ewels/MultiQC/blob/master/LICENSE](https://github.com/ewels/MultiQC/blob/master/LICENSE)|Copyright (C) 2007 Free Software Foundation, Inc <http://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.|
+|Cutadapt|[MIT Licence Copyright (c) 2010-2020 Marcel Martin](Methyl-Seq_3rd_Party_Software_Licenses/cutadapt_LICENSE.pdf)|[https://github.com/marcelm/cutadapt/blob/main/LICENSE](https://github.com/marcelm/cutadapt/blob/main/LICENSE)|Copyright (c) 2010-2020 Marcel Martin <marcel.martin@scilifelab.se> 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:|
+|TrimGalore|[GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007](Methyl-Seq_3rd_Party_Software_Licenses/TrimGalore_LICENSE.pdf)|[https://github.com/FelixKrueger/TrimGalore/blob/master/LICENSE](https://github.com/FelixKrueger/TrimGalore/blob/master/LICENSE)| Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.|
+|Bismark|[GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007](Methyl-Seq_3rd_Party_Software_Licenses/Bismark_LICENSE.pdf)|[https://github.com/FelixKrueger/Bismark/blob/master/license.txt](https://github.com/FelixKrueger/Bismark/blob/master/license.txt)| Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.|
+|bowtie2|[GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007](Methyl-Seq_3rd_Party_Software_Licenses/bowtie2_LICENSE.pdf)|[https://github.com/BenLangmead/bowtie2/blob/master/LICENSE](https://github.com/BenLangmead/bowtie2/blob/master/LICENSE)|Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.|
+|hisat2|[GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007](Methyl-Seq_3rd_Party_Software_Licenses/hisat2_LICENSE.pdf)|[https://github.com/DaehwanKimLab/hisat2/blob/master/LICENSE](https://github.com/DaehwanKimLab/hisat2/blob/master/LICENSE)|Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.|
+|samtools|[The MIT/Expat License Copyright (C) 2008-2020 Genome Research Ltd.](Methyl-Seq_3rd_Party_Software_Licenses/samtools_LICENSE.pdf)|[https://github.com/samtools/samtools/blob/develop/LICENSE](https://github.com/samtools/samtools/blob/develop/LICENSE)|Copyright (C) 2008-2021 Genome Research Ltd. 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:|
+|Qualimap|[GNU GENERAL PUBLIC LICENSE Version 2, June 1991](Methyl-Seq_3rd_Party_Software_Licenses/Qualimap_LICENSE.pdf)|[https://bitbucket.org/kokonech/qualimap/src/master/LICENSE](https://bitbucket.org/kokonech/qualimap/src/master/LICENSE)|Copyright (C) 1989, 1991 Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.|
+|MethylKit|[Artistic 2.0 LICENSE Copyright (c) 2000-2006](Methyl-Seq_3rd_Party_Software_Licenses/MethylKit_LICENSE.pdf)|[https://bioconductor.org/packages/release/bioc/html/methylKit.html](https://bioconductor.org/packages/release/bioc/html/methylKit.html)|Copyright (c) 2000-2006, The Perl Foundation. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.|
+|tidyverse|[MIT Licence Copyright (c) 2021](Methyl-Seq_3rd_Party_Software_Licenses/tidyverse_LICENSE.pdf)|[https://tidyverse.tidyverse.org/LICENSE.html](https://tidyverse.tidyverse.org/LICENSE.html)|MIT License Copyright (c) 2021 tidyverse authors|
+|genomation|[Artistic 2.0 LICENSE Copyright (c) 2000-2006](Methyl-Seq_3rd_Party_Software_Licenses/MethylKit_LICENSE.pdf)|[https://bioconductor.org/packages/release/bioc/html/genomation.html](https://bioconductor.org/packages/release/bioc/html/genomation.html)|Copyright (c) 2000-2006, The Perl Foundation. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.|
+|Nextflow|[Apache License Version 2.0, January 2004](Methyl-Seq_3rd_Party_Software_Licenses/Nextflow_LICENSE.pdf)|[https://github.com/nextflow-io/nextflow/blob/master/COPYING](https://github.com/nextflow-io/nextflow/blob/master/COPYING)| Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form.|