diff --git a/conf/base.config b/conf/base.config index 6dd25142..fbacfc64 100644 --- a/conf/base.config +++ b/conf/base.config @@ -44,7 +44,7 @@ process { memory = { 6.GB * task.attempt } } - withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:CUSTOMPROCESSING.*' { + withName: 'CUSTOMPROCESSING.*' { memory = { 10.GB * task.attempt } } @@ -89,31 +89,18 @@ process { memory = { 1.GB * task.attempt } } - withName: 'BBGTOOLS:DEEPCSA:OMEGANONPROT.*:SUBSETPANEL*' { - cpus = { 2 * task.attempt } - memory = { 4.GB * task.attempt } - } - withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:POSTPROCESSVEPPANEL*' { cpus = { 2 * task.attempt } memory = { 8.GB * task.attempt } } - withName: 'BBGTOOLS:DEEPCSA:MUTRATE.*:MUTRATE*' { - memory = { 8.GB * task.attempt } - } - - withName: 'BBGTOOLS:DEEPCSA:OMEGA.*:(PREPROCESSING|ESTIMATOR).*' { - memory = { 4.GB * task.attempt } - } - - // Catch-all for other OMEGA estimators not explicitly configured - // Keep conservative settings until we have usage data - withName: 'BBGTOOLS:DEEPCSA:OMEGA.*:ESTIMATOR_.*' { + // BBGTOOLS:DEEPCSA:OMEGA:ESTIMATOR and BBGTOOLS:DEEPCSA:OMEGA:PREPROCESSING + withName: 'PREPROCESSING|ESTIMATOR' { memory = { 4.GB * task.attempt } } - withName: 'BBGTOOLS:DEEPCSA:SIGNATURESNONPROT:SIGPROFILERASSIGNMENT*' { + // BBGTOOLS:DEEPCSA:SIGNATURESNONPROT:SIGPROFILERASSIGNMENT + withName: 'SIGPROFILERASSIGNMENT' { memory = { 2.GB * task.attempt } } @@ -127,7 +114,7 @@ process { memory = { 4.GB * task.attempt } } - withName: 'BBGTOOLS:DEEPCSA:MUTATEDCELLSVAF:MUTATEDGENOMESFROMVAFAM' { + withName: 'MUTATEDGENOMESFROMVAFAM' { errorStrategy = 'ignore' maxRetries = 1 } @@ -145,7 +132,7 @@ process { memory = { 30.GB * task.attempt } } - withName: 'BBGTOOLS:DEEPCSA:MUT_PREPROCESSING:FILTERNANOSEQSNP' { + withName: 'FILTERNANOSEQSNP' { memory = { 8.GB * task.attempt } } diff --git a/conf/exome.config b/conf/exome.config index ce7dbac5..a74e952a 100644 --- a/conf/exome.config +++ b/conf/exome.config @@ -93,17 +93,14 @@ process { - withName: '(BBGTOOLS:DEEPCSA:MUT_PREPROCESSING:SOMATICMUTATIONS*|BBGTOOLS:DEEPCSA:OMEGANONPROT.*:SUBSETPANEL*)' { + withName: 'BBGTOOLS:DEEPCSA:MUT_PREPROCESSING:SOMATICMUTATIONS*' { cpus = { 2 * task.attempt } memory = { 4.GB * task.attempt } time = { 360.min * task.attempt } } - - withName: 'BBGTOOLS:DEEPCSA:MUTRATE.*:MUTRATE*' { - memory = { 8.GB * task.attempt } - } - - withName: '(BBGTOOLS:DEEPCSA:OMEGA.*:(PREPROCESSING|ESTIMATOR).*|BBGTOOLS:DEEPCSA:MULTIQC)' { + + // BBGTOOLS:DEEPCSA:OMEGA:ESTIMATOR and BBGTOOLS:DEEPCSA:OMEGA:PREPROCESSING + withName: 'PREPROCESSING|ESTIMATOR|BBGTOOLS:DEEPCSA:MULTIQC' { memory = { 4.GB * task.attempt } } diff --git a/conf/modules.config b/conf/modules.config index 9d3dbe0b..76adb318 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -132,22 +132,11 @@ process { ] } - withName: SUBSETPILEUP { - ext.prefix = { ".subset_pileup" } - ext.args = '' - ext.args2 = '-s 1 -b 2 -e 2' - ext.args3 = '-h' - ext.extension = 'tsv' - ext.header = 'pile' - publishDir = [ - enabled: false - ] - } - withName: 'BBGTOOLS:DEEPCSA:.*ALL:.*' { ext.prefix = { ".all" } } + // Gated by params.profileintrons; "no matching selector" warning is expected when the feature is off withName: 'BBGTOOLS:DEEPCSA:.*INTRONS:.