MIN Update links to HTTPS where possible

luispedro · luispedro · commit a918f1223d4b · 2022-06-04T17:49:41.000+02:00
diff --git a/CITATION.cff b/CITATION.cff
@@ -5,7 +5,7 @@ title: 'NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-
 authors:
 - family-names: Coelho
   given-names: Luis Pedro
-  orcid: http://orcid.org/0000-0002-9280-7885
+  orcid: https://orcid.org/0000-0002-9280-7885
 - family-names: Alves
   given-names: Renato
   orcid: null
diff --git a/NGLess/Citations.hs b/NGLess/Citations.hs
@@ -21,7 +21,7 @@ citations =
 
 nglessCitation :: T.Text
 nglessCitation =
-    "Coelho, L.P., Alves, R., Monteiro, P., Huerta-Cepas, J., Freitas, A.T., and Bork, P., NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language. in Microbiome 7:84 (2019). DOI: http://doi.org/10.1186/s40168-019-0684-8"
+    "Coelho, L.P., Alves, R., Monteiro, P., Huerta-Cepas, J., Freitas, A.T., and Bork, P., NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language. in Microbiome 7:84 (2019). DOI: https://doi.org/10.1186/s40168-019-0684-8"
 
 
 collectCitations :: [Module] -> Script -> [T.Text]
diff --git a/docs/presentations/ngless.html b/docs/presentations/ngless.html
@@ -1,5 +1,5 @@
 <html>
-<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
 <script src="https://rawgithub.com/markdalgleish/fathom/master/fathom.min.js" type="text/javascript"></script>
 <link href="https://raw.github.com/markdalgleish/fathom/master/fathom.sample.css" rel="stylesheet"/>
 <style>
diff --git a/docs/sources/Functions.rst b/docs/sources/Functions.rst
@@ -536,7 +536,7 @@ expansion <searchpath.html>`__.
 The ``functional_map`` should be a tab-separated file where the first column is
 the sequence name and the other columns are the annotations. This is often used
 for gene catalogues and can be produced by `eggnog-mapper
-<http://eggnog-mapper.embl.de/>`__.
+<https://eggnog-mapper.embl.de/>`__.
 
 ``features``: which features to count. If a GFF file is used, this refers to
 the "features" field.
diff --git a/docs/sources/Makefile b/docs/sources/Makefile
@@ -9,7 +9,7 @@ BUILDDIR      = _build
 
 # User-friendly check for sphinx-build
 ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
-$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from https://sphinx-doc.org/)
 endif
 
 # Internal variables.
diff --git a/docs/sources/Mapping.rst b/docs/sources/Mapping.rst
@@ -4,7 +4,7 @@ Mapping
 Mapping is one of the major functions of NGLess. Here we describe, in more
 detail, some of its functionality.
 
-Mapping is implemented using `bwa <http://bio-bwa.sourceforge.net/>`__. As of
+Mapping is implemented using `bwa <https://bio-bwa.sourceforge.net/>`__. As of
 version 1.4, NGLess uses *bwa 0.7.17* by default.
 
 By default, bwa is called with default parameters. If the ``mode_all`` argument
diff --git a/docs/sources/Organisms.rst b/docs/sources/Organisms.rst
@@ -54,7 +54,7 @@ The following table represents organisms provided by default:
 +-----------+-----------------------------+-------------------+---------+
 
 These archives are all created using versions 75, 85 and 90 of `Ensembl
-<http://www.ensembl.org/>`__.
+<https://www.ensembl.org/>`__.
 
 Automatic installation
 ----------------------
diff --git a/docs/sources/_static/gut-metagenomics-tutorial-presentation/gut_specI_tutorial.html b/docs/sources/_static/gut-metagenomics-tutorial-presentation/gut_specI_tutorial.html
@@ -30,7 +30,7 @@
 
 # Metagenomics analysis with NGLess
 
-[Luis Pedro Coelho](http://luispedro.org)
+[Luis Pedro Coelho](https://luispedro.org)
 
 [@luispedrocoelho](https://twitter.com/luispedrocoelho)
 
diff --git a/docs/sources/command-line-wrappers.md b/docs/sources/command-line-wrappers.md
@@ -9,7 +9,7 @@ Python package management tools:
 All of the wrappers can install NGLess if passed the `--auto-install` flag.
 
 All of these wrappers also have [Common Workflow
-Language](http://www.commonwl.org/) so that they can be used in larger
+Language](https://www.commonwl.org/) so that they can be used in larger
 pipelines.
 
 ## ngless-install.py
diff --git a/docs/sources/configuration.rst b/docs/sources/configuration.rst
@@ -40,7 +40,7 @@ auto-detection (see below).
 ``strict-threads``: by default, NGLess will, in certain conditions, use more
 CPUs than specified by the ``jobs`` argument (in bursts of activity). This
 happens, for example, when it calls an external short-read-mapper (such as `bwa
-<http://bio-bwa.sourceforge.net/bwa.shtml>`__). By default, it will pass the
+<https://bio-bwa.sourceforge.net/bwa.shtml>`__). By default, it will pass the
 threads argument through to ``bwa``. However, it will still be processing
 ``bwa``'s output using its own threads. This will results in small bursts of
 activity where the CPU usage is above ``jobs``. If you specify
diff --git a/docs/sources/faq.md b/docs/sources/faq.md
@@ -52,7 +52,7 @@ Add new model organisms can similarly be done with simple YAML file.
 More advanced extensions can be done in Haskell, but this is considered a
 solution for advanced users.
 
