Skip to content

Commit

Permalink
add additional vcfs to reference_indexing_mutlti
Browse files Browse the repository at this point in the history
  • Loading branch information
@aidaanva
aidaanva committed Oct 25, 2024
1 parent 50b87b3 commit 2447756
Showing 1 changed file with 34 additions and 31 deletions.
65 changes: 34 additions & 31 deletions subworkflows/local/reference_indexing_multi.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -19,25 +19,26 @@ workflow REFERENCE_INDEXING_MULTI {
// Import reference sheet and change empty arrays to empty strings for compatibility with single reference input
ch_splitreferencesheet_for_branch = Channel.fromSamplesheet("fasta_sheet")
.map{
meta, fasta, fai, dict, mapper_index, circular_target, circularmapper_elongatedfasta, circularmapper_elongatedindex, mitochondrion, capture_bed, pileupcaller_bed, pileupcaller_snp, hapmap, pmd_masked_fasta, pmd_bed_for_masking, sexdet_bed, bedtools_feature, genotyping_gatk_dbsnp ->
meta.ploidy = meta.genotyping_ploidy != null ? meta.genotyping_ploidy : params.genotyping_reference_ploidy
fai = fai != [] ? fai : ""
dict = dict != [] ? dict : ""
mapper_index = mapper_index != [] ? mapper_index : ""
circular_target = circular_target != [] ? circular_target : ""
circularmapper_elongatedfasta = circularmapper_elongatedfasta != [] ? circularmapper_elongatedfasta : ""
circularmapper_elongatedindex = circularmapper_elongatedindex != [] ? circularmapper_elongatedindex : ""
mitochondrion = mitochondrion != [] ? mitochondrion : ""
capture_bed = capture_bed != [] ? capture_bed : ""
pileupcaller_bed = pileupcaller_bed != [] ? pileupcaller_bed : ""
pileupcaller_snp = pileupcaller_snp != [] ? pileupcaller_snp : ""
hapmap = hapmap != [] ? hapmap : ""
pmd_masked_fasta = pmd_masked_fasta != [] ? pmd_masked_fasta : ""
pmd_bed_for_masking = pmd_bed_for_masking != [] ? pmd_bed_for_masking : ""
sexdet_bed = sexdet_bed != [] ? sexdet_bed : ""
bedtools_feature = bedtools_feature != [] ? bedtools_feature : ""
genotyping_gatk_dbsnp = genotyping_gatk_dbsnp != [] ? genotyping_gatk_dbsnp : ""
[ meta - meta.subMap('genotyping_ploidy'), fasta, fai, dict, mapper_index, circular_target, circularmapper_elongatedfasta, circularmapper_elongatedindex, mitochondrion, capture_bed, pileupcaller_bed, pileupcaller_snp, hapmap, pmd_masked_fasta, pmd_bed_for_masking, sexdet_bed, bedtools_feature, genotyping_gatk_dbsnp ]
meta, fasta, fai, dict, mapper_index, circular_target, circularmapper_elongatedfasta, circularmapper_elongatedindex, mitochondrion, capture_bed, pileupcaller_bed, pileupcaller_snp, hapmap, pmd_masked_fasta, pmd_bed_for_masking, sexdet_bed, bedtools_feature, genotyping_gatk_dbsnp, consensus_multivcfanalyzer_additional_vcf_files ->
meta.ploidy = meta.genotyping_ploidy != null ? meta.genotyping_ploidy : params.genotyping_reference_ploidy
fai = fai != [] ? fai : ""
dict = dict != [] ? dict : ""
mapper_index = mapper_index != [] ? mapper_index : ""
circular_target = circular_target != [] ? circular_target : ""
circularmapper_elongatedfasta = circularmapper_elongatedfasta != [] ? circularmapper_elongatedfasta : ""
circularmapper_elongatedindex = circularmapper_elongatedindex != [] ? circularmapper_elongatedindex : ""
mitochondrion = mitochondrion != [] ? mitochondrion : ""
capture_bed = capture_bed != [] ? capture_bed : ""
pileupcaller_bed = pileupcaller_bed != [] ? pileupcaller_bed : ""
pileupcaller_snp = pileupcaller_snp != [] ? pileupcaller_snp : ""
hapmap = hapmap != [] ? hapmap : ""
pmd_masked_fasta = pmd_masked_fasta != [] ? pmd_masked_fasta : ""
pmd_bed_for_masking = pmd_bed_for_masking != [] ? pmd_bed_for_masking : ""
sexdet_bed = sexdet_bed != [] ? sexdet_bed : ""
bedtools_feature = bedtools_feature != [] ? bedtools_feature : ""
genotyping_gatk_dbsnp = genotyping_gatk_dbsnp != [] ? genotyping_gatk_dbsnp : ""
consensus_multivcfanalyzer_additional_vcf_files = consensus_multivcfanalyzer_additional_vcf_files != [] ? consensus_multivcfanalyzer_additional_vcf_files : ""
[ meta - meta.subMap('genotyping_ploidy'), fasta, fai, dict, mapper_index, circular_target, circularmapper_elongatedfasta, circularmapper_elongatedindex, mitochondrion, capture_bed, pileupcaller_bed, pileupcaller_snp, hapmap, pmd_masked_fasta, pmd_bed_for_masking, sexdet_bed, bedtools_feature, genotyping_gatk_dbsnp, consensus_multivcfanalyzer_additional_vcf_files ]
}

