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Move evaluation subworkflow to an independent workflow #3

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48 changes: 41 additions & 7 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ nextflow.enable.dsl = 2
*/

include { MULTIPLESEQUENCEALIGN } from './workflows/multiplesequencealign'
include { EVALUATEMSA } from './workflows/evaluatemsa'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_multiplesequencealign_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_multiplesequencealign_pipeline'

Expand Down Expand Up @@ -52,6 +53,29 @@ workflow NFCORE_MULTIPLESEQUENCEALIGN {
multiqc_report = MULTIPLESEQUENCEALIGN.out.multiqc

}

workflow NFCORE_EVALUATEMSA {

take:
msa_alignment // channel: [ meta, /path/to/file.aln ]
ch_refs // channel: [ meta, /path/to/file.aln ]
ch_structures_template // channel: [ meta, /path/to/file.pdb ]
stats_summary // channel: [ meta, /path/to/file.csv ]

main:
ch_versions = Channel.empty()

//
// WORKFLOW: Run evaluation pipelines
//
EVALUATEMSA (
msa_alignment,
ch_refs,
ch_structures_template,
stats_summary,
ch_versions
)
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN MAIN WORKFLOW
Expand All @@ -76,13 +100,23 @@ workflow {
params.tools
)

//
// WORKFLOW: Run main workflow
//
NFCORE_MULTIPLESEQUENCEALIGN (
PIPELINE_INITIALISATION.out.samplesheet,
PIPELINE_INITIALISATION.out.tools
)
if (params.evaluate) {
// WORKFLOW: Run evaluation workflow
NFCORE_EVALUATEMSA (
PIPELINE_INITIALISATION.out.msa_alignment,
PIPELINE_INITIALISATION.out.ch_refs,
PIPELINE_INITIALISATION.out.ch_structures_template,
PIPELINE_INITIALISATION.out.stats_summary
)
} else {
//
// WORKFLOW: Run main workflow
//
NFCORE_MULTIPLESEQUENCEALIGN (
PIPELINE_INITIALISATION.out.samplesheet,
PIPELINE_INITIALISATION.out.tools
)
}

//
// SUBWORKFLOW: Run completion tasks
Expand Down
1 change: 1 addition & 0 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ params {
extract_plddt = false

// Evaluation
evaluate = false
skip_eval = false
calc_sp = true
calc_tc = true
Expand Down
111 changes: 111 additions & 0 deletions workflows/evaluatemsa.nf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,111 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

// MODULES
include { MULTIQC } from '../modules/local/multiqc'
include { PREPARE_MULTIQC } from '../modules/local/prepare_multiqc'
include { PREPARE_SHINY } from '../modules/local/prepare_shiny'

//SUBWORKFLOWS
include { EVALUATE } from '../subworkflows/local/evaluate'

// FUNCTIONS
include { paramsSummaryMap } from 'plugin/nf-validation'
include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline'
include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'

workflow EVALUATEMSA {

take:
msa_alignment
ch_refs
ch_structures_template
stats_summary
ch_versions

main:
evaluation_summary = Channel.empty()
stats_and_evaluation_summary = Channel.empty()
ch_multiqc_table = Channel.empty()

//
// Evaluate the quality of the alignment
//
if (!params.skip_eval) {
EVALUATE (msa_alignment, ch_refs, ch_structures_template)
ch_versions = ch_versions.mix(EVALUATE.out.versions)
evaluation_summary = evaluation_summary.mix(EVALUATE.out.eval_summary)
}

//
// Combine stats and evaluation reports into a single CSV
//
if (!params.skip_stats || !params.skip_eval) {
stats_summary_csv = stats_summary.map{ meta, csv -> csv }
eval_summary_csv = evaluation_summary.map{ meta, csv -> csv }
stats_summary_csv.mix(eval_summary_csv)
.collect()
.map {
csvs ->
[ [ id:"summary_stats_eval" ], csvs ]
}
.set { stats_and_evaluation }
MERGE_STATS_EVAL (stats_and_evaluation)
stats_and_evaluation_summary = MERGE_STATS_EVAL.out.csv
ch_versions = ch_versions.mix(MERGE_STATS_EVAL.out.versions)
}

//
// MODULE: Shiny
//
if (!params.skip_shiny) {
shiny_app = Channel.fromPath(params.shiny_app)
PREPARE_SHINY (stats_and_evaluation_summary, shiny_app)
ch_shiny_stats = PREPARE_SHINY.out.data.toList()
ch_versions = ch_versions.mix(PREPARE_SHINY.out.versions)
}

softwareVersionsToYAML(ch_versions)
.collectFile(
storeDir: "${params.outdir}/pipeline_info",
name: 'nf_core_pipeline_software_mqc_versions.yml',
sort: true,
newLine: true
).set { ch_collated_versions }

