Trailing spaces Open
as crashing of any of the agents for whatever reason doesn't stop the rest of the system from running. - Read upRead up
- Exclude checks
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
- Read upRead up
- Exclude checks
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 hereTo fix this, delete the offending lines:
Some text here
Some more text hereNote: this rule will not be triggered if there are multiple consecutive blank lines inside code blocks.
Multiple consecutive blank lines Open
- Read upRead up
- Exclude checks
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 hereTo fix this, delete the offending lines:
Some text here
Some more text hereNote: this rule will not be triggered if there are multiple consecutive blank lines inside code blocks.
Multiple consecutive blank lines Open
- Read upRead up
- Exclude checks
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 hereTo fix this, delete the offending lines:
Some text here
Some more text hereNote: this rule will not be triggered if there are multiple consecutive blank lines inside code blocks.
Headers should be surrounded by blank lines Open
Beekeeper- Read upRead up
- Exclude checks
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 2To 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 2Rationale: 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.
Lists should be surrounded by blank lines Open
* **LOCAL**. A simple meadow that submits jobs locally via `system()` (i.e. `fork()`). It is inherently limited by the specification of the machine beekeeper is running on.- Read upRead up
- Exclude checks
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 textTo 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 textRationale: 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
okayLists should be surrounded by blank lines Open
* **SGE**. A meadow that supports Sun Grid Engine (now known as Oracle Grid Engine). Available for download on GitHub at [Ensembl/ensembl-hive-sge](https://github.com/Ensembl/ensembl-hive-sge).- Read upRead up
- Exclude checks
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 textTo 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 textRationale: 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
okayLine length Open
* Semaphore rules define dependencies between individual Jobs on a more fine-grained level- Read upRead up
- Exclude checks
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
These tasks (we call them Jobs) are claimed and processed by "Worker bees" or just Workers - autonomous processes- Read upRead up
- Exclude checks
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
Jobs that share same code, common parameters and resource requirements are typically grouped into Analyses,- Read upRead up
- Exclude checks
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
* Control rules define dependencies between Analyses as Jobs' containers ("Jobs of Analysis Y can only start when all Jobs of Analysis X are done")- Read upRead up
- Exclude checks
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
* **SGE**. A meadow that supports Sun Grid Engine (now known as Oracle Grid Engine). Available for download on GitHub at [Ensembl/ensembl-hive-sge](https://github.com/Ensembl/ensembl-hive-sge).- Read upRead up
- Exclude checks
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
| Post-mortem inspection of resource usage | Not available | Yes | Not implemented |- Read upRead up
- Exclude checks
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
Analyses- Read upRead up
- Exclude checks
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 2To 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 2Rationale: 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
The main entry point is in [**docs/index.html**](https://rawgit.com/Ensembl/ensembl-hive/version/2.4/docs/index.html) and can also be browsed offline.- Read upRead up
- Exclude checks
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- Read upRead up
- Exclude checks
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 2To 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 2Rationale: 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.
Headers should be surrounded by blank lines Open
Contact us (mailing list)- Read upRead up
- Exclude checks
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 2To 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 2Rationale: 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
eHive is a system for running computation pipelines on distributed computing resources - clusters, farms or grids.- Read upRead up
- Exclude checks
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
or claim some more. When a Worker discovers that its predefined time is up or that there are no more Jobs to do,- Read upRead up
- Exclude checks
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
Available documentation- Read upRead up
- Exclude checks
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 2To 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 2Rationale: 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
(with their code, parameters and resource requirements) and edges are various dependency rules:- Read upRead up
- Exclude checks
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
| :--------------------------------------- | ------------- | ----| --------------- |- Read upRead up
- Exclude checks
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.
Lists should be surrounded by blank lines Open
* what should be automatically done with a Job if it needs more memory/time,- Read upRead up
- Exclude checks
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 textTo 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 textRationale: 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
okayMultiple consecutive blank lines Open
- Read upRead up
- Exclude checks
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 hereTo fix this, delete the offending lines:
Some text here
Some more text hereNote: this rule will not be triggered if there are multiple consecutive blank lines inside code blocks.
