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Merge pull request #289 from RoanKanninga/b37_gearshift
updates for new GATK4 pipeline on new diagnostic clusters
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@@ -21,8 +21,7 @@ batchID | |
| 20 | ||
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| 22 | ||
| Xp | ||
| Xnp | ||
| X | ||
| Y | ||
| MT | ||
| NC_001422.1 | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,31 @@ | ||
| #!/bin/bash | ||
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||
| # | ||
| # Use either WORKSPACE location for Jenkins or | ||
| # resolve path to scripts we need to check | ||
| # when executed manually outside Jenkins. | ||
| # | ||
| if [[ -z "${WORKSPACE:-}" ]]; then | ||
| MYDIR="$(cd -P "$(dirname "${0}")" && pwd)" | ||
| WORKSPACE="$(dirname ${MYDIR})" | ||
| fi | ||
|
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||
| echo '#####################################################################################' | ||
| echo ' Bash code must be indented with TABs. Checking for lines indented with spaces ... ' | ||
| echo '#####################################################################################' | ||
| grep -n '^[[:space:]]* [[:space:]]*' "${WORKSPACE:-../}"/{protocols,scripts}/*.*sh | ||
| grep_exit_status="${?}" | ||
| if [[ "${grep_exit_status}" -eq 0 ]]; then | ||
| echo '#####################################################################################' | ||
| echo ' ERROR: found Bash files containing lines (partially) indented with spaces.' | ||
| echo '#####################################################################################' | ||
| exit 1 | ||
| elif [[ "${grep_exit_status}" -eq 1 ]]; then | ||
| echo ' Ok: all Bash files indented with TABs.' | ||
| echo '####################################################################################' | ||
| exit 0 | ||
| else | ||
| echo ' FAILED: indentation sanity check failed.' | ||
| echo '####################################################################################' | ||
| exit 1 | ||
| fi |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,108 @@ | ||
| #!/bin/bash | ||
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| # | ||
| # Disable some shellcheck warnings: | ||
| # * SC2004: $/${} is unnecessary on arithmetic variables. | ||
| # But for consistency we prefer to always use ${} anyway. | ||
| # * SC2015: Note that A && B || C is not if-then-else. C may run when A is true. | ||
| # We know and use this construct regularly to create "transactions" | ||
| # where C is only executed when both A and B have succeeded. | ||
| # * SC2154: Due to Molgenis Compute string initialization the warning is not valid | ||
| # | ||
| # * SC2148: the shebang is declared in the header.ftl not in the protocols | ||
| # | ||
|
|
||
| export SHELLCHECK_OPTS="-e SC2004 -e SC2015 -e SC2154 -e SC2148" | ||
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||
| function showHelp() { | ||
| # | ||
| # Display commandline help on STDOUT. | ||
| # | ||
| cat <<EOH | ||
| =============================================================================================================== | ||
| Script for sanity checking of Bash code of this repo using ShellCheck. | ||
| Usage: | ||
| $(basename "${0}") OPTIONS | ||
| Options: | ||
| -h Show this help. | ||
| -v Enables verbose output. | ||
| =============================================================================================================== | ||
| EOH | ||
| exit 0 | ||
| } | ||
|
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||
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|
||
| # | ||
| # Parse commandline options | ||
| # | ||
| while getopts ":hv" opt | ||
| do | ||
| case "${opt}" in | ||
| h) | ||
| showHelp | ||
| ;; | ||
| v) | ||
| verbose='1' | ||
| ;; | ||
| \?) | ||
| printf '%s\n' "FATAL: Invalid option -${OPTARG}. Try $(basename "${0}") -h for help." | ||
| exit 1 | ||
| ;; | ||
| :) | ||
| printf '%s\n' "FATAL: Option -${OPTARG} requires an argument. Try $(basename "${0}") -h for help." | ||
| exit 1 | ||
| ;; | ||
| *) | ||
| printf '%s\n' "FATAL Unhandled option. Try $(basename "${0}") -h for help." | ||
| exit 1 | ||
| ;; | ||
| esac | ||
| done | ||
|
|
||
| # | ||
| # Check if ShellCheck is installed. | ||
| # | ||
| which shellcheck 2>&1 >/dev/null \ | ||
| || { | ||
| printf '%s\n' 'FATAL: cannot find shellcheck; make sure it is installed and can be found in ${PATH}.' | ||
| exit 1 | ||
| } | ||
|
|
||
| # | ||
| # Run ShellCheck for all Bash scripts in the bin/ subdir. | ||
| # * Includes sourced files, so the libraries from the lib/ subfolder | ||
| # are checked too as long a they are used in at least one script. | ||
| # * Select format and output based on whether this script is | ||
| # executed by Jenkins or by a regular user. | ||
| # | ||
| if [[ -n "${WORKSPACE:-}" ]] | ||
| then | ||
| # | ||
| # Exclude SC2154 (warning for variables that are referenced but not assigned), | ||
| # because we cannot easily resolve variables sourced from etc/*.cfg config files. | ||
| # | ||
| export SHELLCHECK_OPTS="${SHELLCHECK_OPTS} -e SC2154" | ||
| # | ||
| # ShellCheck for Jenkins. | ||
| # | ||
| shellcheck -a -x -o all -f checkstyle "${WORKSPACE}"/protocols/*.sh | tee checkstyle-result.xml | ||
| # | ||
| # Reformat the generated report to add hyperlinks to the ShellCheck issues on the wiki: | ||
| # https://github.com/koalaman/shellcheck/wiki/SC${ISSUENUMBER} | ||
| # explaining what is wrong with the code / style and how to improve it. | ||
| # | ||
| perl -pi -e "s|message='([^']+)'\s+source='ShellCheck.(SC[0-9]+)'|message='<a href="https://github.com/koalaman/shellcheck/wiki/\$2">\$2: \$1</a>' source='ShellCheck.\$2'|" checkstyle-result.xml | ||
| else | ||
| # | ||
| # ShellCheck for regular user on the commandline. | ||
| # | ||
| MYDIR="$(cd -P "$(dirname "${0}")" && pwd)" | ||
| if [[ "${verbose:-0}" -eq 1 ]] | ||
| then | ||
| cd "${MYDIR}/.." | ||
| shellcheck -a -x -o all -f tty protocols/*.sh # cannot use the printf construct used below for non-vebose output as it destroys the terminal colors. | ||
| cd '-' # Goes back to previous directory before we changed to ${MYDIR}. | ||
| else | ||
| printf '%s\n' "$(cd "${MYDIR}/.." && shellcheck -a -x -o all -f gcc protocols/*.sh)" | ||
| fi | ||
| fi |
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