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Subworkflow language server fixes #593

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Subworkflow language server fixes #593

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23b8cd0
Fix nallo utils wip
fellen31 Mar 3, 2025
7736597
fix subworkflow
fellen31 Mar 4, 2025
c8db68a
CHANGELOG
fellen31 Mar 4, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Changed`

- [#591](https://github.com/genomic-medicine-sweden/nallo/pull/591) - Updated version to 0.6.0dev
- [#593](https://github.com/genomic-medicine-sweden/nallo/pull/593) - Updated local subworkflow to fix Nextflow language server issues

### `Removed`

Expand Down
251 changes: 119 additions & 132 deletions subworkflows/local/utils_nfcore_nallo_pipeline/main.nf
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Expand Up @@ -17,109 +17,6 @@ include { imNotification } from '../../nf-core/utils_nfcore_pipeline'
include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline'
include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DEFINE DEPENDENCIES (FILES AND WORKFLOWS) FOR OTHER WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

//
// nf-validation does not support contitional file and params validation,
// add these here.
//

//
// Define subworkflows and their associated "--skip"
//
def workflowSkips = [
assembly : "skip_genome_assembly",
mapping : "skip_alignment",
snv_calling : "skip_snv_calling",
snv_annotation : "skip_snv_annotation",
sv_calling : "skip_sv_calling",
sv_annotation : "skip_sv_annotation",
call_paralogs : "skip_call_paralogs",
cnv_calling : "skip_cnv_calling",
phasing : "skip_phasing",
rank_variants : "skip_rank_variants",
repeat_calling : "skip_repeat_calling",
repeat_annotation: "skip_repeat_annotation",
methylation : "skip_methylation_pileups",
qc : "skip_qc",
]

//
// E.g., the CNV-calling workflow depends on mapping and snv_calling and can't run without them.
//
def workflowDependencies = [
call_paralogs : ["mapping"],
snv_calling : ["mapping"],
qc : ["mapping"],
sv_calling : ["mapping"],
sv_annotation : ["mapping", "cnv_calling", "sv_calling"],
snv_annotation : ["mapping", "snv_calling"],
cnv_calling : ["mapping", "snv_calling"],
phasing : ["mapping", "snv_calling"],
rank_variants : ["mapping", "snv_calling", "snv_annotation", "sv_annotation"],
repeat_calling : ["mapping", "snv_calling", "phasing"],
repeat_annotation: ["mapping", "snv_calling", "phasing", "repeat_calling"],
methylation : ["mapping", "snv_calling"]
]

//
// E.g., the par_regions file is required by the assembly workflow and the assembly workflow can't run without par_regions
//
def fileDependencies = [
mapping : ["fasta", "somalier_sites"],
assembly : ["fasta"], // The assembly workflow should perhaps be split into two - assembly and alignment (requires ref)
snv_calling : ["fasta", "par_regions"],
snv_annotation : ["echtvar_snv_databases", "vep_cache", "vep_plugin_files", "variant_consequences_snvs"],
sv_calling : ["fasta"],
sv_annotation : ["svdb_sv_databases", "vep_cache", "vep_plugin_files", "variant_consequences_svs"],
cnv_calling : ["hificnv_expected_xy_cn", "hificnv_expected_xx_cn", "hificnv_excluded_regions"],
rank_variants : ["genmod_reduced_penetrance", "genmod_score_config_snvs", "genmod_score_config_svs"],
repeat_calling : ["trgt_repeats"],
repeat_annotation: ["stranger_repeat_catalog"],
]

