Use HTTPS for links where available (#325)

* Fix broken or http-only links.

* Change links to HTTPS where available

docs/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://www.sphinx-doc.org/)
 endif
 
 # Internal variables.

docs/executing/cluster-cloud.rst

@@ -236,7 +236,7 @@ and forward it to the cluster scheduler:
 
     $ snakemake --cluster "qsub --runtime {params.runtime}"
 
-If your cluster system supports `DRMAA <http://www.drmaa.org/>`_, Snakemake can make use of that to increase the control over jobs.
+If your cluster system supports `DRMAA <https://www.drmaa.org/>`_, Snakemake can make use of that to increase the control over jobs.
 E.g. jobs can be cancelled upon pressing ``Ctrl+C``, which is not possible with the generic ``--cluster`` support.
 With DRMAA, no ``qsub`` command needs to be provided, but system specific arguments can still be given as a string, e.g.
 

docs/executing/interoperability.rst

@@ -9,7 +9,7 @@ Interoperability
 CWL export
 ----------
 
-Snakemake workflows can be exported to `CWL <http://www.commonwl.org/>`_, such that they can be executed in any `CWL-enabled workflow engine <https://www.commonwl.org/#Implementations>`_.
+Snakemake workflows can be exported to `CWL <https://www.commonwl.org/>`_, such that they can be executed in any `CWL-enabled workflow engine <https://www.commonwl.org/#Implementations>`_.
 Since, CWL is less powerful for expressing workflows than Snakemake (most importantly Snakemake offers more flexible scatter-gather patterns, since full Python can be used), export works such that every Snakemake job is encoded into a single step in the CWL workflow.
 Moreover, every step of that workflow calls Snakemake again to execute the job. The latter enables advanced Snakemake features like scripts, benchmarks and remote files to work inside CWL.
 So, when exporting keep in mind that the resulting CWL file can become huge, depending on the number of jobs in your workflow.

docs/index.rst

@@ -113,7 +113,7 @@ Support
 Citation
 --------
 
-`Köster, Johannes and Rahmann, Sven. "Snakemake - A scalable bioinformatics workflow engine". Bioinformatics 2012. <http://bioinformatics.oxfordjournals.org/content/28/19/2520>`_
+`Köster, Johannes and Rahmann, Sven. "Snakemake - A scalable bioinformatics workflow engine". Bioinformatics 2012. <https://bioinformatics.oxfordjournals.org/content/28/19/2520>`_
 
 See :doc:`Citations <project_info/citations>` for more information.
 