Line length Open
that are continuously running on the compute farm and connect to the pipeline database to report about the progress of Jobs- Read upRead up
- Exclude checks
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- Read upRead up
- Exclude checks
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
and generally an Analysis can be viewed as a "base class" for the Jobs that belong to it.- Read upRead up
- Exclude checks
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
eHive pipeline databases are molded according to PipeConfig files which are Perl modules conforming to a special interface.- Read upRead up
- Exclude checks
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
| Query job status | Yes | Yes | Yes |- Read upRead up
- Exclude checks
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
* **LOCAL**. A simple meadow that submits jobs locally via `system()` (i.e. `fork()`). It is inherently limited by the specification of the machine beekeeper is running on.- Read upRead up
- Exclude checks
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
PipeConfig file defines Analyses and dependency rules of the pipeline- Read upRead up
- Exclude checks
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 2To 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 2Rationale: 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.
Lists should be surrounded by blank lines Open
* how many Workers can simultaneously work on a given Analysis,- Read upRead up
- Exclude checks
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 textTo 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 textRationale: 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
okayBare URL used Open
To subscribe to it please visit (http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users)- Read upRead up
- Exclude checks
MD034 - Bare URL used
Tags: links, url
Aliases: no-bare-urls
This rule is triggered whenever a URL is given that isn't surrounded by angle brackets:
For more information, see http://www.example.com/.To fix this, add angle brackets around the URL:
For more information, see <http:></http:>.Rationale: Without angle brackets, the URL isn't converted into a link in many markdown parsers.
Note: if you do want a bare URL without it being converted into a link, enclose it in a code block, otherwise in some markdown parsers it will be converted:
`http://www.example.com`Line length Open
| Job limiter and resource management | Not available | Yes | Yes |- Read upRead up
- Exclude checks
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
In the centre of each running pipeline is a database that acts as a blackboard with individual tasks to be run.- Read upRead up
- Exclude checks
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
It regularly checks the states of both the blackboard and the farm and submits more Workers when needed.- Read upRead up
- Exclude checks
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
| Submit jobs | Yes | Yes | Yes |- Read upRead up
- Exclude checks
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
into a separate software tool and is used in many projects both in Genome Campus, Cambridge and outside.- Read upRead up
- Exclude checks
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
as crashing of any of the agents for whatever reason doesn't stop the rest of the system from running. - Read upRead up
- Exclude checks
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
eHive has a generic interface named _Meadow_ that describes how to interact with an underlying grid scheduler (submit jobs, query job's status, etc). eHive ships two meadow implementations:- Read upRead up
- Exclude checks
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
Both are extensively used by the Ensembl project and are regularly updated. The LSF meadow supports workloads reaching thousands of parallel jobs.- Read upRead up
- Exclude checks
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
The table below lists the capabilities of each meadow, and whether they are available and implemented:- Read upRead up
- Exclude checks
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
documentation](https://rawgit.com/Ensembl/ensembl-hive/version/2.4/wrappers/python3/doxygen/index.html) and- Read upRead up
- Exclude checks
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.
Lists should be surrounded by blank lines Open
* Dataflow rules define how data that flows out of an Analysis can be used to trigger creation of Jobs in other Analyses- Read upRead up
- Exclude checks
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 textTo 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 textRationale: 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
okayLine length Open
| Kill job | Yes | Yes | Yes |- Read upRead up
- Exclude checks
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
There is no direct communication between Beekeeper and Workers, which makes the system rather fault-tolerant,- Read upRead up
- Exclude checks
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
* Dataflow rules define how data that flows out of an Analysis can be used to trigger creation of Jobs in other Analyses- Read upRead up
- Exclude checks
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
| Capability | LOCAL | LSF | SGE |- Read upRead up
- Exclude checks
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.