Taskvalidate_read_group
Validate a ReadGroup struct's fields are defined and well-formed
sprocket run --entrypoint validate_read_group data_structures/read_group.wdldata_structures\read_group.wdl [INPUTS]...
Inputs
Required Inputs
Name
Type
Description
read_group
ReadGroup
ReadGroup struct to validate
ReadGroup struct to validate
Other Inputs
Name
Type
Default
Description
required_fields
Array[String]
[]
Array of read group fields that must be defined. The ID field is always required and does not need to be specified.
Array of read group fields that must be defined. The ID field is always required and does not need to be specified.
[]
restrictive
Boolean
true
If true, run a stricter validation of field values. Otherwise, check against SAM spec-defined values.
If true, run a stricter validation of field values. Otherwise, check against SAM spec-defined values.
true
Outputs
Name
Type
Default
Description
Default Runtime Attributes
Attribute
Value
container
"ghcr.io/stjudecloud/util:2.3.1"
Command
exit_code=0
if ~{restrictive}; then
if [[ ~{read_group.ID} =~ ^~{id_pattern}$ ]] \
|| [[ ~{read_group.ID} =~ ~{restrictive_pattern} ]]
then
>&2 echo "ID (~{read_group.ID}) must not match patterns:"
>&2 echo "'~{id_pattern}' or '~{restrictive_pattern}'"
exit_code=1
fi
fi
if [[ ! "~{read_group.ID}" =~ ^~{sam_spec_pattern}$ ]]; then
>&2 echo "ID must match pattern ~{sam_spec_pattern}"
exit_code=1
fi
if [ "$(echo "~{sep(" ", required_fields)}" | grep -Ewc "SM")" -eq 1 ]; then
if [ -z "~{read_group.SM}" ]; then
>&2 echo "SM is required"
exit_code=1
fi
fi
if ~{defined(read_group.SM)}; then
if ~{restrictive}; then
if [[ "~{read_group.SM}" =~ ^~{sample_pattern}$ ]] \
|| [[ "~{read_group.SM}" =~ ~{restrictive_pattern} ]]
then
>&2 echo "SM must not match patterns:"
>&2 echo "'~{sample_pattern}' or '~{restrictive_pattern}'"
exit_code=1
fi
fi
if [[ ! "~{read_group.SM}" =~ ^~{sam_spec_pattern}$ ]]; then
>&2 echo "SM must match pattern ~{sam_spec_pattern}"
exit_code=1
fi
fi
if [ "$(echo "~{sep(" ", required_fields)}" | grep -Ewc "BC")" -eq 1 ]; then
if [ -z "~{read_group.BC}" ]; then
>&2 echo "BC is required"
exit_code=1
fi
fi
if ~{defined(read_group.BC)}; then
if [[ ! "~{read_group.BC}" =~ ^~{sam_spec_pattern}$ ]]; then
>&2 echo "BC must match pattern ~{sam_spec_pattern}"
exit_code=1
fi
fi
if [ "$(echo "~{sep(" ", required_fields)}" | grep -Ewc "CN")" -eq 1 ]; then
if [ -z "~{read_group.CN}" ]; then
>&2 echo "CN is required"
exit_code=1
fi
fi
if ~{defined(read_group.CN)}; then
if [[ ! "~{read_group.CN}" =~ ^~{sam_spec_pattern}$ ]]; then
>&2 echo "CN must match pattern ~{sam_spec_pattern}"
exit_code=1
fi
fi
if [ "$(echo "~{sep(" ", required_fields)}" | grep -Ewc "DS")" -eq 1 ]; then
if [ -z "~{read_group.DS}" ]; then
>&2 echo "DS is required"
exit_code=1
fi
fi
if ~{defined(read_group.DS)}; then
if [[ ! "~{read_group.DS}" =~ ^~{sam_spec_pattern}$ ]]; then
>&2 echo "DS must match pattern ~{sam_spec_pattern}"
exit_code=1
fi
