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Run getmlst.py once and cache the result per pipeline run #93

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Oct 3, 2024
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Run getmlst.py once and cache the result per pipeline run #93

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7 changes: 5 additions & 2 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ include {serotyping} from './modules/serotyping.nf'
include {srst2_for_res_typing; split_target_RES_seq_from_sam_file; split_target_RES_sequences; freebayes} from './modules/res_alignments.nf'
include {res_typer} from './modules/res_typer.nf'
include {surface_typer} from './modules/surface_typer.nf'
include {srst2_for_mlst; get_mlst_allele_and_pileup} from './modules/mlst.nf'
include {getmlst_for_srst2; srst2_for_mlst; get_mlst_allele_and_pileup} from './modules/mlst.nf'
include {get_pbp_genes; get_pbp_alleles} from './modules/pbp_typer.nf'
include {finalise_sero_res_results; finalise_surface_typer_results; finalise_pbp_existing_allele_results; combine_results} from './modules/combine.nf'
include {get_version} from './modules/version.nf'
Expand Down Expand Up @@ -187,8 +187,11 @@ workflow MLST {
reads

main:
// Get MLST database for all downstream processes
getmlst_for_srst2()

// Run SRST2 MLST
srst2_for_mlst(reads, params.mlst_min_coverage)
srst2_for_mlst(getmlst_for_srst2.out.getmlst_results, reads, params.mlst_min_coverage)

// Get new consensus allele and pileup data
get_mlst_allele_and_pileup(srst2_for_mlst.out.bam_and_srst2_results, params.mlst_min_read_depth)
Expand Down
17 changes: 14 additions & 3 deletions modules/mlst.nf
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Original file line number Diff line number Diff line change
@@ -1,6 +1,19 @@
process getmlst_for_srst2 {
output:
tuple path(mlst_fasta), path(mlst_profile_csv), emit: getmlst_results

script:
mlst_fasta="Streptococcus_agalactiae.fasta"
mlst_profile_csv="profiles_csv"
"""
getmlst.py --species 'Streptococcus agalactiae'
"""
}

process srst2_for_mlst {

input:
tuple path(mlst_fasta), path(mlst_profile_csv) // mlst database
tuple val(pair_id), file(reads) // ID and paired read files
val(min_coverage) // String of minimum coverage parameter(s) for SRST2

Expand All @@ -13,12 +26,10 @@ process srst2_for_mlst {
script:
mlst_db="Streptococcus_agalactiae.fasta"
mlst_name="Streptococcus_agalactiae"

"""
set +e

getmlst.py --species 'Streptococcus agalactiae'
srst2 --samtools_args '\\-A' --input_pe ${reads[0]} ${reads[1]} --output ${pair_id} --save_scores --mlst_db ${mlst_db} --mlst_definitions profiles_csv --mlst_delimiter '_' --min_coverage ${min_coverage}
srst2 --samtools_args '\\-A' --input_pe ${reads[0]} ${reads[1]} --output ${pair_id} --save_scores --mlst_db ${mlst_fasta} --mlst_definitions ${mlst_profile_csv} --mlst_delimiter '_' --min_coverage ${min_coverage}

touch ${pair_id}__mlst__${mlst_name}__results.txt

Expand Down
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