@@ -154,41 +154,41 @@ Please consider to add your own.
 * Goormaghtigh et al. 2018. `Reassessing the Role of Type II Toxin-Antitoxin Systems in Formation of Escherichia coli Type II Persister Cells <https://mbio.asm.org/content/mbio/9/3/e00640-18.full.pdf>`_. mBio.
 * Ramirez et al. 2018. `Detecting macroecological patterns in bacterial communities across independent studies of global soils <https://www.nature.com/articles/s41564-017-0062-x>`_. Nature microbiology.
 * Amato et al. 2018. `Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes <https://www.nature.com/articles/s41396-018-0175-0>`_. The ISME journal.
-* Uhlitz et al. 2017. `An immediate–late gene expression module decodes ERK signal duration <http://msb.embopress.org/content/13/5/928>`_. Molecular Systems Biology.
-* Akkouche et al. 2017. `Piwi Is Required during Drosophila Embryogenesis to License Dual-Strand piRNA Clusters for Transposon Repression in Adult Ovaries <http://www.sciencedirect.com/science/article/pii/S1097276517302071>`_. Molecular Cell.
+* Uhlitz et al. 2017. `An immediate–late gene expression module decodes ERK signal duration <https://msb.embopress.org/content/13/5/928>`_. Molecular Systems Biology.
+* Akkouche et al. 2017. `Piwi Is Required during Drosophila Embryogenesis to License Dual-Strand piRNA Clusters for Transposon Repression in Adult Ovaries <https://www.sciencedirect.com/science/article/pii/S1097276517302071>`_. Molecular Cell.
 * Beatty et al. 2017. `Giardia duodenalis induces pathogenic dysbiosis of human intestinal microbiota biofilms <https://www.ncbi.nlm.nih.gov/pubmed/28237889>`_. International Journal for Parasitology.
 * Meyer et al. 2017. `Differential Gene Expression in the Human Brain Is Associated with Conserved, but Not Accelerated, Noncoding Sequences <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5400397/>`_. Molecular Biology and Evolution.
-* Lonardo et al. 2017. `Priming of soil organic matter: Chemical structure of added compounds is more important than the energy content <http://www.sciencedirect.com/science/article/pii/S0038071716304539>`_. Soil Biology and Biochemistry.
+* Lonardo et al. 2017. `Priming of soil organic matter: Chemical structure of added compounds is more important than the energy content <https://www.sciencedirect.com/science/article/pii/S0038071716304539>`_. Soil Biology and Biochemistry.
 * Beisser et al. 2017. `Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes <https://peerj.com/articles/2832/>`_. PeerJ.
 * Piro et al 2017. `MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling <https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0318-y>`_. Microbiome.
 * Dimitrov et al 2017. `Successive DNA extractions improve characterization of soil microbial communities <https://peerj.com/articles/2915/>`_. PeerJ.
-* de Bourcy et al. 2016. `Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging <http://www.pnas.org/content/114/5/1105.short>`_. PNAS.
-* Bray et al. 2016. `Near-optimal probabilistic RNA-seq quantification <http://www.nature.com/nbt/journal/v34/n5/abs/nbt.3519.html>`_. Nature Biotechnology.
+* de Bourcy et al. 2016. `Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging <https://www.pnas.org/content/114/5/1105.short>`_. PNAS.
+* Bray et al. 2016. `Near-optimal probabilistic RNA-seq quantification <https://www.nature.com/nbt/journal/v34/n5/abs/nbt.3519.html>`_. Nature Biotechnology.
 * Etournay et al. 2016. `TissueMiner: a multiscale analysis toolkit to quantify how cellular processes create tissue dynamics <https://elifesciences.org/content/5/e14334>`_. eLife Sciences.
-* Townsend et al. 2016. `The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice <http://www.cell.com/cancer-cell/abstract/S1535-6108%2816%2930090-3>`_. Cancer Cell.
-* Burrows et al. 2016. `Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs <http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005793>`_. PLOS Genetics.
-* Ziller et al. 2015. `Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing <http://www.nature.com/nmeth/journal/v12/n3/full/nmeth.3152.html>`_. Nature Methods.
+* Townsend et al. 2016. `The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice <https://www.cell.com/cancer-cell/abstract/S1535-6108%2816%2930090-3>`_. Cancer Cell.
+* Burrows et al. 2016. `Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs <https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005793>`_. PLOS Genetics.
+* Ziller et al. 2015. `Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing <https://www.nature.com/nmeth/journal/v12/n3/full/nmeth.3152.html>`_. Nature Methods.
 * Li et al. 2015. `Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0843-6>`_. Genome Biology.
-* Schmied et al. 2015. `An automated workflow for parallel processing of large multiview SPIM recordings <http://bioinformatics.oxfordjournals.org/content/32/7/1112>`_. Bioinformatics.
-* Chung et al. 2015. `Whole-Genome Sequencing and Integrative Genomic Analysis Approach on Two 22q11.2 Deletion Syndrome Family Trios for Genotype to Phenotype Correlations <http://onlinelibrary.wiley.com/doi/10.1002/humu.22814/full>`_. Human Mutation.
-* Kim et al. 2015. `TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms <http://emboj.embopress.org/content/34/13/1801.long>`_. The EMBO Journal.
-* Park et al. 2015. `Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone <http://doi.org/10.1016/j.cell.2015.06.007>`_. Cell.
-* Břinda et al. 2015. `RNF: a general framework to evaluate NGS read mappers <http://bioinformatics.oxfordjournals.org/content/early/2015/09/30/bioinformatics.btv524>`_. Bioinformatics.
-* Břinda et al. 2015. `Spaced seeds improve k-mer-based metagenomic classification <http://bioinformatics.oxfordjournals.org/content/early/2015/08/10/bioinformatics.btv419>`_. Bioinformatics.
