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Blank line inside blockquote
Open
Severity: Info
Found in docs/Slack_howto.md by markdownlint

MD028 - Blank line inside blockquote

Tags: blockquote, whitespace

Aliases: no-blanks-blockquote

This rule is triggered when two blockquote blocks are separated by nothing except for a blank line:

> This is a blockquote
> which is immediately followed by

> this blockquote. Unfortunately
> In some parsers, these are treated as the same blockquote.

To fix this, ensure that any blockquotes that are right next to each other have some text in between:

> This is a blockquote.

And Jimmy also said:

> This too is a blockquote.

Alternatively, if they are supposed to be the same quote, then add the blockquote symbol at the beginning of the blank line:

> This is a blockquote.
>
> This is the same blockquote.

Rationale: Some markdown parsers will treat two blockquotes separated by one or more blank lines as the same blockquote, while others will treat them as separate blockquotes.

Ordered list item prefix
Open

3. Use the WebHook in eHive
Severity: Info
Found in docs/Slack_howto.md by markdownlint

MD029 - Ordered list item prefix

Tags: ol

Aliases: ol-prefix

Parameters: style ("one", "ordered"; default "one")

This rule is triggered on ordered lists that do not either start with '1.' or do not have a prefix that increases in numerical order (depending on the configured style, which defaults to 'one').

Example valid list if the style is configured as 'one':

1. Do this.
1. Do that.
1. Done.

Example valid list if the style is configured as 'ordered':

1. Do this.
2. Do that.
3. Done.

Line length
Open

* `"#f:beta#"`: returns `f(beta)` as is (assuming that `f` is a function available in
Severity: Info
Found in wrappers/README.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Headers should be surrounded by blank lines
Open

Blackboard, Jobs and Workers
Severity: Info
Found in README.md by markdownlint

MD022 - Headers should be surrounded by blank lines

Tags: headers, blank_lines

Aliases: blanks-around-headers

This rule is triggered when headers (any style) are either not preceded or not followed by a blank line:

# Header 1
Some text

Some more text
## Header 2

To fix this, ensure that all headers have a blank line both before and after (except where the header is at the beginning or end of the document):

# Header 1

Some text

Some more text

## Header 2

Rationale: Aside from aesthetic reasons, some parsers, including kramdown, will not parse headers that don't have a blank line before, and will parse them as regular text.

Line length
Open

We won't discuss the inner parts of the modules, but real examples can be found in the [ensembl-compara](https://github.com/Ensembl/ensembl-compara) repository. It ships modules used for phylogenetic trees inference: [RAxML](https://github.com/Ensembl/ensembl-compara/blob/release/77/modules/Bio/EnsEMBL/Compara/RunnableDB/ProteinTrees/RAxML.pm) and [ExaML](https://github.com/Ensembl/ensembl-compara/blob/feature/update_pipeline/modules/Bio/EnsEMBL/Compara/RunnableDB/ProteinTrees/ExaML.pm). They look very light-weight (only command-line definitions) because most of the logic is in the base class (*GenericRunnable*), but nevertheless show the command lines used and the parametrization of multi-core and MPI runs.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

1. You need to setup a resource class that encodes those requirements e.g. *16 cores and 24Gb of RAM*:
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

9. On the "master" branch increment the version of Bio::EnsEMBL::Hive::Version to x.(y+1)
Severity: Info
Found in docs/release_checklist.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Ordered list item prefix
Open

3. Review README.md, install.html and running_eHive_pipelines.html
Severity: Info
Found in docs/release_checklist.md by markdownlint

MD029 - Ordered list item prefix

Tags: ol

Aliases: ol-prefix

Parameters: style ("one", "ordered"; default "one")

This rule is triggered on ordered lists that do not either start with '1.' or do not have a prefix that increases in numerical order (depending on the configured style, which defaults to 'one').

Example valid list if the style is configured as 'one':

1. Do this.
1. Do that.
1. Done.

Example valid list if the style is configured as 'ordered':

1. Do this.
2. Do that.
3. Done.

Lists should be surrounded by blank lines
Open

   3. The page now shows advanced configuration for the integration. The most
Severity: Info
Found in docs/Slack_howto.md by markdownlint

MD032 - Lists should be surrounded by blank lines

Tags: bullet, ul, ol, blank_lines

Aliases: blanks-around-lists

This rule is triggered when lists (of any kind) are either not preceded or not followed by a blank line:

Some text
* Some
* List

1. Some
2. List
Some text

To fix this, ensure that all lists have a blank line both before and after (except where the block is at the beginning or end of the document):

Some text

* Some
* List

1. Some
2. List

Some text

Rationale: Aside from aesthetic reasons, some parsers, including kramdown, will not parse lists that don't have blank lines before and after them.