def parameterStatus = [
workflow: [
skip_snv_calling : params.skip_snv_calling,
skip_phasing : params.skip_phasing,
skip_methylation_pileups : params.skip_methylation_pileups,
skip_rank_variants : params.skip_rank_variants,
skip_repeat_calling : params.skip_repeat_calling,
skip_repeat_annotation : params.skip_repeat_annotation,
skip_snv_annotation : params.skip_snv_annotation,
skip_sv_calling : params.skip_sv_calling,
skip_sv_annotation : params.skip_sv_annotation,
skip_call_paralogs : params.skip_call_paralogs,
skip_cnv_calling : params.skip_cnv_calling,
skip_alignment : params.skip_alignment,
skip_qc : params.skip_qc,
skip_genome_assembly : params.skip_genome_assembly,
],
files: [
par_regions : params.par_regions,
echtvar_snv_databases : params.echtvar_snv_databases,
svdb_sv_databases : params.svdb_sv_databases,
somalier_sites : params.somalier_sites,
vep_cache : params.vep_cache,
hificnv_expected_xy_cn : params.hificnv_expected_xy_cn,
hificnv_expected_xx_cn : params.hificnv_expected_xx_cn,
hificnv_excluded_regions : params.hificnv_excluded_regions,
fasta : params.fasta,
trgt_repeats : params.trgt_repeats,
stranger_repeat_catalog : params.stranger_repeat_catalog,
genmod_reduced_penetrance: params.genmod_reduced_penetrance,
genmod_score_config_snvs : params.genmod_score_config_snvs,
genmod_score_config_svs : params.genmod_score_config_svs,
variant_consequences_snvs: params.variant_consequences_snvs,
variant_consequences_svs : params.variant_consequences_svs,
vep_plugin_files : params.vep_plugin_files,
]
]

/*
SUBWORKFLOW TO INITIALISE PIPELINE
*/
Expand Down Expand Up @@ -164,6 +61,103 @@ workflow PIPELINE_INITIALISATION {
nextflow_cli_args
)

//
// nf-validation does not support contitional file and params validation,
// add these here.
//

//
// Define subworkflows and their associated "--skip"
//
def workflowSkips = [
assembly : "skip_genome_assembly",
mapping : "skip_alignment",
snv_calling : "skip_snv_calling",
snv_annotation : "skip_snv_annotation",
sv_calling : "skip_sv_calling",
sv_annotation : "skip_sv_annotation",
call_paralogs : "skip_call_paralogs",
cnv_calling : "skip_cnv_calling",
phasing : "skip_phasing",
rank_variants : "skip_rank_variants",
repeat_calling : "skip_repeat_calling",
repeat_annotation: "skip_repeat_annotation",
methylation : "skip_methylation_pileups",
qc : "skip_qc",
]

//
// E.g., the CNV-calling workflow depends on mapping and snv_calling and can't run without them.
//
def workflowDependencies = [
call_paralogs : ["mapping"],
snv_calling : ["mapping"],
qc : ["mapping"],
sv_calling : ["mapping"],
sv_annotation : ["mapping", "cnv_calling", "sv_calling"],
snv_annotation : ["mapping", "snv_calling"],
cnv_calling : ["mapping", "snv_calling"],
phasing : ["mapping", "snv_calling"],
rank_variants : ["mapping", "snv_calling", "snv_annotation", "sv_annotation"],
repeat_calling : ["mapping", "snv_calling", "phasing"],
repeat_annotation: ["mapping", "snv_calling", "phasing", "repeat_calling"],
methylation : ["mapping", "snv_calling"]
]

//
// E.g., the par_regions file is required by the assembly workflow and the assembly workflow can't run without par_regions
//
def fileDependencies = [
mapping : ["fasta", "somalier_sites"],
assembly : ["fasta"], // The assembly workflow should perhaps be split into two - assembly and alignment (requires ref)
snv_calling : ["fasta", "par_regions"],
snv_annotation : ["echtvar_snv_databases", "vep_cache", "vep_plugin_files", "variant_consequences_snvs"],
sv_calling : ["fasta"],
sv_annotation : ["svdb_sv_databases", "vep_cache", "vep_plugin_files", "variant_consequences_svs"],
cnv_calling : ["hificnv_expected_xy_cn", "hificnv_expected_xx_cn", "hificnv_excluded_regions"],
rank_variants : ["genmod_reduced_penetrance", "genmod_score_config_snvs", "genmod_score_config_svs"],
repeat_calling : ["trgt_repeats"],
repeat_annotation: ["stranger_repeat_catalog"],
]

