Skip to content

Commit

Permalink
updated cma docker image and fixed template updates
Browse files Browse the repository at this point in the history
  • Loading branch information
@wsjung
wsjung committed Feb 13, 2024
1 parent 75da2a3 commit 9a34980
Show file tree
Hide file tree
Showing 4 changed files with 176 additions and 72 deletions.
4 changes: 2 additions & 2 deletions modules/local/cma/cma/main.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ process CMA {

label 'process_low'

container 'docker://jungwooseok/cma:1.2.6' // TODO: replace when released on bioconductor
container 'docker://jungwooseok/cma:1.2.7' // TODO: replace when released on bioconductor

input:
path input_files // list of input files to CMA (to accomodate arbitrary number of files)
Expand Down Expand Up @@ -34,7 +34,7 @@ process CMA {
cat <<-END_VERSIONS > versions.yml
"${task.process}":
R: \$(R --version | head -n1)
CMA: \$(Rscript -e "print(packageVersion('CMA'))")
CMA: \$(Rscript -e "print(packageVersion('corrmeta'))")
dplyr: \$(Rscript -e "print(packageVersion('dplyr'))")
END_VERSIONS
"""
Expand Down
5 changes: 0 additions & 5 deletions modules/nf-core/custom/dumpsoftwareversions/main.nf
View file

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

13 changes: 0 additions & 13 deletions nextflow.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -151,19 +151,6 @@ profiles {
charliecloud {
charliecloud.enabled = true
conda.enabled = false
<<<<<<< HEAD
=======
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
conda.enabled = false
>>>>>>> TEMPLATE
docker.enabled = false
singularity.enabled = false
podman.enabled = false
Expand Down
226 changes: 174 additions & 52 deletions workflows/omicsgenetraitassociation.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
include { paramsSummaryLog; paramsSummaryMap; fromSamplesheet } from 'plugin/nf-validation'

def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
Expand All @@ -15,27 +15,42 @@ log.info logo + paramsSummaryLog(workflow) + citation

WorkflowOmicsgenetraitassociation.initialise(params, log)

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CONFIG FILES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
// /*
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// CONFIG FILES
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// */

ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
// ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
// ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
// ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
// ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT LOCAL MODULES/SUBWORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

//
// MODULES: local modules
//
include { PASCAL } from '../modules/local/pascal'
include { MMAP } from '../modules/local/mmap/mmap'
include { MMAP_PARSE } from '../modules/local/mmap/mmap_parse'
include { PREPROCESS_PASCAL } from '../modules/local/mea/preprocess'
include { RUN_PASCAL } from '../modules/local/mea/pascal'
include { POSTPROCESS_PASCAL } from '../modules/local/mea/postprocess'
include { GO_ANALYSIS } from '../modules/local/mea/go_analysis'
include { MERGE_ORA_AND_SUMMARY } from '../modules/local/mea/merge_ora_and_summary'

//
// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
//
include { INPUT_CHECK } from '../subworkflows/local/input_check'
// include { INPUT_CHECK } from '../subworkflows/local/input_check'
include { PASCAL_SUBWORKFLOW } from '../subworkflows/local/pascal'
include { MMAP_SUBWORKFLOW } from '../subworkflows/local/mmap'
include { CMA_SUBWORKFLOW } from '../subworkflows/local/cma'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand All @@ -46,9 +61,9 @@ include { INPUT_CHECK } from '../subworkflows/local/input_check'
//
// MODULE: Installed directly from nf-core/modules
//
include { FASTQC } from '../modules/nf-core/fastqc/main'
include { MULTIQC } from '../modules/nf-core/multiqc/main'
include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
// include { FASTQC } from '../modules/nf-core/fastqc/main'
// include { MULTIQC } from '../modules/nf-core/multiqc/main'
// include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand All @@ -57,57 +72,171 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft
*/

// Info required for completion email and summary
def multiqc_report = []
// def multiqc_report = []

workflow OMICSGENETRAITASSOCIATION {

ch_versions = Channel.empty()
ch_mea_preprocess_input = Channel.empty()

//
// Validate and parse samplesheet
//
// TODO: deal with additional sources
Channel.fromSamplesheet("input")
.multiMap{ sample, trait, pascal, twas, additional_sources ->
def num_additional_sources = 0
if (additional_sources) {
num_additional_sources = additional_sources.countLines()
}
def meta = ["id": sample, "trait": trait]
pascal: [meta, pascal]
twas: [meta, twas]
num_additional_sources: [meta, num_additional_sources]
}
.set { ch_input }
// ch_input.pascal.view()
// ch_input.twas.view()
// ch_input.num_additional_sources.view()


//
// SUBWORKFLOW: Read in samplesheet, validate and stage input files
// MODULE: PASCAL
//
INPUT_CHECK (
file(params.input)
PASCAL_SUBWORKFLOW (
ch_input.pascal,
params.pascal_gene_annotation,
params.pascal_ref_panel
)
ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
// TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input")
// See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/
// ! There is currently no tooling to help you write a sample sheet schema
ch_pascal_output = PASCAL_SUBWORKFLOW.out.pascal_output
ch_pascal_cma_format = PASCAL_SUBWORKFLOW.out.cma_format_output
ch_versions = ch_versions.mix(PASCAL_SUBWORKFLOW.out.versions)

// ch_pascal_output.view()