-## Couldn't you just use Docker/[Bioboxes](http://bioboxes.org/)?
+## Couldn't you just use Docker/[Bioboxes](https://bioboxes.org/)?
 
 Short answer: Bioboxes gets us part of the way there, but not all of it;
 however, if we think of these technologies as complements, we might get more
@@ -74,7 +74,8 @@ experience than is possible with a generic tool. In particular, when the user
 makes a mistake (and all users will make mistakes), we can diagnose it faster
 and provide a better error message than is possible to do with Bioboxes.
 
-## What is the relationship of ngless to the [Common Workflow Language](http://common-workflow-language.github.io/)?
+## What is the relationship of ngless to the [Common Workflow
+Language](https://common-workflow-language.github.io/)?
 
 Like for the question above, we consider ngless to be related to but not
 overlapping with the CWL (Common Workflow Language).
diff --git a/docs/sources/index.rst b/docs/sources/index.rst
@@ -55,7 +55,7 @@ Basic functionality
 
 -  preprocessing and quality control of FastQ files
 -  mapping to a reference genome (implemented through
-   `bwa <http://bio-bwa.sourceforge.net/>`__ by default)
+   `bwa <https://bio-bwa.sourceforge.net/>`__ by default)
 -  assembly of contigs
 -  annotation and summarization of the alignments using reference gene
    annotations
@@ -164,11 +164,11 @@ from another programme (not just ``cat``).
 Authors
 -------
 
--  `Luis Pedro Coelho <http://luispedro.org>`__ (email: coelho@embl.de)
+-  `Luis Pedro Coelho <https://luispedro.org>`__ (email: coelho@embl.de)
    (on twitter: `@luispedrocoelho <https://twitter.com/luispedrocoelho>`__)
 -  Paulo Monteiro
 -  Renato Alves
--  `Ana Teresa Freitas <http://web.tecnico.ulisboa.pt/ana.freitas/>`__
+-  `Ana Teresa Freitas <https://web.tecnico.ulisboa.pt/ana.freitas/>`__
 -  Peer Bork
 
 
diff --git a/docs/sources/install.md b/docs/sources/install.md
@@ -3,7 +3,7 @@
 ## Bioconda (binary)
 
 The recommended way to install NGLess is through
-[bioconda](http://bioconda.github.io):
+[bioconda](https://bioconda.github.io):
 
     conda install -c bioconda ngless 
 
diff --git a/docs/sources/preprocess.rst b/docs/sources/preprocess.rst
@@ -13,7 +13,7 @@ Filtering reads based on quality is performed with the ``preprocess`` function,
 which takes a block of code. This block of code will be executed for each read.
 For example::
 
-    ngless "0.8"
+    ngless "1.4"
 
     input = fastq('input.fq.gz')
 
@@ -45,7 +45,7 @@ Within the preprocess block, you can modify the read in several ways:
   method).
 
 You can combine these in different ways. For example, the behaviour of the
-`fastx quality trimmer <http://hannonlab.cshl.edu/fastx_toolkit/>`__ can be
+`fastx quality trimmer <https://hannonlab.cshl.edu/fastx_toolkit/>`__ can be
 recreated as::
 
     preprocess(input) using |r|:
diff --git a/docs/sources/tutorial-assembly-gp.rst b/docs/sources/tutorial-assembly-gp.rst
@@ -8,7 +8,7 @@ metagenomes.
 .. note::
     This tutorial uses the full Ocean Microbial Reference Gene Catalog
     presented in `Structure and function of the global ocean microbiome
-    <http://science.sciencemag.org/content/348/6237/1261359.long>`__ Sunagawa,
+    <https://science.sciencemag.org/content/348/6237/1261359.long>`__ Sunagawa,
     Coelho, Chaffron, et al., Science, 2015
 
 
diff --git a/docs/sources/tutorial-gut-metagenomics.rst b/docs/sources/tutorial-gut-metagenomics.rst
@@ -135,7 +135,7 @@ Now, we will use the ``input`` object which has been filtered of human reads.
 
