More cohesion between subworkflows

CHANGELOG.md

@@ -44,7 +44,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#466](https://github.com/nf-core/sarek/pull/466), [#478](https://github.com/nf-core/sarek/pull/478), [#492](https://github.com/nf-core/sarek/pull/492), [#521](https://github.com/nf-core/sarek/pull/521) - Move some local modules to `nf-core/modules`
 - [#466](https://github.com/nf-core/sarek/pull/466), [#485](https://github.com/nf-core/sarek/pull/485), [#492](https://github.com/nf-core/sarek/pull/492), [#494](https://github.com/nf-core/sarek/pull/494), [#515](https://github.com/nf-core/sarek/pull/515) - Improve preprocessing subworkflows
 - [#474](https://github.com/nf-core/sarek/pull/474), [#475](https://github.com/nf-core/sarek/pull/475) - Sync `TEMPLATE` with `tools` `2.2`
-- [#487](https://github.com/nf-core/sarek/pull/487), [#489](https://github.com/nf-core/sarek/pull/489), [#492](https://github.com/nf-core/sarek/pull/492), [#497](https://github.com/nf-core/sarek/pull/497), [#522](https://github.com/nf-core/sarek/pull/522) - Improve variant calling subworkflows
+- [#487](https://github.com/nf-core/sarek/pull/487), [#489](https://github.com/nf-core/sarek/pull/489), [#492](https://github.com/nf-core/sarek/pull/492), [#497](https://github.com/nf-core/sarek/pull/497), [#522](https://github.com/nf-core/sarek/pull/522), [#583](https://github.com/nf-core/sarek/pull/583) - Improve variant calling subworkflows
 - [#498](https://github.com/nf-core/sarek/pull/498) - Update docs
 - [#501](https://github.com/nf-core/sarek/pull/501) - Sync `TEMPLATE` with `tools` `2.3`
 - [#511](https://github.com/nf-core/sarek/pull/511) - Sync `TEMPLATE` with `tools` `2.3.2`
@@ -54,7 +54,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#544](https://github.com/nf-core/sarek/pull/544) - `Mutect2` is no longer compatible with `--no_intervals`
 - [#551](https://github.com/nf-core/sarek/pull/551) - Sync `TEMPLATE` with `tools` `2.4`
 - [#563](https://github.com/nf-core/sarek/pull/563) - Updated subway map
-- [#571](https://github.com/nf-core/sarek/pull/571) - Including and using GATK4's mergeVcfs. Removing the local module `concat_vcf`.
+- [#571](https://github.com/nf-core/sarek/pull/571) - Including and using GATK4's mergeVcfs
 - [#572](https://github.com/nf-core/sarek/pull/572) - Adjusted subway map svg for firefox compatibility
 - [#578](https://github.com/nf-core/sarek/pull/578) - Updated module deeptools/bamcoverage
 
@@ -94,6 +94,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#539](https://github.com/nf-core/sarek/pull/539) - `--cadd_cache`, `--cadd_indels`, `--cadd_indels_tbi`, `--cadd_wg_snvs`, `--cadd_wg_snvs_tbi` have been removed
 - [#539](https://github.com/nf-core/sarek/pull/539) - `--genesplicer` has been removed
 - [#539](https://github.com/nf-core/sarek/pull/539) - `conf/genomes.config` and `params.genomes_base` have been removed
+- [#571](https://github.com/nf-core/sarek/pull/571) - Removed the local module `concat_vcf`.
 
