Merge branch 'nextflow-version' into 'dev'
nf version See merge request epi2melabs/workflows/wf-transcriptomes!117
This commit is contained in:
Sarah Griffiths
commit
dd8466e62d
@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [updated]
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### Changed
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- Nextflow minimum required version to 23.04.2
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## [v0.2.1]
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### Changed
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- Any sample aliases that contain spaces will be replaced with underscores.
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@ -182,8 +182,8 @@ class NfcoreSchema {
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println ''
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log.error 'ERROR: Validation of pipeline parameters failed!'
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JSONObject exceptionJSON = e.toJSON()
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printExceptions(exceptionJSON, params_json, log, enums)
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println ''
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HashSet<String> observed_exceptions = []
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printExceptions(exceptionJSON, params_json, log, enums, raw_schema, observed_exceptions)
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has_error = true
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}
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@ -196,7 +196,7 @@ class NfcoreSchema {
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warn_msg = warn_msg + "\n* --${unexpectedParam}: ${params[unexpectedParam].toString()}"
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}
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log.warn warn_msg
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log.info "- ${colors.dim}Ignore this warning: params.schema_ignore_params = \"${unexpectedParams.join(',')}\" ${colors.reset}"
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log.info "${colors.dim}- Ignore this warning: params.schema_ignore_params = \"${unexpectedParams.join(',')}\" ${colors.reset}"
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println ''
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}
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@ -361,16 +361,150 @@ class NfcoreSchema {
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return output
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}
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// Traverse the raw_schema to resolve a $ref, returning a JSONObject or JSONArray.
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private static def getSchemaLocation(raw_schema, schema_components) {
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// a quick search did not reveal how to resolve a $ref inside a
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// JSONObject so we'll go with traversing it ourselves!
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def head = raw_schema
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for (component in schema_components) {
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if (component == '#') {
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continue
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}
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else if (component.isNumber()) {
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// assume numeric components are indexing an array
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head = head[component as int]
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}
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else {
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// otherwise grab by key
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head = head[component]
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}
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}
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return head
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}
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// Return a map of dependencies for a path in a schema, that relate to a key that is known to be missing.
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// Each key in the map is a parameter that has been switched on and has a requirement on the missing key.
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// The value of each key in the map is a list of all parameters that are required by the corresponding key.
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private static HashMap<String, String> getSchemaDependencies(raw_schema, schema_components, missing_key) {
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def head = getSchemaLocation(raw_schema, schema_components[1..-1] + 'dependencies')
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HashMap<String, String> requirements = []
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for (key in head.keySet()) {
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if (head[key].contains(missing_key)) {
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requirements[key] = head[key]
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}
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}
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return requirements
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}
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// Return a list of all required parameters that are adjacent to a given path in a schema
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private static ArrayList getSchemaRequirements(raw_schema, schema_components) {
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def head = getSchemaLocation(raw_schema, schema_components[1..-2])
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ArrayList requirements = []
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for (entry in head) {
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// this could be an allOf with more allOf/oneOf/anyOf inside
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// we'll ignore anything that isn't a required key
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if (entry.has("required")) {
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requirements += entry["required"]
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}
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}
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return requirements
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}
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//
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// Loop over nested exceptions and print the causingException
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//
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private static void printExceptions(ex_json, params_json, log, enums) {
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private static void printExceptions(ex_json, params_json, log, enums, raw_schema, observed_exceptions) {
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def causingExceptions = ex_json['causingExceptions']
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if (causingExceptions.length() == 0) {
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def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/
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// Missing required param
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if (m.matches()) {
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log.error "* Missing required parameter: --${m[0][1]}"
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// Missing required param...
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if (ex_json["keyword"] == "required") {
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def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/
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// ...but what sort of required param
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ArrayList schema_components = ex_json['schemaLocation'].split('/')
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if (schema_components[-1].isNumber()) {
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// schemaLocation ends in array position, indicating use of
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// xOf in the schema. this is some sort of complex definition
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String schema_error_location = schema_components[1..-2].join('.')