 .. note::
     This section of the tutorial uses the `Integrated Gene Catalogue
-    <http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html>`__ and
+    <https://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html>`__ and
     requires ca. **15GiB** of RAM. Skip to step 9 if your machine does not have
     this much memory.
 
diff --git a/docs/sources/tutorial-ocean-metagenomics.rst b/docs/sources/tutorial-ocean-metagenomics.rst
@@ -15,7 +15,7 @@ metagenomes.
 .. note::
     This tutorial uses the full Ocean Microbial Reference Gene Catalog
     presented in `Structure and function of the global ocean microbiome
-    <http://science.sciencemag.org/content/348/6237/1261359.long>`__ Sunagawa,
+    <https://science.sciencemag.org/content/348/6237/1261359.long>`__ Sunagawa,
     Coelho, Chaffron, et al., Science, 2015
 
     This catalog contains ca. 40 million genes and requires **56GiB** of RAM
diff --git a/docs/sources/tutorial.rst b/docs/sources/tutorial.rst
@@ -8,7 +8,7 @@ Example
 -------
 
 This example will use data from a real experiment stored at EMBL-EBI. The data
-can be accessed at http://www.ebi.ac.uk/ena/data/view/SRP023199 and represent
+can be accessed at https://www.ebi.ac.uk/ena/data/view/SRP023199 and represent
 **HeLa cells**. The idea is to preprocess the data set, map it against the
 human genome and count the reads that overlap with known genes.
 
diff --git a/docs/sources/whatsnew.rst b/docs/sources/whatsnew.rst
@@ -121,7 +121,7 @@ User-visible improvements
 - More flexible loading of ``functional_map`` arguments in `count
   <https://ngless.embl.de/Functions.html#count>`__ to accept multiple comment
   lines at the top of the file as produced by `eggnog-mapper
-  <http://eggnog-mapper.embl.de/>`__.
+  <https://eggnog-mapper.embl.de/>`__.
 - Added ``sense`` argument to the `count
   <https://ngless.embl.de/Functions.html#count>`__ function, generalizing the
   previous ``strand`` argument (which is deprecated). Whereas before it was
diff --git a/tests/argv/expected.stdout.txt b/tests/argv/expected.stdout.txt
@@ -5,7 +5,7 @@ When publishing results from this script, please cite the following references:
 
 	 - Coelho, L.P., Alves, R., Monteiro, P., Huerta-Cepas, J., Freitas, A.T., and Bork, P.,
 	 NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language. in
-	 Microbiome 7:84 (2019). DOI: http://doi.org/10.1186/s40168-019-0684-8
+	 Microbiome 7:84 (2019). DOI: https://doi.org/10.1186/s40168-019-0684-8
 
 
 argv.ngl
diff --git a/tests/error-ofile-complex/expected.stdout.txt b/tests/error-ofile-complex/expected.stdout.txt
@@ -5,7 +5,7 @@ When publishing results from this script, please cite the following references:
 
 	 - Coelho, L.P., Alves, R., Monteiro, P., Huerta-Cepas, J., Freitas, A.T., and Bork, P.,
 	 NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language. in
-	 Microbiome 7:84 (2019). DOI: http://doi.org/10.1186/s40168-019-0684-8
+	 Microbiome 7:84 (2019). DOI: https://doi.org/10.1186/s40168-019-0684-8
 
 
 Should print
diff --git a/tests/exampleModule/expected.stdout.txt b/tests/exampleModule/expected.stdout.txt
@@ -5,7 +5,7 @@ When publishing results from this script, please cite the following references:
 
 	 - Coelho, L.P., Alves, R., Monteiro, P., Huerta-Cepas, J., Freitas, A.T., and Bork, P.,
 	 NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language. in
-	 Microbiome 7:84 (2019). DOI: http://doi.org/10.1186/s40168-019-0684-8
+	 Microbiome 7:84 (2019). DOI: https://doi.org/10.1186/s40168-019-0684-8
 
 
 Called example function 'example'
diff --git a/tests/len_list/expected.stdout.txt b/tests/len_list/expected.stdout.txt
@@ -5,7 +5,7 @@ When publishing results from this script, please cite the following references:
 
 	 - Coelho, L.P., Alves, R., Monteiro, P., Huerta-Cepas, J., Freitas, A.T., and Bork, P.,
 	 NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language. in
-	 Microbiome 7:84 (2019). DOI: http://doi.org/10.1186/s40168-019-0684-8
+	 Microbiome 7:84 (2019). DOI: https://doi.org/10.1186/s40168-019-0684-8
 
 
 three
diff --git a/tests/parse_odd_corners/expected.stdout.txt b/tests/parse_odd_corners/expected.stdout.txt
@@ -5,7 +5,7 @@ When publishing results from this script, please cite the following references:
 
 	 - Coelho, L.P., Alves, R., Monteiro, P., Huerta-Cepas, J., Freitas, A.T., and Bork, P.,
 	 NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language. in
-	 Microbiome 7:84 (2019). DOI: http://doi.org/10.1186/s40168-019-0684-8
+	 Microbiome 7:84 (2019). DOI: https://doi.org/10.1186/s40168-019-0684-8
 
 
 one
diff --git a/tests/readlines/expected.stdout.txt b/tests/readlines/expected.stdout.txt
@@ -5,7 +5,7 @@ When publishing results from this script, please cite the following references:
 
 	 - Coelho, L.P., Alves, R., Monteiro, P., Huerta-Cepas, J., Freitas, A.T., and Bork, P.,
 	 NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language. in
-	 Microbiome 7:84 (2019). DOI: http://doi.org/10.1186/s40168-019-0684-8
+	 Microbiome 7:84 (2019). DOI: https://doi.org/10.1186/s40168-019-0684-8
 
 
 line 1