 ## [2.7.1](https://github.com/nf-core/sarek/releases/tag/2.7.1) - Pårtejekna
 

subworkflows/local/annotate.nf

@@ -8,15 +8,15 @@ include { ANNOTATION_ENSEMBLVEP                     } from '../nf-core/annotatio
 
 workflow ANNOTATE {
     take:
-    vcf          // channel: [ val(meta), vcf ]
-    tools
-    snpeff_db
-    snpeff_cache
-    vep_genome
-    vep_species
-    vep_cache_version
-    vep_cache
-    vep_extra_files
+        vcf                           // channel: [ val(meta), vcf ]
+        tools                         // Mandatory, list of tools to apply
+        snpeff_db
+        snpeff_cache
+        vep_genome
+        vep_species
+        vep_cache_version
+        vep_cache
+        vep_extra_files
 
     main:
     ch_reports  = Channel.empty()

subworkflows/local/germline_variant_calling.nf

@@ -7,21 +7,22 @@ include { RUN_FREEBAYES       } from '../nf-core/variantcalling/freebayes/main.n
 include { RUN_HAPLOTYPECALLER } from '../nf-core/variantcalling/haplotypecaller/main.nf'
 include { RUN_MANTA_GERMLINE  } from '../nf-core/variantcalling/manta/germline/main.nf'
 include { RUN_STRELKA_SINGLE  } from '../nf-core/variantcalling/strelka/single/main.nf'
-include { RUN_CNVKIT_GERMLINE  } from '../nf-core/variantcalling/cnvkit/germline/main.nf'
+include { RUN_CNVKIT_GERMLINE } from '../nf-core/variantcalling/cnvkit/germline/main.nf'
 //include { TIDDIT          } from './variantcalling/tiddit.nf'
 
 workflow GERMLINE_VARIANT_CALLING {
     take:
-        cram_recalibrated            // channel: [mandatory] cram
-        dbsnp                        // channel: [mandatory] dbsnp
-        dbsnp_tbi                    // channel: [mandatory] dbsnp_tbi
-        dict                         // channel: [mandatory] dict
-        fasta                        // channel: [mandatory] fasta
-        fasta_fai                    // channel: [mandatory] fasta_fai
-        intervals                    // channel: [mandatory] intervals/target regions
-        intervals_bed_gz_tbi         // channel: [mandatory] intervals/target regions index zipped and indexed
-        intervals_bed_combined       // channel: [mandatory] intervals/target regions in one file unzipped
-        // joint_germline               // val: true/false on whether to run joint_germline calling, only works in combination with haplotypecaller at the moment
+        tools                         // Mandatory, list of tools to apply
+        cram_recalibrated             // channel: [mandatory] cram
+        dbsnp                         // channel: [mandatory] dbsnp
+        dbsnp_tbi                     // channel: [mandatory] dbsnp_tbi
+        dict                          // channel: [mandatory] dict
+        fasta                         // channel: [mandatory] fasta
+        fasta_fai                     // channel: [mandatory] fasta_fai
+        intervals                     // channel: [mandatory] intervals/target regions
+        intervals_bed_gz_tbi          // channel: [mandatory] intervals/target regions index zipped and indexed
+        intervals_bed_combined        // channel: [mandatory] intervals/target regions in one file unzipped
+        // joint_germline                // val: true/false on whether to run joint_germline calling, only works in combination with haplotypecaller at the moment
 
     main:
 
@@ -60,7 +61,7 @@ workflow GERMLINE_VARIANT_CALLING {
 
     // CNVKIT
 
-    if(params.tools.contains('cnvkit')){
+    if(tools.contains('cnvkit')){
         cram_recalibrated_cnvkit_germline = cram_recalibrated
             .map{ meta, cram, crai ->
                 [meta, [], cram]
@@ -75,15 +76,15 @@ workflow GERMLINE_VARIANT_CALLING {
     }
 
     // DEEPVARIANT
-    if(params.tools.contains('deepvariant')){
+    if(tools.contains('deepvariant')){
         RUN_DEEPVARIANT(cram_recalibrated_intervals, dict, fasta, fasta_fai)
 
         deepvariant_vcf = Channel.empty().mix(RUN_DEEPVARIANT.out.deepvariant_vcf,RUN_DEEPVARIANT.out.deepvariant_gvcf)
         ch_versions     = ch_versions.mix(RUN_DEEPVARIANT.out.versions)
     }
 
     // FREEBAYES
-    if (params.tools.contains('freebayes')){
+    if (tools.contains('freebayes')){
         // Remap channel for Freebayes
         cram_recalibrated_intervals_freebayes = cram_recalibrated_intervals
             .map{ meta, cram, crai, intervals ->
@@ -96,7 +97,7 @@ workflow GERMLINE_VARIANT_CALLING {
     }
 
