Fixing failing subworkflow tests

subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_gatk/main.nf

@@ -2,13 +2,6 @@
 // Run GATK mutect2 in tumor normal mode, getepileupsummaries, calculatecontamination, learnreadorientationmodel and filtermutectcalls
 //
 
-params.mutect2_options          = [:]
-params.learnorientation_options = [:]
-params.getpileup_tumor_options  = [suffix: '_tumor']
-params.getpileup_normal_options = [suffix: '_normal']
-params.calccontam_options       = [:]
-params.filtercalls_options      = [suffix: '_filtered']
-
 include { GATK4_MUTECT2                   as MUTECT2 }                   from '../../../modules/nf-core/gatk4/mutect2/main'
 include { GATK4_LEARNREADORIENTATIONMODEL as LEARNREADORIENTATIONMODEL } from '../../../modules/nf-core/gatk4/learnreadorientationmodel/main'
 include { GATK4_GETPILEUPSUMMARIES        as GETPILEUPSUMMARIES_TUMOR }  from '../../../modules/nf-core/gatk4/getpileupsummaries/main'
@@ -18,16 +11,15 @@ include { GATK4_FILTERMUTECTCALLS         as FILTERMUTECTCALLS }         from '.
 
 workflow BAM_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING_GATK {
     take:
-    ch_input                     // channel: [ val(meta), path(input), path(input_index), val(which_norm) ]
-    ch_fasta                     // channel: [ path(fasta) ]
-    ch_fai                       // channel: [ path(fai) ]
-    ch_dict                      // channel: [ path(dict) ]
-    ch_germline_resource         // channel: [ path(germline_resource) ]
-    ch_germline_resource_tbi     // channel: [ path(germline_resource_tbi) ]
-    ch_panel_of_normals          // channel: [ path(panel_of_normals) ]
-    ch_panel_of_normals_tbi      // channel: [ path(panel_of_normals_tbi) ]
-    ch_interval_file             // channel: [ path(interval_file) ]
-
+    ch_input                 // channel: [ val(meta), path(input), path(input_index), val(which_norm) ]
+    ch_fasta                 // channel: /path/to/reference/fasta
+    ch_fai                   // channel: /path/to/reference/fasta/index
+    ch_dict                  // channel: /path/to/reference/fasta/dictionary
+    ch_germline_resource     // channel: /path/to/germline/resource
+    ch_germline_resource_tbi // channel: /path/to/germline/index
+    ch_panel_of_normals      // channel: /path/to/panel/of/normals
+    ch_panel_of_normals_tbi  // channel: /path/to/panel/of/normals/index
+    ch_interval_file         // channel: /path/to/interval/file
 
     main:
     ch_versions = Channel.empty()
@@ -45,62 +37,68 @@ workflow BAM_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING_GATK {
         ch_panel_of_normals,
         ch_panel_of_normals_tbi
     )
+
     ch_versions = ch_versions.mix(MUTECT2.out.versions)
 
     //
     // Generate artifactpriors using learnreadorientationmodel on the f1r2 output of mutect2.
     //
-    ch_learnread_in = MUTECT2.out.f1r2.collect()
-    LEARNREADORIENTATIONMODEL (ch_learnread_in)
-    ch_versions = ch_versions.mix(LEARNREADORIENTATIONMODEL.out.versions.firs())
+    LEARNREADORIENTATIONMODEL (MUTECT2.out.f1r2.collect())
+    ch_versions = ch_versions.mix(LEARNREADORIENTATIONMODEL.out.versions)
 
     //
     // Generate pileup summary tables using getepileupsummaries. tumor sample should always be passed in as the first input and input list entries of ch_mutect2_in,
     // to ensure correct file order for calculatecontamination.
     //
-    ch_pileup_tumor_input = ch_input.map {
-        meta, input_file, input_index, which_norm ->
-        [meta, input_file[0], input_index[0]]
+    ch_pileup_tumor_input = ch_input.combine(ch_interval_file).map {
+        meta, input_file, input_index, which_norm, intervals ->
+        [meta, input_file[0], input_index[0], intervals]
     }
 