// GENERAL DESCRIPTION FOR NEXT SECTIONS
Expand All @@ -53,7 +54,7 @@ workflow REFERENCE_INDEXING_MULTI {

ch_input_from_referencesheet = ch_splitreferencesheet_for_branch
.multiMap {
meta, fasta, fai, dict, mapper_index, circular_target, circularmapper_elongatedfasta, circularmapper_elongatedindex, mitochondrion, capture_bed, pileupcaller_bed, pileupcaller_snp, hapmap, pmd_masked_fasta, pmd_bed_for_masking, sexdet_bed, bedtools_feature, genotyping_gatk_dbsnp ->
meta, fasta, fai, dict, mapper_index, circular_target, circularmapper_elongatedfasta, circularmapper_elongatedindex, mitochondrion, capture_bed, pileupcaller_bed, pileupcaller_snp, hapmap, pmd_masked_fasta, pmd_bed_for_masking, sexdet_bed, bedtools_feature, genotyping_gatk_dbsnp, consensus_multivcfanalyzer_additional_vcf_files ->
generated: [ meta, fasta, fai, dict, mapper_index ]
circularmapper: [ meta, circular_target, circularmapper_elongatedfasta, circularmapper_elongatedindex ]
mitochondrion_header: [ meta, mitochondrion ]
Expand All @@ -65,6 +66,7 @@ workflow REFERENCE_INDEXING_MULTI {
sexdeterrmine_bed: [ meta, sexdet_bed ]
bedtools_feature: [ meta, bedtools_feature ]
dbsnp: [ meta, genotyping_gatk_dbsnp ]
mva_additional_vcfs: [ meta, consensus_multivcfanalyzer_additional_vcf_files ]
}

// Detect if fasta is gzipped or not
Expand Down Expand Up @@ -201,16 +203,17 @@ workflow REFERENCE_INDEXING_MULTI {
ch_indexmapper_for_reference = ch_fasta_for_mapperindex.skip.mix(ch_indexed_formix)

emit:
reference = ch_indexmapper_for_reference // [ meta, fasta, fai, dict, mapindex ]
elongated_reference = ch_input_from_referencesheet.circularmapper // [ meta, circular_target, circularmapper_elongatedfasta, circularmapper_elongatedindex ]
mitochondrion_header = ch_input_from_referencesheet.mitochondrion_header // [ meta, mitochondrion ]
hapmap = ch_input_from_referencesheet.angsd_hapmap // [ meta, hapmap ]
pmd_masked_fasta = ch_input_from_referencesheet.pmd_masked_fasta // [ meta, pmd_masked_fasta ]
pmd_bed_for_masking = ch_input_from_referencesheet.pmd_bed_for_masking // [ meta, pmd_bed_for_masking ]
snp_capture_bed = ch_input_from_referencesheet.snp_bed // [ meta, capture_bed ]
pileupcaller_bed_snp = ch_input_from_referencesheet.pileupcaller_bed_snp // [ meta, pileupcaller_bed, pileupcaller_snp ]
sexdeterrmine_bed = ch_input_from_referencesheet.sexdeterrmine_bed // [ meta, sexdet_bed ]
bedtools_feature = ch_input_from_referencesheet.bedtools_feature // [ meta, bedtools_feature ]
dbsnp = ch_input_from_referencesheet.dbsnp // [ meta, genotyping_gatk_dbsnp ]
reference = ch_indexmapper_for_reference // [ meta, fasta, fai, dict, mapindex ]
elongated_reference = ch_input_from_referencesheet.circularmapper // [ meta, circular_target, circularmapper_elongatedfasta, circularmapper_elongatedindex ]
mitochondrion_header = ch_input_from_referencesheet.mitochondrion_header // [ meta, mitochondrion ]
hapmap = ch_input_from_referencesheet.angsd_hapmap // [ meta, hapmap ]
pmd_masked_fasta = ch_input_from_referencesheet.pmd_masked_fasta // [ meta, pmd_masked_fasta ]
pmd_bed_for_masking = ch_input_from_referencesheet.pmd_bed_for_masking // [ meta, pmd_bed_for_masking ]
snp_capture_bed = ch_input_from_referencesheet.snp_bed // [ meta, capture_bed ]
pileupcaller_bed_snp = ch_input_from_referencesheet.pileupcaller_bed_snp // [ meta, pileupcaller_bed, pileupcaller_snp ]
sexdeterrmine_bed = ch_input_from_referencesheet.sexdeterrmine_bed // [ meta, sexdet_bed ]
bedtools_feature = ch_input_from_referencesheet.bedtools_feature // [ meta, bedtools_feature ]
dbsnp = ch_input_from_referencesheet.dbsnp // [ meta, genotyping_gatk_dbsnp ]
mva_additional_vcfs = ch_input_from_referencesheet.mva_additional_vcfs // [ meta, consensus_multivcfanalyzer_additional_vcf_files ]
versions = ch_versions
}

0 comments on commit 2447756

Please sign in to comment.