Showing 87 of 87 total issues
don't use underscores in Go names; var lib_type_dir should be libTypeDir Open
lib_type_dir := strings.ReplaceAll(cram.Library_type, " ", "_")
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Line length Open
curl -s https://api.github.com/repos/seanlaidlaw/iRODS-Downloader/releases/latest | grep browser_download_url | cut -d '"' -f 4 | wget -qi -
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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.
Dollar signs used before commands without showing output Open
```{bash}
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MD014 - Dollar signs used before commands without showing output
Tags: code
Aliases: commands-show-output
This rule is triggered when there are code blocks showing shell commands to be typed, and the shell commands are preceded by dollar signs ($):
$ ls
$ cat foo
$ less bar
The dollar signs are unnecessary in the above situation, and should not be included:
ls
cat foo
less bar
However, an exception is made when there is a need to distinguish between typed commands and command output, as in the following example:
$ ls
foo bar
$ cat foo
Hello world
$ cat bar
baz
Rationale: it is easier to copy and paste and less noisy if the dollar signs are omitted when they are not needed. See http://www.cirosantilli.com/markdown-styleguide/#dollar-signs-in-shell-code for more information.
don't use underscores in Go names; var checkpoint_file should be checkpointFile Open
checkpoint_file := fmt.Sprintf("checkpoint_%d.json", step)
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don't use underscores in Go names; func parameter cram_list should be cramList Open
cram_list *[]cram_file,
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don't use underscores in Go names; var bjobs_output_filename should be bjobsOutputFilename Open
bjobs_output_filename := submitted_jobs_map[func_cram.Filename]
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don't use underscores in Go names; struct field Imeta_downloaded should be ImetaDownloaded Open
Imeta_downloaded bool
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don't use underscores in Go names; struct field Cram_is_phix should be CramIsPhix Open
Cram_is_phix bool
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don't use underscores in Go names; struct field Fastq_2_path should be Fastq2Path Open
Fastq_2_path string
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don't use underscores in Go names; struct field Fastq_extracted_success should be FastqExtractedSuccess Open
Fastq_extracted_success bool
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don't use underscores in Go names; struct field Cram_download_success should be CramDownloadSuccess Open
Cram_download_success bool
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don't use underscores in Go names; struct field Symlinked_fq_1 should be SymlinkedFq1 Open
Symlinked_fq_1 string
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don't use underscores in Go names; struct field Imeta_parsed should be ImetaParsed Open
Imeta_parsed bool
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don't use underscores in Go names; var bwa_ram should be bwaRAM Open
bwa_ram := viper.GetString("bwa_ram")
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don't use underscores in Go names; struct field Realigned_quickcheck_success should be RealignedQuickcheckSuccess Open
Realigned_quickcheck_success bool
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don't use underscores in Go names; var job_err should be jobErr Open
job_err := out_folder + "/D_realignement_RNA_" + cram.Sample_name + ".e"
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don't use underscores in Go names; var cram_list should be cramList Open
var cram_list []cram_file
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don't use underscores in Go names; var star_exec should be starExec Open
star_exec := viper.GetString("star_exec")
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don't use underscores in Go names; var cram_exists_map should be cramExistsMap Open
cram_exists_map := make(map[string]string)
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don't use underscores in Go names; var library_type should be libraryType Open
library_type := ""
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