     // HAPLOTYPECALLER
-    if (params.tools.contains('haplotypecaller')){
+    if (tools.contains('haplotypecaller')){
         RUN_HAPLOTYPECALLER(cram_recalibrated_intervals,
                         fasta,
                         fasta_fai,
@@ -110,7 +111,7 @@ workflow GERMLINE_VARIANT_CALLING {
     }
 
     // MANTA
-    if (params.tools.contains('manta')){
+    if (tools.contains('manta')){
         RUN_MANTA_GERMLINE (cram_recalibrated_intervals_gz_tbi,
                         dict,
                         fasta,
@@ -121,7 +122,7 @@ workflow GERMLINE_VARIANT_CALLING {
     }
 
     // STRELKA
-    if (params.tools.contains('strelka')){
+    if (tools.contains('strelka')){
         RUN_STRELKA_SINGLE(cram_recalibrated_intervals_gz_tbi,
                 dict,
                 fasta,

subworkflows/local/pair_variant_calling.nf

@@ -11,7 +11,7 @@ include { RUN_CNVKIT_SOMATIC                        } from '../nf-core/variantca
 
 workflow PAIR_VARIANT_CALLING {
     take:
-        tools
+        tools                         // Mandatory, list of tools to apply
         cram_pair                     // channel: [mandatory] cram
         dbsnp                         // channel: [mandatory] dbsnp
         dbsnp_tbi                     // channel: [mandatory] dbsnp_tbi

subworkflows/local/tumor_variant_calling.nf

@@ -12,20 +12,20 @@ include { RUN_CNVKIT_TUMORONLY                    } from '../nf-core/variantcall
 
 workflow TUMOR_ONLY_VARIANT_CALLING {
     take:
-        tools                        // Mandatory, list of tools to apply
-        cram_recalibrated            // channel: [mandatory] cram
-        dbsnp                        // channel: [mandatory] dbsnp
-        dbsnp_tbi                    // channel: [mandatory] dbsnp_tbi
-        dict                         // channel: [mandatory] dict
-        fasta                        // channel: [mandatory] fasta
-        fasta_fai                    // channel: [mandatory] fasta_fai
-        intervals                    // channel: [mandatory] intervals/target regions
-        intervals_bed_gz_tbi         // channel: [mandatory] intervals/target regions index zipped and indexed
+        tools                         // Mandatory, list of tools to apply
+        cram_recalibrated             // channel: [mandatory] cram
+        dbsnp                         // channel: [mandatory] dbsnp
+        dbsnp_tbi                     // channel: [mandatory] dbsnp_tbi
+        dict                          // channel: [mandatory] dict
+        fasta                         // channel: [mandatory] fasta
+        fasta_fai                     // channel: [mandatory] fasta_fai
+        intervals                     // channel: [mandatory] intervals/target regions
+        intervals_bed_gz_tbi          // channel: [mandatory] intervals/target regions index zipped and indexed
         intervals_bed_combined        // channel: [mandatory] intervals/target regions in one file unzipped
-        germline_resource            // channel: [optional]  germline_resource
-        germline_resource_tbi        // channel: [optional]  germline_resource_tbi
-        panel_of_normals             // channel: [optional]  panel_of_normals
-        panel_of_normals_tbi         // channel: [optional]  panel_of_normals_tbi
+        germline_resource             // channel: [optional]  germline_resource
+        germline_resource_tbi         // channel: [optional]  germline_resource_tbi
+        panel_of_normals              // channel: [optional]  panel_of_normals
+        panel_of_normals_tbi          // channel: [optional]  panel_of_normals_tbi
         chr_files
         mappability
 

workflows/sarek.nf

@@ -770,6 +770,7 @@ workflow SAREK {
 
         // GERMLINE VARIANT CALLING
         GERMLINE_VARIANT_CALLING(
+            params.tools,
             cram_variant_calling_status_normal,
             dbsnp,
             dbsnp_tbi,