fi
if [ "$(echo "~{sep(" ", required_fields)}" | grep -Ewc "DT")" -eq 1 ]; then
if [ -z "~{read_group.DT}" ]; then
>&2 echo "DT is required"
exit_code=1
fi
fi
if ~{defined(read_group.DT)}; then
if [[ ! "~{read_group.DT}" =~ ^~{sam_spec_pattern}$ ]]; then
>&2 echo "DT must match pattern ~{sam_spec_pattern}"
exit_code=1
fi
fi
if [ "$(echo "~{sep(" ", required_fields)}" | grep -Ewc "FO")" -eq 1 ]; then
if [ -z "~{read_group.FO}" ]; then
>&2 echo "FO is required"
exit_code=1
fi
fi
if ~{defined(read_group.FO)}; then
if [[ ! "~{read_group.FO}" =~ ^\*|[ACMGRSVTWYHKDBN]+$ ]]; then
>&2 echo "FO must match pattern \*|[ACMGRSVTWYHKDBN]+"
exit_code=1
fi
fi
if [ "$(echo "~{sep(" ", required_fields)}" | grep -Ewc "KS")" -eq 1 ]; then
if [ -z "~{if defined(read_group.KS) then read_group.KS else ""}" ]; then
>&2 echo "KS is required"
exit_code=1
fi
fi
if ~{defined(read_group.KS)}; then
if [[ ! "~{read_group.KS}" =~ ^~{sam_spec_pattern}$ ]]; then
>&2 echo "KS must match pattern ~{sam_spec_pattern}"
exit_code=1
fi
fi
if [ "$(echo "~{sep(" ", required_fields)}" | grep -Ewc "LB")" -eq 1 ]; then
if [ -z "~{read_group.LB}" ]; then
>&2 echo "LB is required"
exit_code=1
fi
fi
if ~{defined(read_group.LB)}; then
if [[ ! "~{read_group.LB}" =~ ^~{sam_spec_pattern}$ ]]; then
>&2 echo "LB must match pattern ~{sam_spec_pattern}"
exit_code=1
fi
fi
if [ "$(echo "~{sep(" ", required_fields)}" | grep -Ewc "PG")" -eq 1 ]; then
if [ -z "~{read_group.PG}" ]; then
>&2 echo "PG is required"
exit_code=1
fi
fi
if ~{defined(read_group.PG)}; then
if [[ ! "~{read_group.PG}" =~ ^~{sam_spec_pattern}$ ]]; then
>&2 echo "PG must match pattern ~{sam_spec_pattern}"
exit_code=1
fi
fi
if [ "$(echo "~{sep(" ", required_fields)}" | grep -Ewc "PI")" -eq 1 ]; then
if [ -z "~{read_group.PI}" ]; then
>&2 echo "PI is required"
exit_code=1
fi
fi
if ~{defined(read_group.PI)}; then
if [[ ! "~{read_group.PI}" =~ ^[0-9]+$ ]]; then
>&2 echo "PI must match pattern [0-9]+"
exit_code=1
fi
fi
if [ "$(echo "~{sep(" ", required_fields)}" | grep -Ewc "PL")" -eq 1 ]; then
if [ -z "~{read_group.PL}" ]; then
>&2 echo "PL is required"
exit_code=1
fi
fi
if ~{defined(read_group.PL)}; then
if [[ ! "~{read_group.PL}" =~ ^~{sep("|", platforms)}$ ]]; then
>&2 echo "PL must match pattern ~{sep("|", platforms)}"
exit_code=1
fi
fi
if [ "$(echo "~{sep(" ", required_fields)}" | grep -Ewc "PM")" -eq 1 ]; then
if [ -z "~{read_group.PM}" ]; then
>&2 echo "PM is required"
exit_code=1
fi
fi
if ~{defined(read_group.PM)}; then
if [[ ! "~{read_group.PM}" =~ ^~{sam_spec_pattern}$ ]]; then
>&2 echo "PM must match pattern ~{sam_spec_pattern}"
exit_code=1
fi
fi
if [ "$(echo "~{sep(" ", required_fields)}" | grep -Ewc "PU")" -eq 1 ]; then
if [ -z "~{read_group.PU}" ]; then
>&2 echo "PU is required"
exit_code=1
fi
fi
if ~{defined(read_group.PU)}; then
if [[ ! "~{read_group.PU}" =~ ^~{sam_spec_pattern}$ ]]; then
>&2 echo "PU must match pattern ~{sam_spec_pattern}"
exit_code=1
fi
fi
exit $exit_code 