//
// MODULE: Run FastQC
// SUBWORKFLOW: MMAP_SUBWORKFLOW
//
FASTQC (
INPUT_CHECK.out.reads
MMAP_SUBWORKFLOW (
params.mmap_gene_list,
params.trait,
ch_input.twas,
params.mmap_pedigree_file,
params.mmap_cov_matrix_file
)
ch_versions = ch_versions.mix(FASTQC.out.versions.first())
ch_mmap_parsed = MMAP_SUBWORKFLOW.out.parsed_mmap_output
ch_mmap_cma_format = MMAP_SUBWORKFLOW.out.cma_format_output
ch_versions = ch_versions.mix(MMAP_SUBWORKFLOW.out.versions)

//
// MODULE: run CMA
//

CUSTOM_DUMPSOFTWAREVERSIONS (
ch_versions.unique().collectFile(name: 'collated_versions.yml')
// ch_pascal_cma_format.view()
// ch_mmap_cma_format.view()

ch_cma_input_files = ch_pascal_cma_format
.mix(ch_mmap_cma_format)
.toList()

CMA_SUBWORKFLOW (
ch_cma_input_files,
params.trait,
[]
)
ch_pval = CMA_SUBWORKFLOW.out.pval
.collect()
ch_versions = ch_versions.mix(CMA_SUBWORKFLOW.out.versions)

//
// MODULE: MultiQC
// MODULE: PREPROCESSFORPASCAL
//
workflow_summary = WorkflowOmicsgenetraitassociation.paramsSummaryMultiqc(workflow, summary_params)
ch_workflow_summary = Channel.value(workflow_summary)
ch_mea_preprocess_input = ch_pval
.multiMap{ pval ->
gene_score_file: pval
meta: tuple ( params.pipeline, params.trait, params.gene_col_name, params.pval_col_name)
}

methods_description = WorkflowOmicsgenetraitassociation.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params)
ch_methods_description = Channel.value(methods_description)
ch_module_files = Channel.fromPath("${params.module_file_dir}/*.txt")
.map { module_file ->
tuple ( module_file.baseName, module_file)
}

ch_multiqc_files = Channel.empty()
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
ch_preprocess_input = ch_mea_preprocess_input.gene_score_file
.combine(ch_module_files)
.combine(ch_mea_preprocess_input.meta)
.multiMap { gene_score_file, module_id, module_file_dir, pipeline, trait, gene_col_name, pval_col_name ->
gene_score_file: gene_score_file
module_file: tuple (module_id, module_file_dir)
meta: tuple (pipeline, trait, gene_col_name, pval_col_name)
}

MULTIQC (
ch_multiqc_files.collect(),
ch_multiqc_config.toList(),
ch_multiqc_custom_config.toList(),
ch_multiqc_logo.toList()
PREPROCESS_PASCAL (
ch_preprocess_input
)
multiqc_report = MULTIQC.out.report.toList()
ch_mea_paths = PREPROCESS_PASCAL.out.paths
ch_mea_meta = PREPROCESS_PASCAL.out.meta
ch_versions = ch_versions.mix(PREPROCESS_PASCAL.out.versions)

//
// MODULE: MEA PASCAL
//
RUN_PASCAL (
ch_mea_paths,
ch_mea_meta
)

ch_pascal_paths = RUN_PASCAL.out.paths
ch_pascal_meta = RUN_PASCAL.out.meta
ch_versions = ch_versions.mix(RUN_PASCAL.out.versions)

//
// MODULE: POSTPROCESS_PASCAL
//
POSTPROCESS_PASCAL (
ch_pascal_paths,
ch_pascal_meta,
params.numtests,
params.alpha
)
ch_postprocess_paths = POSTPROCESS_PASCAL.out.paths
ch_postprocess_meta = POSTPROCESS_PASCAL.out.meta
ch_versions = ch_versions.mix(POSTPROCESS_PASCAL.out.versions)

//
// MODULE: GO analysis
//
GO_ANALYSIS (
ch_postprocess_paths,
ch_postprocess_meta
)
ch_go_paths = GO_ANALYSIS.out.paths
ch_go_meta = GO_ANALYSIS.out.meta
ch_versions = ch_versions.mix(GO_ANALYSIS.out.versions)

//
// MODULE: MERGE_ORA_AND_SUMMARY
// TODO: each run of MERGE_ORA_AND_SUMMARY overwrites contents of summary_dir. should not happen
//
MERGE_ORA_AND_SUMMARY (
ch_go_paths,
ch_go_meta
)
ch_merge_summary_dir = MERGE_ORA_AND_SUMMARY.out.summary_dir
ch_merge_summary_files = MERGE_ORA_AND_SUMMARY.out.summary_files
ch_merge_meta = MERGE_ORA_AND_SUMMARY.out.meta
ch_merge_trait = MERGE_ORA_AND_SUMMARY.out.trait

// ch_merge_summary_files.collect().view()

// concatenate summary slices and write to master_summary_<trait>.csv
ch_master_summary = ch_merge_summary_files
.collectFile(name: "master_summary_${params.trait}.csv",
cache: false,
keepHeader: true,
skip: 1,
storeDir: "${params.outdir}/mea/"
)
}

/*
Expand All @@ -118,7 +247,7 @@ workflow OMICSGENETRAITASSOCIATION {

workflow.onComplete {
if (params.email || params.email_on_fail) {
NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
}
NfcoreTemplate.dump_parameters(workflow, params)
NfcoreTemplate.summary(workflow, params, log)
Expand All @@ -127,13 +256,6 @@ workflow.onComplete {
}
}

workflow.onError {
if (workflow.errorReport.contains("Process requirement exceeds available memory")) {
println("🛑 Default resources exceed availability 🛑 ")
println("💡 See here on how to configure pipeline: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources 💡")
}
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
Expand Down

0 comments on commit 9a34980

Please sign in to comment.