*' { ext.prefix = { ".introns" } } @@ -415,6 +404,7 @@ process { ] } + // Gated by params.profilenonprot; "no matching selector" warning is expected when the feature is off withName: '.*NONPROT:SUBSETMUTPROFILE' { ext.filters = { [ @@ -569,13 +559,6 @@ process { ] } - withName: READSPOSBED { - ext.tool = "readsxposition" - publishDir = [ - enabled: false - ] - } - withName: ONCODRIVECLUSTL { ext.args = "-sim region_restricted \ -kmer 3 \ @@ -650,7 +633,7 @@ process { } // BBGRegressions output configuration - withName: '.*:REGRESSIONS.*:EDITCONFIG' { + withName: 'EDITCONFIG' { publishDir = [ [ mode: params.publish_dir_mode, @@ -661,7 +644,8 @@ process { ] } - withName: '.*:REGRESSIONS.*:CREATE_INPUT' { + // REGRESSIONS:CREATE_INPUT + withName: 'CREATE_INPUT' { publishDir = [ [ mode: params.publish_dir_mode, @@ -672,7 +656,8 @@ process { ] } - withName: '.*:REGRESSIONS.*:MODELS' { + // REGRESSIONS:MODELS + withName: 'MODELS' { publishDir = [ [ mode: params.publish_dir_mode, @@ -682,7 +667,8 @@ process { ] } - withName: '.*:REGRESSIONS.*:PLOT' { + // REGRESSIONS:PLOT + withName: 'PLOT' { publishDir = [ [ mode: params.publish_dir_mode, diff --git a/conf/tmp_quick_fixes.config b/conf/tmp_quick_fixes.config index 4a473f0b..a47f7d25 100644 --- a/conf/tmp_quick_fixes.config +++ b/conf/tmp_quick_fixes.config @@ -15,11 +15,12 @@ process { errorStrategy = 'ignore' } - withName: 'BBGTOOLS:DEEPCSA:MUTATEDCELLSVAF:MUTATEDGENOMESFROMVAFAM' { + withName: 'MUTATEDGENOMESFROMVAFAM' { errorStrategy = 'ignore' maxRetries = 1 } + // Gated by params.expected_mutated_cells; "no matching selector" warning is expected when the feature is off withName: "BBGTOOLS:DEEPCSA:EXPECTEDMUTATEDCELLS:.*" { errorStrategy = 'ignore' maxRetries = 1 diff --git a/conf/tools/omega.config b/conf/tools/omega.config index c5bc60b5..9f8cee7b 100644 --- a/conf/tools/omega.config +++ b/conf/tools/omega.config @@ -73,6 +73,7 @@ process { ext.prefix = { ".multi" } } + // Gated by params.profilenonprot && params.positive_selection_non_protein_affecting && params.omega_multi; "no matching selector" warning is expected when the feature is off withName: 'BBGTOOLS:DEEPCSA:OMEGANONPROTMULTI:.*' { ext.prefix = { ".non_prot_aff.multi" } } @@ -86,6 +87,7 @@ process { ext.prefix = { ".multi.global_loc" } } + // Gated by params.omega_globalloc (+ params.profilenonprot && params.positive_selection_non_protein_affecting); "no matching selector" warning is expected when the feature is off withName: 'BBGTOOLS:DEEPCSA:OMEGANONPROT:.*GLOBALLOC' { ext.prefix = { ".non_prot_aff.global_loc" } } @@ -106,6 +108,7 @@ process { ] } + // BBGTOOLS:DEEPCSA:OMEGA:ESTIMATOR withName: ESTIMATOR { ext.option = 'mle' ext.args = "" @@ -185,8 +188,8 @@ process { ] } - - withName: 'PREPROCESSING.*|ESTIMATOR.*' { + // BBGTOOLS:DEEPCSA:OMEGA:ESTIMATOR and BBGTOOLS:DEEPCSA:OMEGA:PREPROCESSING + withName: 'PREPROCESSING|ESTIMATOR' { ext.assembly = params.vep_genome == 'GRCh38' ? 