-* Spjuth et al. 2015. `Experiences with workflows for automating data-intensive bioinformatics <http://www.biologydirect.com/content/10/1/43>`_. Biology Direct.
-* Schramm et al. 2015. `Mutational dynamics between primary and relapse neuroblastomas <http://www.nature.com/ng/journal/v47/n8/full/ng.3349.html>`_. Nature Genetics.
-* Berulava et al. 2015. `N6-Adenosine Methylation in MiRNAs <http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118438>`_. PLOS ONE.
-* The Genome of the Netherlands Consortium 2014. `Whole-genome sequence variation, population structure and demographic history of the Dutch population <http://www.nature.com/ng/journal/v46/n8/full/ng.3021.html>`_. Nature Genetics.
-*  Patterson et al. 2014. `WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads <http://online.liebertpub.com/doi/10.1089/cmb.2014.0157>`_. Journal of Computational Biology.
-* Fernández et al. 2014. `H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells <http://genome.cshlp.org/content/25/1/27.long>`_. Genome Research.
+* Schmied et al. 2015. `An automated workflow for parallel processing of large multiview SPIM recordings <https://bioinformatics.oxfordjournals.org/content/32/7/1112>`_. Bioinformatics.
+* Chung et al. 2015. `Whole-Genome Sequencing and Integrative Genomic Analysis Approach on Two 22q11.2 Deletion Syndrome Family Trios for Genotype to Phenotype Correlations <https://onlinelibrary.wiley.com/doi/10.1002/humu.22814/full>`_. Human Mutation.
+* Kim et al. 2015. `TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms <https://emboj.embopress.org/content/34/13/1801.long>`_. The EMBO Journal.
+* Park et al. 2015. `Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone <https://doi.org/10.1016/j.cell.2015.06.007>`_. Cell.
+* Břinda et al. 2015. `RNF: a general framework to evaluate NGS read mappers <https://bioinformatics.oxfordjournals.org/content/early/2015/09/30/bioinformatics.btv524>`_. Bioinformatics.
+* Břinda et al. 2015. `Spaced seeds improve k-mer-based metagenomic classification <https://bioinformatics.oxfordjournals.org/content/early/2015/08/10/bioinformatics.btv419>`_. Bioinformatics.
+* Spjuth et al. 2015. `Experiences with workflows for automating data-intensive bioinformatics <https://biologydirect.biomedcentral.com/articles/10.1186/s13062-015-0071-8>`_. Biology Direct.
+* Schramm et al. 2015. `Mutational dynamics between primary and relapse neuroblastomas <https://www.nature.com/ng/journal/v47/n8/full/ng.3349.html>`_. Nature Genetics.
+* Berulava et al. 2015. `N6-Adenosine Methylation in MiRNAs <https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118438>`_. PLOS ONE.
+* The Genome of the Netherlands Consortium 2014. `Whole-genome sequence variation, population structure and demographic history of the Dutch population <https://www.nature.com/ng/journal/v46/n8/full/ng.3021.html>`_. Nature Genetics.
+*  Patterson et al. 2014. `WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads <https://online.liebertpub.com/doi/10.1089/cmb.2014.0157>`_. Journal of Computational Biology.
+* Fernández et al. 2014. `H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells <https://genome.cshlp.org/content/25/1/27.long>`_. Genome Research.
 * Köster et al. 2014. `Massively parallel read mapping on GPUs with the q-group index and PEANUT <https://peerj.com/articles/606/>`_. PeerJ.
-* Chang et al. 2014. `TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications <http://www.cell.com/molecular-cell/abstract/S1097-2765(14)00121-X>`_. Molecular Cell.
-* Althoff et al. 2013. `MiR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A <http://onlinelibrary.wiley.com/doi/10.1002/ijc.28091/abstract;jsessionid=33613A834E2A2FDCCA49246C23DF777E.f04t02>`_. International Journal of Cancer.
-* Marschall et al. 2013. `MATE-CLEVER: Mendelian-Inheritance-Aware Discovery and Genotyping of Midsize and Long Indels <http://bioinformatics.oxfordjournals.org/content/29/24/3143.long>`_. Bioinformatics.
-* Rahmann et al. 2013. `Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data <http://www.sciencedirect.com/science/article/pii/S1046202312002605>`_. Methods.
-* Martin et al. 2013. `Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3 <http://www.nature.com/ng/journal/v45/n8/full/ng.2674.html>`_. Nature Genetics.
-* Czeschik et al. 2013. `Clinical and mutation data in 12 patients with the clinical diagnosis of Nager syndrome <http://link.springer.com/article/10.1007%2Fs00439-013-1295-2>`_. Human Genetics.
-* Marschall et al. 2012. `CLEVER: Clique-Enumerating Variant Finder <http://bioinformatics.oxfordjournals.org/content/28/22/2875.long>`_. Bioinformatics.
+* Chang et al. 2014. `TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications <https://www.cell.com/molecular-cell/abstract/S1097-2765(14)00121-X>`_. Molecular Cell.
+* Althoff et al. 2013. `MiR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A <https://onlinelibrary.wiley.com/doi/10.1002/ijc.28091/abstract;jsessionid=33613A834E2A2FDCCA49246C23DF777E.f04t02>`_. International Journal of Cancer.
+* Marschall et al. 2013. `MATE-CLEVER: Mendelian-Inheritance-Aware Discovery and Genotyping of Midsize and Long Indels <https://bioinformatics.oxfordjournals.org/content/29/24/3143.long>`_. Bioinformatics.
+* Rahmann et al. 2013. `Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data <https://www.sciencedirect.com/science/article/pii/S1046202312002605>`_. Methods.
+* Martin et al. 2013. `Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3 <https://www.nature.com/ng/journal/v45/n8/full/ng.2674.html>`_. Nature Genetics.
+* Czeschik et al. 2013. `Clinical and mutation data in 12 patients with the clinical diagnosis of Nager syndrome <https://link.springer.com/article/10.1007%2Fs00439-013-1295-2>`_. Human Genetics.
+* Marschall et al. 2012. `CLEVER: Clique-Enumerating Variant Finder <https://bioinformatics.oxfordjournals.org/content/28/22/2875.long>`_. Bioinformatics.
 