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String composition_type = schema_components[-2]
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if (schema_error_location in observed_exceptions){
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return
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}
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// try to check the schema to get the adjacent requirements
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ArrayList requirement_group = []
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try {
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requirement_group = getSchemaRequirements(raw_schema, schema_components)
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}
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catch (groovy.lang.MissingPropertyException e) {}
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if (requirement_group.size() == 0) {
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// fall back to old error if we cannot read the schema
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log.error "* Missing required parameter: --${m[0][1]}"
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return
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}
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else if (composition_type == "allOf") {
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// similarly, use the old error for all members of an allOf
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for (choice in requirement_group) {
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log.error "* Missing required parameter: --${choice}"
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}
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return
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}
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// construct an appropriate message for the other types of composition
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String stderr_msg_prefix = "* Bad parameter configuration. "
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if (composition_type == "oneOf") {
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stderr_msg_prefix += "You must select only one option of:"
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}
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else if (composition_type == "anyOf") {
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stderr_msg_prefix += "You must select at least one of:"
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}
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ArrayList stderr_msg = [stderr_msg_prefix]
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// glue choices to error
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for (choice in requirement_group) {
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stderr_msg += " --${choice}"
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}
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log.error stderr_msg.join('\n')
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// suppress similar warnings
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observed_exceptions.add(schema_error_location)
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}
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else {
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// boring simple required
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log.error "* Missing required parameter: --${m[0][1]}"
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}
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}
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// Missing dependent param
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else if (ex_json['keyword'] == "dependencies") {
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def m = ex_json['message'] =~ /property \[([^\]]+)\] is required/
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HashMap<String, String> dependent_group = []
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ArrayList schema_components = ex_json['schemaLocation'].split('/')
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// try to check the schema to get the dependencies
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try {
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dependent_group = getSchemaDependencies(raw_schema, schema_components, m[0][1])
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}
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catch (groovy.lang.MissingPropertyException e) {}
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if (dependent_group.size() == 0) {
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// fall back to old error if we cannot read the schema
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log.error "* Missing required parameter: --${m[0][1]}"
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return
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}
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// we don't actually get told which parameter triggered the dependency
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// only the name of the parameter that is actually missing.
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// dependent_group will contain a list of triggering keys and their
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// deps so we can print them all out for the user.
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for (trigger_key in dependent_group.keySet()) {
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String schema_error_location = "${ex_json.schemaLocation}/dependencies/${trigger_key}"
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if (schema_error_location in observed_exceptions){
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return
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}
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String stderr_msg_prefix = "* Missing parameter(s) that are required by --${trigger_key}:"
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ArrayList stderr_msg = [stderr_msg_prefix]
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// list dependencies of trigger_key that are not in the params_json
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for (dep_key in dependent_group[trigger_key]) {
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if (!params_json.has(dep_key)) {
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stderr_msg += " --${dep_key}"
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}
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}
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log.error stderr_msg.join('\n')
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// suppress similar warnings
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observed_exceptions.add(schema_error_location)
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}
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}
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// Other base-level error
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else if (ex_json['pointerToViolation'] == '#') {
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@ -381,11 +515,11 @@ class NfcoreSchema {
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def param = ex_json['pointerToViolation'] - ~/^#\//
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def param_val = params_json[param].toString()
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if (ex_json['message'] =~ /.*not a valid enum value.*/) {
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String stderr_msg = "* --${param}: ${param_val} is not a valid choice, pick one of:\n"
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ArrayList stderr_msg = ["* --${param}: ${param_val} is not a valid choice, pick one of:"]
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for (choice in enums[param]) {
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stderr_msg += " - ${choice}\n"
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stderr_msg += " - ${choice}"
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}
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log.error stderr_msg // avoid silly new lines between choices
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log.error stderr_msg.join('\n') // avoid silly new lines between choices by printing one string
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}
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else {
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log.error "* --${param}: ${ex_json['message']} (${param_val})"
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@ -393,7 +527,7 @@ class NfcoreSchema {
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}
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}
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for (ex in causingExceptions) {
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printExceptions(ex, params_json, log, enums)
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printExceptions(ex, params_json, log, enums, raw_schema, observed_exceptions)
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}
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}
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1
main.nf
1
main.nf
@ -545,6 +545,7 @@ workflow pipeline {
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// So map this reference to all sample_ids
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seq_for_transcriptome_build = sample_ids.flatten().combine(ref_genome)
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}
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get_transcriptome(
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merge_gff_bundles.out.gff
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.join(run_gffcompare.out.gffcmp_dir)
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@ -114,7 +114,7 @@ manifest {
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homePage = 'https://github.com/epi2me-labs/wf-transcriptomes'
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description = 'Transcriptome analysis including gene fusions, differential expression as well as assembly and annotation of cDNA and direct RNA sequencing data.'
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mainScript = 'main.nf'
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nextflowVersion = '>=22.10.8'
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nextflowVersion = '>=23.04.2'
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version = 'v0.2.1'
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}
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@ -162,7 +162,8 @@ workflow differential_expression {
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main:
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checkSampleSheetCondition(sample_sheet)
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t_index = build_minimap_index_transcriptome(ref_transcriptome)
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mapped = map_transcriptome(full_len_reads.combine(t_index))
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mapped = map_transcriptome(full_len_reads.combine(t_index)
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.map{meta, fastq, reference, transcriptome -> tuple(meta, fastq, reference) })
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count_transcripts(mapped.bam.combine(t_index.map{ mmi, reference -> reference}))
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merged = mergeCounts(count_transcripts.out.counts.collect())
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merged_TPM = mergeTPM(count_transcripts.out.counts.collect())
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