-    ch_pileup_normal_input = ch_input.map {
-        meta, input_file, input_index, which_norm ->
-        [meta, input_file[1], input_index[1]]
+    ch_pileup_normal_input = ch_input.combine(ch_interval_file).map {
+        meta, input_file, input_index, which_norm, intervals ->
+        [meta, input_file[1], input_index[1], intervals]
     }
 
     GETPILEUPSUMMARIES_TUMOR (
         ch_pileup_tumor_input,
+        ch_fasta,
+        ch_fai,
+        ch_dict,
         ch_germline_resource,
-        ch_germline_resource_tbi,
-        ch_interval_file
+        ch_germline_resource_tbi
     )
+
     GETPILEUPSUMMARIES_NORMAL (
         ch_pileup_normal_input,
+        ch_fasta,
+        ch_fai,
+        ch_dict,
         ch_germline_resource,
-        ch_germline_resource_tbi,
-        ch_interval_file
+        ch_germline_resource_tbi
     )
+
     ch_versions = ch_versions.mix(GETPILEUPSUMMARIES_TUMOR.out.versions.first())
     ch_versions = ch_versions.mix(GETPILEUPSUMMARIES_NORMAL.out.versions.first())
 
     //
     // Contamination and segmentation tables created using calculatecontamination on the pileup summary table.
     //
-    ch_pileup_tumor     = GETPILEUPSUMMARIES_TUMOR.out.table.collect()
-    ch_pileup_normal    = GETPILEUPSUMMARIES_NORMAL.out.table.collect()
-    ch_calccon_in       = ch_pileup_tumor.join(ch_pileup_normal, failOnDuplicate: true, failOnMismatch: true)
-    CALCULATECONTAMINATION ( ch_calccon_in, true )
+    ch_pileup_tumor = GETPILEUPSUMMARIES_TUMOR.out.table.collect()
+    ch_pileup_normal = GETPILEUPSUMMARIES_NORMAL.out.table.collect()
+    ch_calccon_in = ch_pileup_tumor.join(ch_pileup_normal, failOnDuplicate: true, failOnMismatch: true)
+    CALCULATECONTAMINATION ( ch_calccon_in )
     ch_versions   = ch_versions.mix(CALCULATECONTAMINATION.out.versions)
 
     //
     // Mutect2 calls filtered by filtermutectcalls using the artifactpriors, contamination and segmentation tables.
     //
-    ch_vcf                   = MUTECT2.out.vcf.collect()
-    ch_tbi                   = MUTECT2.out.tbi.collect()
-    ch_stats                 = MUTECT2.out.stats.collect()
-    ch_orientation           = LEARNREADORIENTATIONMODEL.out.artifactprior.collect()
-    ch_segment               = CALCULATECONTAMINATION.out.segmentation.collect()
-    ch_contamination         = CALCULATECONTAMINATION.out.contamination.collect()
+    ch_vcf           = MUTECT2.out.vcf.collect()
+    ch_tbi           = MUTECT2.out.tbi.collect()
+    ch_stats         = MUTECT2.out.stats.collect()
+    ch_orientation   = LEARNREADORIENTATIONMODEL.out.artifactprior.collect()
+    ch_segment       = CALCULATECONTAMINATION.out.segmentation.collect()
+    ch_contamination = CALCULATECONTAMINATION.out.contamination.collect()
 
     //[] is used as a placeholder for optional input to specify the contamination estimate as a value, since the contamination table is used, this is not needed.
     ch_contamination.add([])