//
// MODULE: MultiQC
//
multiqc_out = Channel.empty()
if (!params.skip_multiqc && (!params.skip_stats || !params.skip_eval)) {
ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))

PREPARE_MULTIQC (stats_and_evaluation_summary)
ch_multiqc_table = ch_multiqc_table.mix(PREPARE_MULTIQC.out.multiqc_table.collect{it[1]}.ifEmpty([]))

MULTIQC (
ch_multiqc_files.collect(),
ch_multiqc_config.toList(),
ch_multiqc_custom_config.toList(),
ch_multiqc_logo.toList(),
ch_multiqc_table
)
multiqc_out = MULTIQC.out.report.toList()
}

emit:
versions = ch_versions // channel: [ path(versions.yml) ]
multiqc = multiqc_out // channel: [ path(multiqc_report.html) ]
}
52 changes: 1 addition & 51 deletions workflows/multiplesequencealign.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -27,15 +27,8 @@ include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_mult
// SUBWORKFLOW: Local subworkflows
//
include { STATS } from '../subworkflows/local/stats'
include { EVALUATE } from '../subworkflows/local/evaluate'
include { CREATE_TCOFFEETEMPLATE } from '../modules/local/create_tcoffee_template'

//
// MODULE: local modules
//
include { PREPARE_MULTIQC } from '../modules/local/prepare_multiqc'
include { PREPARE_SHINY } from '../modules/local/prepare_shiny'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT NF-CORE MODULES/SUBWORKFLOWS
Expand Down Expand Up @@ -74,10 +67,7 @@ workflow MULTIPLESEQUENCEALIGN {

main:
ch_multiqc_files = Channel.empty()
ch_multiqc_table = Channel.empty()
evaluation_summary = Channel.empty()
stats_summary = Channel.empty()
stats_and_evaluation_summary = Channel.empty()
ch_shiny_stats = Channel.empty()

ch_input
Expand Down Expand Up @@ -210,43 +200,6 @@ workflow MULTIPLESEQUENCEALIGN {
msa_alignment.mix(MSA_ALIGNMENT.out.alignment)
}

//
// Evaluate the quality of the alignment
//
if (!params.skip_eval) {
EVALUATE (msa_alignment, ch_refs, ch_structures_template)
ch_versions = ch_versions.mix(EVALUATE.out.versions)
evaluation_summary = evaluation_summary.mix(EVALUATE.out.eval_summary)
}

//
// Combine stats and evaluation reports into a single CSV
//
if (!params.skip_stats || !params.skip_eval) {
stats_summary_csv = stats_summary.map{ meta, csv -> csv }
eval_summary_csv = evaluation_summary.map{ meta, csv -> csv }
stats_summary_csv.mix(eval_summary_csv)
.collect()
.map {
csvs ->
[ [ id:"summary_stats_eval" ], csvs ]
}
.set { stats_and_evaluation }
MERGE_STATS_EVAL (stats_and_evaluation)
stats_and_evaluation_summary = MERGE_STATS_EVAL.out.csv
ch_versions = ch_versions.mix(MERGE_STATS_EVAL.out.versions)
}

//
// MODULE: Shiny
//
if (!params.skip_shiny) {
shiny_app = Channel.fromPath(params.shiny_app)
PREPARE_SHINY (stats_and_evaluation_summary, shiny_app)
ch_shiny_stats = PREPARE_SHINY.out.data.toList()
ch_versions = ch_versions.mix(PREPARE_SHINY.out.versions)
}

softwareVersionsToYAML(ch_versions)
.collectFile(
storeDir: "${params.outdir}/pipeline_info",
Expand All @@ -272,15 +225,12 @@ workflow MULTIPLESEQUENCEALIGN {
ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))

PREPARE_MULTIQC (stats_and_evaluation_summary)
ch_multiqc_table = ch_multiqc_table.mix(PREPARE_MULTIQC.out.multiqc_table.collect{it[1]}.ifEmpty([]))

MULTIQC (
ch_multiqc_files.collect(),
ch_multiqc_config.toList(),
ch_multiqc_custom_config.toList(),
ch_multiqc_logo.toList(),
ch_multiqc_table
[]
)
multiqc_out = MULTIQC.out.report.toList()
}
Expand Down