'hg38' : params.vep_genome == 'GRCm39' diff --git a/conf/tools/panels.config b/conf/tools/panels.config index 19098a6e..16681a58 100644 --- a/conf/tools/panels.config +++ b/conf/tools/panels.config @@ -57,67 +57,7 @@ process { ] } - withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:CREATESAMPLEPANELSALL' { - publishDir = [ - [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/regions/samplepanels/createsamplepanelsall" }, - pattern: "*{tsv,bed}", - ] - ] - } - - withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:CREATESAMPLEPANELSPROTAFFECT' { - publishDir = [ - [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/regions/samplepanels/createsamplepanelsprotaffect" }, - pattern: "*{tsv,bed}", - ] - ] - } - - withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:CREATESAMPLEPANELSNONPROTAFFECT' { - publishDir = [ - [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/regions/samplepanels/createsamplepanelsnonprotaffect" }, - pattern: "*{tsv,bed}", - ] - ] - } - - withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:CREATESAMPLEPANELSEXONS' { - publishDir = [ - [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/regions/samplepanels/createsamplepanelsexons" }, - pattern: "*{tsv,bed}", - ] - ] - } - - withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:CREATESAMPLEPANELSINTRONS' { - publishDir = [ - [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/regions/samplepanels/createsamplepanelsintrons" }, - pattern: "*{tsv,bed}", - ] - ] - } - - withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:CREATESAMPLEPANELSSYNONYMOUS' { - publishDir = [ - [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/regions/samplepanels/createsamplepanelssynonymous" }, - pattern: "*{tsv,bed}", - ] - ] - } - - withName: 'BBGTOOLS:DEEPCSA:ENRICHPANELS:EXPANDREGIONSALL' { + withName: 'EXPANDREGIONSALL|EXPANDREGIONSNONPROT|EXPANDREGIONSPROT|EXPANDREGIONSSYNONYMOUS|EXPANDREGIONSEXONS' { publishDir = [ [ mode: params.publish_dir_mode, @@ -127,43 +67,4 @@ process { ] } - withName: 'BBGTOOLS:DEEPCSA:ENRICHPANELS:EXPANDREGIONSNONPROT' { - publishDir = [ - [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/regions/expandedregions/" }, - pattern: "*{tsv,json}", - ] - ] - } - - withName: 'BBGTOOLS:DEEPCSA:ENRICHPANELS:EXPANDREGIONSPROT' { - publishDir = [ - [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/regions/expandedregions/" }, - pattern: "*{tsv,json}", - ] - ] - } - - withName: 'BBGTOOLS:DEEPCSA:ENRICHPANELS:EXPANDREGIONSSYNONYMOUS' { - publishDir = [ - [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/regions/expandedregions/" }, - pattern: "*{tsv,json}", - ] - ] - } - - withName: 'BBGTOOLS:DEEPCSA:ENRICHPANELS:EXPANDREGIONSEXONS' { - publishDir = [ - [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/regions/expandedregions/" }, - pattern: "*{tsv,json}", - ] - ] - } } diff --git a/modules/local/createpanels/sample/main.nf b/modules/local/createpanels/sample/main.nf deleted file mode 100644 index 02db32ef..00000000 --- a/modules/local/createpanels/sample/main.nf +++ /dev/null @@ -1,59 +0,0 @@ -process CREATESAMPLEPANELS { - tag "$meta.id" - label 'process_single' - label 'time_low' - - conda "bioconda::pybedtools=0.9.1--py38he0f268d_0" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pybedtools:0.9.1--py38he0f268d_0' : - 'biocontainers/pybedtools:0.9.1--py38he0f268d_0' }" - - - input: - tuple val(meta) , path(compact_captured_panel_annotation) - tuple val(meta2), path(depths) - val(min_depth) - - output: - path("*.tsv") , emit: sample_specific_panel - path("*.bed") , emit: sample_specific_panel_bed - path "versions.yml" , topic: versions - - - script: - def prefix = task.ext.prefix ?: "" - prefix = "${meta.id}${prefix}" - // TODO min_depth should be provided from modules.config - """ - create_panel4sample.py \\ - --compact-annot-panel-path ${compact_captured_panel_annotation} \\ - --depths-path all_samples.depths.tsv.gz \\ - --panel-name ${prefix} \\ - --min-depth ${min_depth} - - for sample_panel in \$(ls *${prefix}.tsv ); do - bedtools merge \\ - -i <( - tail -n +2 \$sample_panel | \\ - awk -F'\\t' '{print \$1, \$2-1, \$2}' OFS='\\t' | uniq - ) > \${sample_panel%.tsv}.bed; - done - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //g') - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "TargetRegions" - """ - touch ${prefix}.tsv - touch ${prefix}.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //g') - END_VERSIONS - """ -} diff --git a/subworkflows/local/enrichpanels/main.nf b/subworkflows/local/enrichpanels/main.nf index 5cc6ecc6..de56bcf1 100644 --- a/subworkflows/local/enrichpanels/main.nf +++ b/subworkflows/local/enrichpanels/main.nf @@ -38,25 +38,25 @@ workflow ENRICHPANELS { if (params.create_subgenic_regions){ EXPANDREGIONSALL(all_consensus_panel, domains_ch, exons_ch, subgenic_ch) - all_expanded_panel = EXPANDREGIONSALL.out.panel_increased + all_expanded_panel = EXPANDREGIONSALL.out.panel_increased.first() EXPANDREGIONSNONPROT(nonprot_consensus_panel, domains_ch, exons_ch, subgenic_ch) - nonprot_expanded_panel = EXPANDREGIONSNONPROT.out.panel_increased + nonprot_expanded_panel = EXPANDREGIONSNONPROT.out.panel_increased.first() EXPANDREGIONSPROT(prot_consensus_panel, domains_ch, exons_ch, subgenic_ch) - prot_expanded_panel = EXPANDREGIONSPROT.out.panel_increased + prot_expanded_panel = EXPANDREGIONSPROT.out.panel_increased.first() EXPANDREGIONSSYNONYMOUS(synonymous_consensus_panel, domains_ch, exons_ch, subgenic_ch) - synonymous_expanded_panel = EXPANDREGIONSSYNONYMOUS.out.panel_increased + synonymous_expanded_panel = EXPANDREGIONSSYNONYMOUS.out.panel_increased.first() EXPANDREGIONSEXONS(exons_consensus_panel, domains_ch, exons_ch, subgenic_ch) - exons_expanded_panel = EXPANDREGIONSEXONS.out.panel_increased + exons_expanded_panel = EXPANDREGIONSEXONS.out.panel_increased.first() // all_json_subgenic = EXPANDREGIONSALL.out.new_regions_json // nonprot_json_subgenic = EXPANDREGIONSNONPROT.out.new_regions_json // prot_json_subgenic = EXPANDREGIONSPROT.out.new_regions_json // synonymous_json_subgenic = EXPANDREGIONSSYNONYMOUS.out.new_regions_json - exons_json_subgenic = EXPANDREGIONSEXONS.out.new_regions_json + exons_json_subgenic = EXPANDREGIONSEXONS.out.new_regions_json.first() } else { all_expanded_panel = all_consensus_panel @@ -70,13 +70,13 @@ workflow ENRICHPANELS { emit: - all_consensus_expanded_panel = all_expanded_panel.first() - nonprot_consensus_expanded_panel = nonprot_expanded_panel.first() - prot_consensus_expanded_panel = prot_expanded_panel.first() - synonymous_consensus_expanded_panel = synonymous_expanded_panel.first() - exons_consensus_expanded_panel = exons_expanded_panel.first() + all_consensus_expanded_panel = all_expanded_panel + nonprot_consensus_expanded_panel = nonprot_expanded_panel + prot_consensus_expanded_panel = prot_expanded_panel + synonymous_consensus_expanded_panel = synonymous_expanded_panel + exons_consensus_expanded_panel = exons_expanded_panel - exons_json_subgenic = exons_json_subgenic.first() + exons_json_subgenic = exons_json_subgenic dna2protein_mapping_depth_exons = DNA2PROTEINMAPPING.out.depths_exons_positions.first() dna2protein_mapping_panel_exons = DNA2PROTEINMAPPING.out.panel_exons_bed.first() diff --git a/subworkflows/local/mutationpreprocessing/main.nf b/subworkflows/local/mutationpreprocessing/main.nf index d5265230..789903e2 100644 --- a/subworkflows/local/mutationpreprocessing/main.nf +++ b/subworkflows/local/mutationpreprocessing/main.nf @@ -62,7 +62,7 @@ workflow MUTATION_PREPROCESSING { CUSTOMANNOTATION(SUMANNOTATION.out.tab, custom_annotation_tsv) summary_of_mutations = CUSTOMANNOTATION.out.mutations.first() } else { - summary_of_mutations = SUMANNOTATION.out.tab.first() + summary_of_mutations = SUMANNOTATION.out.tab } VCF2MAF(vcfs, summary_of_mutations) diff --git a/subworkflows/local/omega/main.nf b/subworkflows/local/omega/main.nf index d772f826..3bcf8947 100644 --- a/subworkflows/local/omega/main.nf +++ b/subworkflows/local/omega/main.nf @@ -109,7 +109,7 @@ workflow OMEGA_ANALYSIS{ PREPROCESSINGGLOBALLOC(muts_n_depths_n_profile, expanded_panel, - mutationdensities.first(), + mutationdensities, all_samples_mut_profile) PREPROCESSINGGLOBALLOC.out.mutabs_n_mutations_tsv diff --git a/workflows/deepcsa.nf b/workflows/deepcsa.nf index 500954cb..5b9261d2 100644 --- a/workflows/deepcsa.nf +++ b/workflows/deepcsa.nf @@ -323,7 +323,7 @@ workflow DEEPCSA { // Concatenate all outputs into a single file MUTDENSITYADJUSTED.out.mutdensities.map{ it -> it[1]}.flatten() .set{ all_adjusted_mutdensities } - all_adjusted_mutdensities.collectFile(name: "all_adjusted_mutdensities.tsv", storeDir:"${params.outdir}/mutdensity_adjusted", skip: 1, keepHeader: true).set{ all_adjusted_mutdensities_file } + all_adjusted_mutdensities.collectFile(name: "all_adjusted_mutdensities.tsv", storeDir:"${params.outdir}/mutdensity_adjusted", skip: 1, keepHeader: true).first().set{ all_adjusted_mutdensities_file } MUTDENSITYADJUSTED.out.mutdensities_flat.map{ it -> it[1]}.flatten() .set{ all_adjusted_mutdensities_flat } @@ -358,10 +358,10 @@ workflow DEEPCSA { if (run_mutdensity){ // Mutation Density - MUTDENSITYALL(somatic_mutations, DEPTHSALLCONS.out.subset, CREATEPANELS.out.all_consensus_bed, ENRICHPANELS.out.all_consensus_expanded_panel.first()) - MUTDENSITYPROT(somatic_mutations, DEPTHSPROTCONS.out.subset, CREATEPANELS.out.prot_consensus_bed, ENRICHPANELS.out.prot_consensus_expanded_panel.first()) - MUTDENSITYNONPROT(somatic_mutations, DEPTHSNONPROTCONS.out.subset, CREATEPANELS.out.nonprot_consensus_bed, ENRICHPANELS.out.nonprot_consensus_expanded_panel.first()) - MUTDENSITYSYNONYMOUS(somatic_mutations, DEPTHSSYNONYMOUSCONS.out.subset, CREATEPANELS.out.synonymous_consensus_bed, ENRICHPANELS.out.synonymous_consensus_expanded_panel.first()) + MUTDENSITYALL(somatic_mutations, DEPTHSALLCONS.out.subset, CREATEPANELS.out.all_consensus_bed, ENRICHPANELS.out.all_consensus_expanded_panel) + MUTDENSITYPROT(somatic_mutations, DEPTHSPROTCONS.out.subset, CREATEPANELS.out.prot_consensus_bed, ENRICHPANELS.out.prot_consensus_expanded_panel) + MUTDENSITYNONPROT(somatic_mutations, DEPTHSNONPROTCONS.out.subset, CREATEPANELS.out.nonprot_consensus_bed, ENRICHPANELS.out.nonprot_consensus_expanded_panel) + MUTDENSITYSYNONYMOUS(somatic_mutations, DEPTHSSYNONYMOUSCONS.out.subset, CREATEPANELS.out.synonymous_consensus_bed, ENRICHPANELS.out.synonymous_consensus_expanded_panel) // Concatenate all