subworkflows/nf-core/bam_tumor_only_somatic_variant_calling_gatk/main.nf

@@ -0,0 +1,113 @@
+//
+// Run GATK mutect2 in tumor only mode, getepileupsummaries, calculatecontamination and filtermutectcalls
+//
+
+include { GATK4_MUTECT2                as MUTECT2 }                  from '../../../modules/nf-core/gatk4/mutect2/main'
+include { GATK4_GETPILEUPSUMMARIES     as GETPILEUPSUMMARIES }       from '../../../modules/nf-core/gatk4/getpileupsummaries/main'
+include { GATK4_CALCULATECONTAMINATION as CALCULATECONTAMINATION }   from '../../../modules/nf-core/gatk4/calculatecontamination/main'
+include { GATK4_FILTERMUTECTCALLS      as FILTERMUTECTCALLS }        from '../../../modules/nf-core/gatk4/filtermutectcalls/main'
+
+workflow BAM_TUMOR_ONLY_SOMATIC_VARIANT_CALLING_GATK {
+    take:
+    ch_input                 // channel: [ val(meta), [ input ], [ input_index ], [] ]
+    ch_fasta                 // channel: /path/to/reference/fasta
+    ch_fai                   // channel: /path/to/reference/fasta/index
+    ch_dict                  // channel: /path/to/reference/fasta/dictionary
+    ch_germline_resource     // channel: /path/to/germline/resource
+    ch_germline_resource_tbi // channel: /path/to/germline/index
+    ch_panel_of_normals      // channel: /path/to/panel/of/normals
+    ch_panel_of_normals_tbi  // channel: /path/to/panel/of/normals/index
+    ch_interval_file         // channel: /path/to/interval/file
+
+    main:
+    ch_versions = Channel.empty()
+
+    //
+    //Perform variant calling using mutect2 module in tumor single mode.
+    //
+    MUTECT2 (
+        ch_input,
+        ch_fasta,
+        ch_fai,
+        ch_dict,
+        ch_germline_resource,
+        ch_germline_resource_tbi,
+        ch_panel_of_normals,
+        ch_panel_of_normals_tbi
+    )
+
+    ch_versions = ch_versions.mix(MUTECT2.out.versions)
+
+    //
+    //Generate pileup summary table using getpileupsummaries.
+    //
+
+    ch_pileup_input = ch_input.combine(ch_interval_file).map {
+        meta, input_file, input_index, which_norm, intervals ->
+        [meta, input_file, input_index, intervals]
+    }
+
+    GETPILEUPSUMMARIES (
+        ch_pileup_input,
+        ch_fasta,
+        ch_fai,
+        ch_dict,
+        ch_germline_resource,
+        ch_germline_resource_tbi
+    )
+
+    ch_versions = ch_versions.mix(GETPILEUPSUMMARIES.out.versions)
+
+    //
+    //Contamination and segmentation tables created using calculatecontamination on the pileup summary table.
+    //
+    ch_pileup = GETPILEUPSUMMARIES.out.table.collect()
+
+    //[] is a placeholder for the optional input where the matched normal sample would be passed in for tumor-normal samples, which is not necessary for this workflow.
+    ch_pileup.add([])
+
+    CALCULATECONTAMINATION ( ch_pileup )
+
+    ch_versions = ch_versions.mix(CALCULATECONTAMINATION.out.versions)
+
+    //
+    //Mutect2 calls filtered by filtermutectcalls using the contamination and segmentation tables.
+    //
+
+    ch_vcf = MUTECT2.out.vcf.collect()
+    ch_tbi = MUTECT2.out.tbi.collect()
+    ch_stats = MUTECT2.out.stats.collect()
+
+    ch_segment = CALCULATECONTAMINATION.out.segmentation.collect()
+    ch_contamination = CALCULATECONTAMINATION.out.contamination.collect()
+
+    ch_filtermutect_in = ch_vcf
+        .combine(ch_tbi, by: 0)
+        .combine(ch_stats, by: 0)
+        .combine(ch_segment, by: 0)
+        .combine(ch_contamination, by: 0)
+    // Adding [] as a placeholder for the optional input file artifact priors, which is only used for tumor-normal samples and therefor isn't needed in this workflow.
+    // and [] as a placeholder for entering a contamination estimate value, which is not needed as this workflow uses the contamination table instead.
+        .map{ meta, vcf, tbi, stats, segment, contamination -> [meta, vcf, tbi, stats, [], segment, contamination, [] ] }
+
+    ch_filtermutect_in.view()
+
+    FILTERMUTECTCALLS ( ch_filtermutect_in, ch_fasta, ch_fai, ch_dict )
+    ch_versions = ch_versions.mix(FILTERMUTECTCALLS.out.versions)
+
+    emit:
+    mutect2_vcf         = MUTECT2.out.vcf.collect()                          // channel: [ val(meta), [ vcf ] ]
+    mutect2_index       = MUTECT2.out.tbi.collect()                          // channel: [ val(meta), [ tbi ] ]
+    mutect2_stats       = MUTECT2.out.stats.collect()                        // channel: [ val(meta), [ stats ] ]
+
+    pileup_table        = GETPILEUPSUMMARIES.out.table.collect()             // channel: [ val(meta), [ table ] ]
+
+    contamination_table = CALCULATECONTAMINATION.out.contamination.collect() // channel: [ val(meta), [ contamination ] ]
+    segmentation_table  = CALCULATECONTAMINATION.out.segmentation.collect()  // channel: [ val(meta), [ segmentation ] ]
+
+    filtered_vcf        = FILTERMUTECTCALLS.out.vcf.collect()                // channel: [ val(meta), [ vcf ] ]
+    filtered_index      = FILTERMUTECTCALLS.out.tbi.collect()                // channel: [ val(meta), [ tbi ] ]
+    filtered_stats      = FILTERMUTECTCALLS.out.stats.collect()              // channel: [ val(meta), [ stats ] ]
+
+    versions            = ch_versions                                        // channel: [ versions.yml ]
+}