Note: List items without hanging indents are a violation of this rule; list items with hanging indents are okay:

* This is
not okay

* This is
  okay

Line length
Open

In the centre of each running pipeline is a database that acts as a blackboard with individual tasks to be run.
Severity: Info
Found in README.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

A PipeConfig file defines the stucture of the pipeline, which is a graph whose nodes are Analyses
Severity: Info
Found in README.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

_Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place._
Severity: Info
Found in PULL_REQUEST_TEMPLATE.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Inconsistent indentation for list items at the same level
Open

  * `span[ptile=4]`, this option specifies the granularity in which LSF will split the jobs/per node. In this example we ask for at least 4 jobs to be executed in the same machine. This might affect queuing times.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD005 - Inconsistent indentation for list items at the same level

Tags: bullet, ul, indentation

Aliases: list-indent

This rule is triggered when list items are parsed as being at the same level, but don't have the same indentation:

* Item 1
    * Nested Item 1
    * Nested Item 2
   * A misaligned item

Usually this rule will be triggered because of a typo. Correct the indentation for the list to fix it:

* Item 1
  * Nested Item 1
  * Nested Item 2
  * Nested Item 3

Trailing spaces
Open

            # ...
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD009 - Trailing spaces

Tags: whitespace

Aliases: no-trailing-spaces

Parameters: br_spaces (number; default: 0)

This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.

The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.

Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.

Multiple consecutive blank lines
Open
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD012 - Multiple consecutive blank lines

Tags: whitespace, blank_lines

Aliases: no-multiple-blanks

This rule is triggered when there are multiple consecutive blank lines in the document:

Some text here


Some more text here

To fix this, delete the offending lines:

Some text here

Some more text here

Note: this rule will not be triggered if there are multiple consecutive blank lines inside code blocks.

Line length
Open

This can be easily taken care by properly setting up your .bashrc to load the right modules.
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

No space after hash on atx style header
Open

####Otherwise, follow the recommended usage in your institute
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD018 - No space after hash on atx style header

Tags: headers, atx, spaces

Aliases: no-missing-space-atx

This rule is triggered when spaces are missing after the hash characters in an atx style header:

#Header 1

##Header 2

To fix this, separate the header text from the hash character by a single space:

# Header 1

## Header 2

Ordered list item prefix
Open

2. You need to add the analysis to your pipeconfig:
Severity: Info
Found in docs/MPI_howto.md by markdownlint

MD029 - Ordered list item prefix

Tags: ol

Aliases: ol-prefix

Parameters: style ("one", "ordered"; default "one")

This rule is triggered on ordered lists that do not either start with '1.' or do not have a prefix that increases in numerical order (depending on the configured style, which defaults to 'one').

Example valid list if the style is configured as 'one':

1. Do this.
1. Do that.
1. Done.

Example valid list if the style is configured as 'ordered':

1. Do this.
2. Do that.
3. Done.

Ordered list item prefix
Open

9. On the "master" branch increment the version of Bio::EnsEMBL::Hive::Version to x.(y+1)
Severity: Info
Found in docs/release_checklist.md by markdownlint

MD029 - Ordered list item prefix

Tags: ol

Aliases: ol-prefix

Parameters: style ("one", "ordered"; default "one")

This rule is triggered on ordered lists that do not either start with '1.' or do not have a prefix that increases in numerical order (depending on the configured style, which defaults to 'one').

Example valid list if the style is configured as 'one':

1. Do this.
1. Do that.
1. Done.

Example valid list if the style is configured as 'ordered':

1. Do this.
2. Do that.
3. Done.

Ordered list item prefix
Open

   2. Configure the `slack_webhook` parameter in the SlackNotification Runnable
Severity: Info
Found in docs/Slack_howto.md by markdownlint

MD029 - Ordered list item prefix

Tags: ol

Aliases: ol-prefix

Parameters: style ("one", "ordered"; default "one")

This rule is triggered on ordered lists that do not either start with '1.' or do not have a prefix that increases in numerical order (depending on the configured style, which defaults to 'one').

Example valid list if the style is configured as 'one':

1. Do this.
1. Do that.
1. Done.

Example valid list if the style is configured as 'ordered':

1. Do this.
2. Do that.
3. Done.
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