outputs into a single file channel.empty() @@ -461,8 +461,8 @@ workflow DEEPCSA { OMEGA(mutations_in_exons, DEPTHSEXONSCONS.out.subset, MUTPROFILEALL.out.profile, - CREATEPANELS.out.exons_consensus_bed.first(), - ENRICHPANELS.out.exons_consensus_expanded_panel.first(), + CREATEPANELS.out.exons_consensus_bed, + ENRICHPANELS.out.exons_consensus_expanded_panel, custom_groups_table, SYNMUTDENSITY.out.mutdensity.first(), CREATEPANELS.out.panel_annotated_rich, @@ -477,7 +477,7 @@ workflow DEEPCSA { } if (params.omega_globalloc){ positive_selection_results = positive_selection_results.join(OMEGA.out.results_global, remainder: true) - all_compiled_omegasgloballoc = OMEGA.out.all_globalloc_compiled + all_compiled_omegasgloballoc = OMEGA.out.all_globalloc_compiled.first() } if (params.regressions){ @@ -491,8 +491,8 @@ workflow DEEPCSA { OMEGAMULTI(mutations_in_exons, DEPTHSEXONSCONS.out.subset, MUTPROFILEALL.out.profile, - CREATEPANELS.out.exons_consensus_bed.first(), - ENRICHPANELS.out.exons_consensus_expanded_panel.first(), + CREATEPANELS.out.exons_consensus_bed, + ENRICHPANELS.out.exons_consensus_expanded_panel, custom_groups_table, SYNMUTREADSDENSITY.out.mutdensity.first(), CREATEPANELS.out.panel_annotated_rich, @@ -513,8 +513,8 @@ workflow DEEPCSA { OMEGANONPROT(mutations_in_exons, DEPTHSEXONSCONS.out.subset, MUTPROFILENONPROT.out.profile, - CREATEPANELS.out.exons_consensus_bed.first(), - ENRICHPANELS.out.exons_consensus_expanded_panel.first(), + CREATEPANELS.out.exons_consensus_bed, + ENRICHPANELS.out.exons_consensus_expanded_panel, custom_groups_table, SYNMUTDENSITY.out.mutdensity.first(), CREATEPANELS.out.panel_annotated_rich, @@ -527,8 +527,8 @@ workflow DEEPCSA { OMEGANONPROTMULTI(mutations_in_exons, DEPTHSEXONSCONS.out.subset, MUTPROFILENONPROT.out.profile, - CREATEPANELS.out.exons_consensus_bed.first(), - ENRICHPANELS.out.exons_consensus_expanded_panel.first(), + CREATEPANELS.out.exons_consensus_bed, + ENRICHPANELS.out.exons_consensus_expanded_panel, custom_groups_table, SYNMUTREADSDENSITY.out.mutdensity.first(), CREATEPANELS.out.panel_annotated_rich, @@ -604,8 +604,8 @@ workflow DEEPCSA { PLOTTINGQC( somatic_mutations, all_mutdensities_file.first(), - all_adjusted_mutdensities_file.first(), - all_compiled_omegasgloballoc.first(), + all_adjusted_mutdensities_file, + all_compiled_omegasgloballoc, PLOTDEPTHSEXONSCONS.out.average_depth_gene_sample.first(), all_compiled_omegas, // site_comparison_results, @@ -631,19 +631,19 @@ workflow DEEPCSA { PLOTTINGSUMMARY(positive_selection_results_ready, somatic_mutations, all_mutdensities_file.first(), - all_adjusted_mutdensities_file.first(), + all_adjusted_mutdensities_file, site_comparison_results, ANNOTATEDEPTHS.out.all_samples_depths.first(), TABLE2GROUP.out.json_samples.first(), TABLE2GROUP.out.json_allgroups.first(), - CREATEPANELS.out.exons_consensus_panel.first(), - ENRICHPANELS.out.exons_consensus_expanded_panel.first(), - CREATEPANELS.out.panel_annotated_rich.first(), + CREATEPANELS.out.exons_consensus_panel, + ENRICHPANELS.out.exons_consensus_expanded_panel, + CREATEPANELS.out.panel_annotated_rich, seqinfo_df, - CREATEPANELS.out.domains_in_panel.first(), - ENRICHPANELS.out.dna2protein_mapping_depth_exons.first(), + CREATEPANELS.out.domains_in_panel, + ENRICHPANELS.out.dna2protein_mapping_depth_exons, group_keys_ch ) }