tests/config/pytest_modules.yml

@@ -3360,6 +3360,10 @@ subworkflows/bam_tumor_normal_somatic_variant_calling_gatk:
   - subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_gatk/**
   - tests/subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_gatk/**
 
+subworkflows/bam_tumor_only_somatic_variant_calling_gatk:
+  - subworkflows/nf-core/bam_tumor_only_somatic_variant_calling_gatk/**
+  - tests/subworkflows/nf-core/bam_tumor_only_somatic_variant_calling_gatk/**
+
 subworkflows/bam_variant_calling_sort_freebayes_bcftools:
   - subworkflows/nf-core/bam_variant_calling_sort_freebayes_bcftools/**
   - tests/subworkflows/nf-core/bam_variant_calling_sort_freebayes_bcftools/**
@@ -3452,14 +3456,6 @@ subworkflows/gatk_create_som_pon:
   - subworkflows/nf-core/gatk_create_som_pon/**
   - tests/subworkflows/nf-core/gatk_create_som_pon/**
 
-subworkflows/gatk_tumor_normal_somatic_variant_calling:
-  - subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/**
-  - tests/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/**
-
-subworkflows/gatk_tumor_only_somatic_variant_calling:
-  - subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/**
-  - tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/**
-
 subworkflows/homer/groseq:
   - subworkflows/nf-core/homer/groseq/**
   - tests/subworkflows/nf-core/homer/groseq/**

tests/subworkflows/nf-core/bam_create_som_pon_gatk/main.nf

@@ -4,7 +4,7 @@ nextflow.enable.dsl = 2
 
 include { BAM_CREATE_SOM_PON_GATK } from '../../../../subworkflows/nf-core/bam_create_som_pon_gatk/main'
 
-workflow bam_create_som_pon_gatk {
+workflow test_bam_create_som_pon_gatk {
     ch_mutect2_in = Channel.of(
         [
             [ id:'test1' ], // meta map

tests/subworkflows/nf-core/bam_create_som_pon_gatk/test.yml

@@ -1,5 +1,5 @@
 - name: bam_create_som_pon_gatk
-  command: nextflow run ./tests/subworkflows/nf-core/bam_create_som_pon_gatk -entry bam_create_som_pon_gatk -c tests/config/nextflow.config
+  command: nextflow run ./tests/subworkflows/nf-core/bam_create_som_pon_gatk -entry test_bam_create_som_pon_gatk -c tests/config/nextflow.config
   tags:
     - subworkflows
     - subworkflows/bam_create_som_pon_gatk