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Added ont support for A. fumigatus & C. neoformans
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@Michal-Babins
Michal-Babins committed Oct 18, 2024
1 parent 767f33a commit d46d58f
Showing 1 changed file with 46 additions and 15 deletions.
61 changes: 46 additions & 15 deletions workflows/utilities/wf_merlin_magic.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -697,16 +697,32 @@ workflow merlin_magic {
maxsoft = snippy_maxsoft,
docker = snippy_variants_docker_image
}
}

if (assembly_only && ont_data) {
call snippy.snippy_variants as snippy_afumigatus_ont {
input:
reference_genome_file = snippy_reference_afumigatus,
assembly_fasta = assembly,
samplename = samplename,
map_qual = snippy_map_qual,
base_quality = snippy_base_quality,
min_coverage = snippy_min_coverage,
min_frac = snippy_min_frac,
min_quality = snippy_min_quality,
maxsoft = snippy_maxsoft,
docker = snippy_variants_docker_image
}
}
call snippy_gene_query.snippy_gene_query as snippy_gene_query_afumigatus {
input:
samplename = samplename,
snippy_variants_results = snippy_afumigatus.snippy_variants_results,
snippy_variants_results = select_first([snippy_afumigatus.snippy_variants_results, snippy_afumigatus_ont.snippy_variants_results]),
reference = snippy_reference_afumigatus,
query_gene = select_first([snippy_query_gene, "Cyp51A,HapE,AFUA_4G08340"]), # AFUA_4G08340 is COX10 according to MARDy
docker = snippy_gene_query_docker_image
}
}
}
if (merlin_tag == "Cryptococcus neoformans") {
if (!assembly_only && !ont_data) {
call snippy.snippy_variants as snippy_crypto {
Expand All @@ -723,16 +739,31 @@ workflow merlin_magic {
maxsoft = snippy_maxsoft,
docker = snippy_variants_docker_image
}
}
if (assembly_only && ont_data) {
call snippy.snippy_variants as snippy_crypto_ont {
input:
reference_genome_file = snippy_reference_cryptoneo,
assembly_fasta = assembly,
samplename = samplename,
map_qual = snippy_map_qual,
base_quality = snippy_base_quality,
min_coverage = snippy_min_coverage,
min_frac = snippy_min_frac,
min_quality = snippy_min_quality,
maxsoft = snippy_maxsoft,
docker = snippy_variants_docker_image
}
}
call snippy_gene_query.snippy_gene_query as snippy_gene_query_crypto {
input:
samplename = samplename,
snippy_variants_results = snippy_crypto.snippy_variants_results,
snippy_variants_results = select_first([snippy_crypto.snippy_variants_results, snippy_crypto_ont.snippy_variants_results]),
reference = snippy_reference_cryptoneo,
query_gene = select_first([snippy_query_gene, "CNA00300"]), # CNA00300 is ERG11 for this reference genome
docker = snippy_gene_query_docker_image
}
}
}
}
output {
# theiaprok
Expand Down Expand Up @@ -983,20 +1014,20 @@ workflow merlin_magic {
String? cladetyper_docker_image = cladetyper.gambit_cladetyper_docker_image
String? cladetype_annotated_ref = cladetyper.clade_spec_ref
# snippy variants
String snippy_variants_reference_genome = select_first([snippy_cauris.snippy_variants_reference_genome, snippy_cauris_ont.snippy_variants_reference_genome, snippy_afumigatus.snippy_variants_reference_genome, snippy_crypto.snippy_variants_reference_genome, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
String snippy_variants_version = select_first([snippy_cauris.snippy_variants_version, snippy_cauris_ont.snippy_variants_version,snippy_afumigatus.snippy_variants_version, snippy_crypto.snippy_variants_version, "No matching taxon detected"])
String snippy_variants_reference_genome = select_first([snippy_cauris.snippy_variants_reference_genome, snippy_cauris_ont.snippy_variants_reference_genome, snippy_afumigatus.snippy_variants_reference_genome, snippy_afumigatus_ont.snippy_variants_reference_genome, snippy_crypto.snippy_variants_reference_genome, snippy_crypto_ont.snippy_variants_reference_genome, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
