seanlaidlaw/iRODS-Downloader

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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, " ", "_")
Severity: Minor
Found in irods_downloader.go by golint

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 -
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.

Dollar signs used before commands without showing output
Open

```{bash}
Severity: Info
Found in README.md by markdownlint

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)
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; func parameter cram_list should be cramList
Open

    cram_list *[]cram_file,
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; var bjobs_output_filename should be bjobsOutputFilename
Open

            bjobs_output_filename := submitted_jobs_map[func_cram.Filename]
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; struct field Imeta_downloaded should be ImetaDownloaded
Open

    Imeta_downloaded             bool
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; struct field Cram_is_phix should be CramIsPhix
Open

    Cram_is_phix                 bool
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; struct field Fastq_2_path should be Fastq2Path
Open

    Fastq_2_path                 string
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; struct field Fastq_extracted_success should be FastqExtractedSuccess
Open

    Fastq_extracted_success      bool
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; struct field Cram_download_success should be CramDownloadSuccess
Open

    Cram_download_success        bool
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; struct field Symlinked_fq_1 should be SymlinkedFq1
Open

    Symlinked_fq_1               string
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; struct field Imeta_parsed should be ImetaParsed
Open

    Imeta_parsed                 bool
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; var bwa_ram should be bwaRAM
Open

    bwa_ram := viper.GetString("bwa_ram")
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; struct field Realigned_quickcheck_success should be RealignedQuickcheckSuccess
Open

    Realigned_quickcheck_success bool
Severity: Minor
Found in irods_downloader.go by golint

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"
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; var cram_list should be cramList
Open

var cram_list []cram_file
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; var star_exec should be starExec
Open

    star_exec := viper.GetString("star_exec")
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; var cram_exists_map should be cramExistsMap
Open

        cram_exists_map := make(map[string]string)
Severity: Minor
Found in irods_downloader.go by golint

don't use underscores in Go names; var library_type should be libraryType
Open

                library_type := ""
Severity: Minor
Found in irods_downloader.go by golint
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