def parameterStatus = [
workflow: [
skip_snv_calling : params.skip_snv_calling,
skip_phasing : params.skip_phasing,
skip_methylation_pileups : params.skip_methylation_pileups,
skip_rank_variants : params.skip_rank_variants,
skip_repeat_calling : params.skip_repeat_calling,
skip_repeat_annotation : params.skip_repeat_annotation,
skip_snv_annotation : params.skip_snv_annotation,
skip_sv_calling : params.skip_sv_calling,
skip_sv_annotation : params.skip_sv_annotation,
skip_call_paralogs : params.skip_call_paralogs,
skip_cnv_calling : params.skip_cnv_calling,
skip_alignment : params.skip_alignment,
skip_qc : params.skip_qc,
skip_genome_assembly : params.skip_genome_assembly,
],
files: [
par_regions : params.par_regions,
echtvar_snv_databases : params.echtvar_snv_databases,
svdb_sv_databases : params.svdb_sv_databases,
somalier_sites : params.somalier_sites,
vep_cache : params.vep_cache,
hificnv_expected_xy_cn : params.hificnv_expected_xy_cn,
hificnv_expected_xx_cn : params.hificnv_expected_xx_cn,
hificnv_excluded_regions : params.hificnv_excluded_regions,
fasta : params.fasta,
trgt_repeats : params.trgt_repeats,
stranger_repeat_catalog : params.stranger_repeat_catalog,
genmod_reduced_penetrance: params.genmod_reduced_penetrance,
genmod_score_config_snvs : params.genmod_score_config_snvs,
genmod_score_config_svs : params.genmod_score_config_svs,
variant_consequences_snvs: params.variant_consequences_snvs,
variant_consequences_svs : params.variant_consequences_svs,
vep_plugin_files : params.vep_plugin_files,
]
]

//
// Custom validation for pipeline parameters
//
Expand All @@ -187,9 +181,8 @@ workflow PIPELINE_INITIALISATION {
[ sample, metas[0] + [n_files: metas.size() + metas.size() * Math.max(0, params.alignment_processes - 1), single_end:true ], reads ]
}
// Convert back to [ meta, reads ]
.flatMap {
sample, meta, reads ->
reads.collect { return [ meta, it ] }
.flatMap { _sample, meta, reads ->
reads.collect { return [ meta, it ] }
}
.set { ch_samplesheet }

Expand Down Expand Up @@ -271,7 +264,7 @@ def validateInputParameters(statusMap, workflowMap, workflowDependencies, fileDe
//
def validateInputSamplesheet(input) {
// Filenames needs to be unique for each sample to avoid collisions when merging
fileNames = input[2].collect { new File(it.toString()).name }
def fileNames = input[2].collect { new File(it.toString()).name }
if (fileNames.size() != fileNames.unique().size()) {
error "Error: Input filenames needs to be unique for each sample."
}
Expand Down Expand Up @@ -336,7 +329,7 @@ def citationBibliographyText(ch_versions, references_yaml, description) {

def unwantedReferences = ['genomic-medicine-sweden/nallo', 'Nextflow']
// These are not collected in ch_versions but should be referenced
baseTools = Channel.from(['nextflow', 'nf_core', 'bioconda', 'biocontainers', 'multiqc'])
def baseTools = Channel.from(['nextflow', 'nf_core', 'bioconda', 'biocontainers', 'multiqc'])