String snippy_variants_version = select_first([snippy_cauris.snippy_variants_version, snippy_cauris_ont.snippy_variants_version,snippy_afumigatus.snippy_variants_version, snippy_afumigatus_ont.snippy_variants_version, snippy_crypto.snippy_variants_version, snippy_crypto_ont.snippy_variants_version, "No matching taxon detected"])
String snippy_variants_query = select_first([snippy_gene_query_cauris.snippy_variants_query, snippy_gene_query_afumigatus.snippy_variants_query, snippy_gene_query_crypto.snippy_variants_query, "No matching taxon detected"])
String snippy_variants_query_check = select_first([snippy_gene_query_cauris.snippy_variants_query_check, snippy_gene_query_afumigatus.snippy_variants_query_check, snippy_gene_query_crypto.snippy_variants_query_check, "No matching taxon detected"])
String snippy_variants_hits = select_first([snippy_gene_query_cauris.snippy_variants_hits, snippy_gene_query_afumigatus.snippy_variants_hits, snippy_gene_query_crypto.snippy_variants_hits, "No matching taxon detected"])
String snippy_variants_gene_query_results = select_first([snippy_gene_query_cauris.snippy_variants_gene_query_results, snippy_gene_query_afumigatus.snippy_variants_gene_query_results, snippy_gene_query_crypto.snippy_variants_gene_query_results, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
String snippy_variants_outdir_tarball = select_first([snippy_cauris.snippy_variants_outdir_tarball, snippy_cauris_ont.snippy_variants_outdir_tarball, snippy_afumigatus.snippy_variants_outdir_tarball, snippy_crypto.snippy_variants_outdir_tarball, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
String snippy_variants_results = select_first([snippy_cauris.snippy_variants_results, snippy_cauris_ont.snippy_variants_results,snippy_afumigatus.snippy_variants_results, snippy_crypto.snippy_variants_results, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
String snippy_variants_bam = select_first([snippy_cauris.snippy_variants_bam, snippy_cauris_ont.snippy_variants_bam, snippy_afumigatus.snippy_variants_bam, snippy_crypto.snippy_variants_bam, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
String snippy_variants_bai = select_first([snippy_cauris.snippy_variants_bai, snippy_cauris_ont.snippy_variants_bai, snippy_afumigatus.snippy_variants_bai, snippy_crypto.snippy_variants_bai, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
String snippy_variants_summary = select_first([snippy_cauris.snippy_variants_summary, snippy_cauris_ont.snippy_variants_summary, snippy_afumigatus.snippy_variants_summary, snippy_crypto.snippy_variants_summary, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
String snippy_variants_num_reads_aligned = select_first([snippy_cauris.snippy_variants_num_reads_aligned, snippy_cauris_ont.snippy_variants_num_reads_aligned, snippy_afumigatus.snippy_variants_num_reads_aligned, snippy_crypto.snippy_variants_num_reads_aligned, "No matching taxon detected"])
String snippy_variants_coverage_tsv = select_first([snippy_cauris.snippy_variants_coverage_tsv, snippy_cauris_ont.snippy_variants_coverage_tsv, snippy_afumigatus.snippy_variants_coverage_tsv, snippy_crypto.snippy_variants_coverage_tsv, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
String snippy_variants_num_variants = select_first([snippy_cauris.snippy_variants_num_variants, snippy_cauris_ont.snippy_variants_num_variants, snippy_afumigatus.snippy_variants_num_variants, snippy_crypto.snippy_variants_num_reads_aligned, "No matching taxon detected"])