 
 .. toctree::

docs/project_info/citations.rst

@@ -18,19 +18,19 @@ When using Snakemake for a publication, **please cite the following article** in
 Cite This
 =========
 
-`Köster, Johannes and Rahmann, Sven. "Snakemake - A scalable bioinformatics workflow engine". Bioinformatics 2012. <http://bioinformatics.oxfordjournals.org/content/28/19/2520>`_
+`Köster, Johannes and Rahmann, Sven. "Snakemake - A scalable bioinformatics workflow engine". Bioinformatics 2012. <https://bioinformatics.oxfordjournals.org/content/28/19/2520>`_
 
 
 More References
 ===============
 
 Another publication describing more of Snakemake internals:
 
-`Köster, Johannes and Rahmann, Sven. "Building and Documenting Bioinformatics Workflows with Python-based Snakemake". Proceedings of the GCB 2012. <http://drops.dagstuhl.de/opus/volltexte/oasics-complete/oasics-vol26-gcb2012-complete.pdf>`_
+`Köster, Johannes and Rahmann, Sven. "Building and Documenting Bioinformatics Workflows with Python-based Snakemake". Proceedings of the GCB 2012. <https://drops.dagstuhl.de/opus/volltexte/oasics-complete/oasics-vol26-gcb2012-complete.pdf>`_
 
 And my PhD thesis which describes all algorithmic details:
 
-`Johannes Köster, "Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis", TU Dortmund 2014 <http://hdl.handle.net/2003/33940>`_
+`Johannes Köster, "Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis", TU Dortmund 2014 <https://hdl.handle.net/2003/33940>`_
 
 
 Project Pages
@@ -48,4 +48,4 @@ The markdown syntax is
     [![Snakemake](https://img.shields.io/badge/snakemake-≥5.6.0-brightgreen.svg?style=flat)](https://snakemake.readthedocs.io)
 
 Replace the ``3.5.2`` with the minimum required Snakemake version.
-You can also `change the style <http://shields.io/#styles>`_.
+You can also `change the style <https://shields.io/#styles>`_.

docs/project_info/faq.rst

@@ -188,7 +188,7 @@ and have in the Snakefile some Python code that reads this environment variable,
 I get a NameError with my shell command. Are braces unsupported?
 ----------------------------------------------------------------
 
-You can use the entire Python `format minilanguage <http://docs.python.org/3/library/string.html#formatspec>`_ in shell commands. Braces in shell commands that are not intended to insert variable values thus have to be escaped by doubling them:
+You can use the entire Python `format minilanguage <https://docs.python.org/3/library/string.html#formatspec>`_ in shell commands. Braces in shell commands that are not intended to insert variable values thus have to be escaped by doubling them:
 
 This:
 
@@ -315,7 +315,7 @@ On unix, you can make use of the commonly pre-installed `mail` command:
     snakemake 2> snakemake.log
     mail -s "snakemake finished" youremail@provider.com < snakemake.log
 
-In case your administrator does not provide you with a proper configuration of the sendmail framework, you can configure `mail` to work e.g. via Gmail (see `here <http://www.cyberciti.biz/tips/linux-use-gmail-as-a-smarthost.html>`_).
+In case your administrator does not provide you with a proper configuration of the sendmail framework, you can configure `mail` to work e.g. via Gmail (see `here <https://www.cyberciti.biz/tips/linux-use-gmail-as-a-smarthost.html>`_).
 
 I want to pass variables between rules. Is that possible?
 ---------------------------------------------------------