ch_versions
.map { module_yaml -> extractSoftwareFromVersions(module_yaml) }
Expand All @@ -361,19 +354,13 @@ def citationBibliographyText(ch_versions, references_yaml, description) {
def validateParameterCombinations(statusMap, workflowMap, workflowDependencies, fileDependencies) {
// Array to store errors
def errors = []
// For each of the "workflow", "files"
statusMap.each { paramsType, allParams ->
// Go through all params and their status
statusMap[paramsType].each { param, paramStatus ->
switch (paramsType) {
case "files":
checkFileDependencies(param, fileDependencies, statusMap, workflowMap, errors)
break
case "workflow":
checkWorkflowDependencies(param, workflowDependencies, statusMap, workflowMap, errors)
break
default:
break
// For each of the "workflow", "files" - TODO: All errors now are comming from other parts of the workflow
statusMap.each { paramsType, paramsMap ->
paramsMap.each { param, _paramStatus ->
if (paramsType == "files") {
checkFileDependencies(param, fileDependencies, statusMap, workflowMap, errors)
} else if (paramsType == "workflow") {
checkWorkflowDependencies(param, workflowDependencies, statusMap, workflowMap, errors)
}
}
}
Expand All @@ -393,10 +380,10 @@ def validateParameterCombinations(statusMap, workflowMap, workflowDependencies,
def checkWorkflowDependencies(String skip, Map combinationsMap, Map statusMap, Map workflowMap, List errors) {

// Lookup the workflow associated with the --skip_xxx parameter
currentWorkflow = workflowMap.find { key, mapValue -> mapValue == skip }?.key
def currentWorkflow = workflowMap.find { _key, mapValue -> mapValue == skip }?.key

// If the --skip is not set, then the workflow is active, give no error
workflowIsActive = !statusMap["workflow"][skip]
def workflowIsActive = !statusMap["workflow"][skip]
if(workflowIsActive) {
return
}
Expand Down Expand Up @@ -426,7 +413,7 @@ def checkFileDependencies(String file, Map combinationsMap, Map statusMap, Map w
// Get all workflows required by a file
def workflowThatRequiresFile = findKeysForValue(file, combinationsMap)

for (workflow in workflowThatRequiresFile) {
workflowThatRequiresFile.each { workflow ->
// Get the "--skip" for that workflow
def workflowSkip = workflowMap[workflow]
// Get the status of the "--skip", if false then workflow is active
Expand All @@ -449,11 +436,11 @@ def findRequiredSkips(paramType, Set<String> requiredWorkflows, Map statusMap, M

def requiredSkips = []

for (currentWorkflow in requiredWorkflows) {
requiredWorkflows.each { currentWorkflow ->
// Get the skip associated with the workflow
skip = workflowMap[currentWorkflow]
def skip = workflowMap[currentWorkflow]

workflowIsSkipped = !statusMap[paramType][skip]
def workflowIsSkipped = !statusMap[paramType][skip]

if(paramType == "workflow") {
if(workflowIsSkipped) {
Expand All @@ -468,7 +455,7 @@ def findKeysForValue(def valueToFind, Map map) {

def keys = []

for (entry in map) {
map.each { entry ->
def key = entry.key
def value = entry.value

Expand Down Expand Up @@ -505,14 +492,14 @@ def validateAllFamiliesHasAffectedSamples(ch_samplesheet, params) {
}

def familiesWithPhenotypes = ch_samplesheet
.map { meta, reads -> [ meta.family_id, meta.phenotype ] }
.map { meta, _reads -> [ meta.family_id, meta.phenotype ] }
.groupTuple()

def familiesWithoutAffected = familiesWithPhenotypes
.filter { family, phenotype -> !phenotype.contains(2) }
.filter { _family, phenotype -> !phenotype.contains(2) }

familiesWithoutAffected
.map { family, phenotype -> family }
.map { family, _phenotype -> family }
.collect()
.subscribe { familyList ->
if (familyList) {
Expand All @@ -523,7 +510,7 @@ def validateAllFamiliesHasAffectedSamples(ch_samplesheet, params) {

def validateSingleProjectPerRun(ch_samplesheet) {
ch_samplesheet
.map { meta, reads -> meta.project }
.map { meta, _reads -> meta.project }
.unique()
.count()
.map { n ->
Expand Down