String snippy_variants_percent_ref_coverage = select_first([snippy_cauris.snippy_variants_percent_ref_coverage, snippy_cauris_ont.snippy_variants_percent_ref_coverage, snippy_afumigatus.snippy_variants_percent_ref_coverage, snippy_crypto.snippy_variants_percent_ref_coverage, "No matching taxon detected"])
String snippy_variants_outdir_tarball = select_first([snippy_cauris.snippy_variants_outdir_tarball, snippy_cauris_ont.snippy_variants_outdir_tarball, snippy_afumigatus.snippy_variants_outdir_tarball, snippy_afumigatus_ont.snippy_variants_outdir_tarball, snippy_crypto.snippy_variants_outdir_tarball, snippy_crypto_ont.snippy_variants_outdir_tarball, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
String snippy_variants_results = select_first([snippy_cauris.snippy_variants_results, snippy_cauris_ont.snippy_variants_results,snippy_afumigatus.snippy_variants_results, snippy_afumigatus_ont.snippy_variants_results, snippy_crypto.snippy_variants_results, snippy_crypto_ont.snippy_variants_results, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
String snippy_variants_bam = select_first([snippy_cauris.snippy_variants_bam, snippy_cauris_ont.snippy_variants_bam, snippy_afumigatus.snippy_variants_bam, snippy_afumigatus_ont.snippy_variants_bam, snippy_crypto.snippy_variants_bam, snippy_crypto_ont.snippy_variants_bam, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
String snippy_variants_bai = select_first([snippy_cauris.snippy_variants_bai, snippy_cauris_ont.snippy_variants_bai, snippy_afumigatus.snippy_variants_bai, snippy_afumigatus_ont.snippy_variants_bai, snippy_crypto.snippy_variants_bai, snippy_crypto_ont.snippy_variants_bai, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
String snippy_variants_summary = select_first([snippy_cauris.snippy_variants_summary, snippy_cauris_ont.snippy_variants_summary, snippy_afumigatus.snippy_variants_summary, snippy_afumigatus_ont.snippy_variants_summary, snippy_crypto.snippy_variants_summary, snippy_crypto_ont.snippy_variants_summary, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
String snippy_variants_num_reads_aligned = select_first([snippy_cauris.snippy_variants_num_reads_aligned, snippy_cauris_ont.snippy_variants_num_reads_aligned, snippy_afumigatus.snippy_variants_num_reads_aligned, snippy_afumigatus_ont.snippy_variants_num_reads_aligned, snippy_crypto.snippy_variants_num_reads_aligned, snippy_crypto_ont.snippy_variants_num_reads_aligned, "No matching taxon detected"])
String snippy_variants_coverage_tsv = select_first([snippy_cauris.snippy_variants_coverage_tsv, snippy_cauris_ont.snippy_variants_coverage_tsv, snippy_afumigatus.snippy_variants_coverage_tsv, snippy_afumigatus_ont.snippy_variants_coverage_tsv, snippy_crypto.snippy_variants_coverage_tsv, snippy_crypto_ont.snippy_variants_coverage_tsv, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
String snippy_variants_num_variants = select_first([snippy_cauris.snippy_variants_num_variants, snippy_cauris_ont.snippy_variants_num_variants, snippy_afumigatus.snippy_variants_num_variants, snippy_afumigatus_ont.snippy_variants_num_variants, snippy_crypto.snippy_variants_num_reads_aligned, snippy_crypto_ont.snippy_variants_num_variants, "No matching taxon detected"])
String snippy_variants_percent_ref_coverage = select_first([snippy_cauris.snippy_variants_percent_ref_coverage, snippy_cauris_ont.snippy_variants_percent_ref_coverage, snippy_afumigatus.snippy_variants_percent_ref_coverage, snippy_afumigatus_ont.snippy_variants_percent_ref_coverage, snippy_crypto.snippy_variants_percent_ref_coverage, snippy_crypto_ont.snippy_variants_percent_ref_coverage, "No matching taxon detected"])
}
}

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