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Add Subworkflow Build_Indices for switch to DSL2 #238
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e87c4dd
bwamem2 is not working
FriederikeHanssen 97e07be
Add index subworkflow with bwamem2, samtools, gatk, htslib
FriederikeHanssen da2b677
Add intervals building
FriederikeHanssen a87e74c
Fix number of input channels for subworkflow build_indices
FriederikeHanssen 2f6e6ea
Move buidl indices to subworkflow folder
FriederikeHanssen 5c733b0
Fix relativ paths for include
FriederikeHanssen 573761d
Add OR to changelog
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,70 @@ | ||
| /* | ||
| ================================================================================ | ||
| BUILDING INDEXES | ||
| ================================================================================ | ||
| */ | ||
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| // And then initialize channels based on params or indexes that were just built | ||
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| include { HTSLIB_TABIX as HTSLIB_TABIX_DBSNP } from '../nf-core/htslib_tabix' | ||
| include { HTSLIB_TABIX as HTSLIB_TABIX_GERMLINE_RESOURCE } from '../nf-core/htslib_tabix' | ||
| include { HTSLIB_TABIX as HTSLIB_TABIX_KNOWN_INDELS } from '../nf-core/htslib_tabix' | ||
| include { HTSLIB_TABIX as HTSLIB_TABIX_PON } from '../nf-core/htslib_tabix' | ||
| include { BWAMEM2_INDEX as BWAMEM2_INDEX } from '../nf-core/bwamem2_index.nf' | ||
| include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX } from '../nf-core/samtools_faidx.nf' | ||
| include { GATK_CREATE_SEQUENCE_DICTIONARY as GATK_CREATE_SEQUENCE_DICTIONARY } from '../local/gatk_dict.nf' | ||
| include { BUILD_INTERVALS } from '../local/build_intervals.nf' | ||
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| workflow BUILD_INDICES{ | ||
| take: | ||
| step | ||
| ch_fasta | ||
| ch_dbsnp | ||
| ch_germline_resource | ||
| ch_known_indels | ||
| ch_pon | ||
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| main: | ||
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| if(!(params.bwa) && params.fasta && 'mapping' in step) | ||
| BWAMEM2_INDEX(ch_fasta) | ||
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| if(!(params.dict) && params.fasta && !('annotate' in step) && !('controlfreec' in step)) | ||
| GATK_CREATE_SEQUENCE_DICTIONARY(ch_fasta) | ||
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| if(!(params.fasta_fai) && params.fasta && !('annotate' in step)) | ||
| SAMTOOLS_FAIDX(ch_fasta) | ||
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| if(!(params.dbsnp_index) && params.dbsnp && ('mapping' in step || 'preparerecalibration' in step || 'controlfreec' in tools || 'haplotypecaller' in tools || 'mutect2' in tools || 'tnscope' in tools)) | ||
| HTSLIB_TABIX_DBSNP(ch_dbsnp) | ||
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| if(!(params.germline_resource_index) && params.germline_resource && 'mutect2' in tools) | ||
| HTSLIB_TABIX_GERMLINE_RESOURCE(ch_germline_resource) | ||
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| if(!(params.known_indels_index) && params.known_indels && ('mapping' in step || 'preparerecalibration' in step)) | ||
| HTSLIB_TABIX_KNOWN_INDELS(ch_known_indels) | ||
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| if(!(params.pon_index) && params.pon && ('tnscope' in tools || 'mutect2' in tools)) | ||
| HTSLIB_TABIX_PON(ch_pon) | ||
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| if(!(params.intervals) && !('annotate' in step) && !('controlfreec' in step)){ | ||
| ch_fai = params.fasta_fai ? Channel.value(file(params.fasta_fai)) : SAMTOOLS_FAIDX.out | ||
| BUILD_INTERVALS(ch_fai) | ||
| } | ||
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| emit: | ||
| bwa_built = BWAMEM2_INDEX.out | ||
| dictBuilt = GATK_CREATE_SEQUENCE_DICTIONARY.out | ||
| fai_built = SAMTOOLS_FAIDX.out | ||
| dbsnp_tbi = HTSLIB_TABIX_DBSNP.out | ||
| germline_resource_tbi = HTSLIB_TABIX_GERMLINE_RESOURCE.out | ||
| known_indels_tbi = HTSLIB_TABIX_KNOWN_INDELS.out | ||
| pon_tbi = HTSLIB_TABIX_PON.out | ||
| intervalBuilt = BUILD_INTERVALS.out | ||
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| } | ||
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Maybe move this line to DSL2 too, no?
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will do in the next PR coming :)