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kraken -> kraken2
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@cimendes
cimendes committed Oct 25, 2024
1 parent fe5e93d commit a28ff96
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Showing 3 changed files with 45 additions and 45 deletions.
30 changes: 15 additions & 15 deletions workflows/utilities/wf_read_QC_trim_ont.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -29,11 +29,11 @@ workflow read_QC_trim_ont {

# kraken inputs
String? target_organism
Boolean call_kraken = false
Int? kraken_disk_size
Int? kraken_memory
Int? kraken_cpu
File? kraken_db
Boolean call_kraken2 = false
Int? kraken2_disk_size
Int? kraken2_memory
Int? kraken2_cpu
File? kraken2_db

# rasusa downsampling
Float downsampling_coverage = 150
Expand All @@ -57,7 +57,7 @@ workflow read_QC_trim_ont {
samplename = samplename,
read1 = read1,
target_organism = target_organism,
kraken2_db = select_first([kraken_db])
kraken2_db = select_first([kraken2_db])
}
call kraken2.kraken2_parse_classified as kraken2_recalculate_abundances_raw {
input:
Expand All @@ -71,7 +71,7 @@ workflow read_QC_trim_ont {
samplename = samplename,
read1 = ncbi_scrub_se.read1_dehosted,
target_organism = target_organism,
kraken2_db = select_first([kraken_db])
kraken2_db = select_first([kraken2_db])
}
call kraken2.kraken2_parse_classified as kraken2_recalculate_abundances_dehosted {
input:
Expand All @@ -82,24 +82,24 @@ workflow read_QC_trim_ont {
}
}
if ("~{workflow_series}" == "theiaprok") {
if ((call_kraken) && defined(kraken_db)) {
if ((call_kraken2) && defined(kraken2_db)) {
call kraken2.kraken2_standalone as kraken2_theiaprok {
input:
samplename = samplename,
read1 = read1,
kraken2_db = select_first([kraken_db]),
disk_size = kraken_disk_size,
memory = kraken_memory,
cpu = kraken_cpu
kraken2_db = select_first([kraken2_db]),
disk_size = kraken2_disk_size,
memory = kraken2_memory,
cpu = kraken2_cpu
}
call kraken2.kraken2_parse_classified as kraken2_recalculate_abundances {
input:
samplename = samplename,
kraken2_report = kraken2_theiaprok.kraken2_report,
kraken2_classified_report = kraken2_theiaprok.kraken2_classified_report
}
} if ((call_kraken) && ! defined(kraken_db)) {
String kraken_db_warning = "Kraken database not defined"
} if ((call_kraken2) && ! defined(kraken2_db)) {
String kraken2_db_warning = "Kraken2 database not defined"
}

# rasusa for random downsampling
Expand Down Expand Up @@ -140,7 +140,7 @@ workflow read_QC_trim_ont {
String? kraken2_sc2_dehosted = kraken2_recalculate_abundances_dehosted.percent_sc2
String? kraken2_target_organism_dehosted = kraken2_recalculate_abundances_dehosted.percent_target_organism
File? kraken2_report_dehosted = kraken2_recalculate_abundances_dehosted.kraken_report
String kraken2_database = select_first([kraken2_theiacov_raw.kraken2_database, kraken2_theiaprok.kraken2_database, kraken_db_warning, ""])
String kraken2_database = select_first([kraken2_theiacov_raw.kraken2_database, kraken2_theiaprok.kraken2_database, kraken2_db_warning, ""])

# estimated genome length -- by default for TheiaProk this is 5Mb
Int est_genome_length = genome_length
Expand Down
30 changes: 15 additions & 15 deletions workflows/utilities/wf_read_QC_trim_pe.wdl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -24,11 +24,11 @@ workflow read_QC_trim_pe {
Int bbduk_memory = 8
Boolean call_midas = false
File? midas_db
Boolean call_kraken = false
Int? kraken_disk_size
Int? kraken_memory
Int? kraken_cpu
File? kraken_db
Boolean call_kraken2 = false
Int? kraken2_disk_size
Int? kraken2_memory
Int? kraken2_cpu
File? kraken2_db
String? target_organism
File? adapters
File? phix
Expand All @@ -53,15 +53,15 @@ workflow read_QC_trim_pe {
read1 = read1,
read2 = read2,
target_organism = target_organism,
kraken2_db = select_first([kraken_db])
kraken2_db = select_first([kraken2_db])
}
call kraken.kraken2_standalone as kraken2_theiacov_dehosted {
input:
samplename = samplename,
read1 = select_first([ncbi_scrub_pe.read1_dehosted]),
read2 = ncbi_scrub_pe.read2_dehosted,
target_organism = target_organism,
kraken2_db = select_first([kraken_db])
kraken2_db = select_first([kraken2_db])
}
}
if (read_processing == "trimmomatic") {
Expand Down Expand Up @@ -133,19 +133,19 @@ workflow read_QC_trim_pe {
}
}
if ("~{workflow_series}" == "theiaprok") {
if ((call_kraken) && defined(kraken_db)) {
if ((call_kraken2) && defined(kraken2_db)) {
call kraken.kraken2_standalone as kraken2_theiaprok {
input:
samplename = samplename,
read1 = read1,
read2 = read2,
kraken2_db = select_first([kraken_db]),
disk_size = kraken_disk_size,
memory = kraken_memory,
cpu = kraken_cpu
kraken2_db = select_first([kraken2_db]),
disk_size = kraken2_disk_size,
memory = kraken2_memory,
cpu = kraken2_cpu
}
} if ((call_kraken) && ! defined(kraken_db)) {
String kraken_db_warning = "Kraken database not defined"
} if ((call_kraken2) && ! defined(kraken2_db)) {
String kraken2_db_warning = "Kraken2 database not defined"
}
}
if ("~{workflow_series}" == "theiameta") {
Expand Down Expand Up @@ -203,7 +203,7 @@ workflow read_QC_trim_pe {
String? kraken2_target_organism_name = target_organism
File? kraken2_report_dehosted = kraken2_theiacov_dehosted.kraken2_report
String kraken2_docker = select_first([kraken2_theiacov_raw.kraken2_docker, kraken2_theiaprok.kraken2_docker, ""])
String kraken2_database = select_first([kraken2_theiacov_raw.kraken2_database, kraken2_theiaprok.kraken2_database, kraken_db_warning, ""])
String kraken2_database = select_first([kraken2_theiacov_raw.kraken2_database, kraken2_theiaprok.kraken2_database, kraken2_db_warning, ""])

# trimming versioning
String? trimmomatic_version = trimmomatic_pe.version
Expand Down
30 changes: 15 additions & 15 deletions workflows/utilities/wf_read_QC_trim_se.wdl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -27,11 +27,11 @@ workflow read_QC_trim_se {
String? trimmomatic_args
Boolean call_midas = false
File? midas_db
Boolean call_kraken = false
File? kraken_db
Int? kraken_disk_size
Int? kraken_memory
Int? kraken_cpu
Boolean call_kraken2 = false
File? kraken2_db
Int? kraken2_disk_size
Int? kraken2_memory
Int? kraken2_cpu
String read_processing = "trimmomatic" # options: trimmomatic, fastp
String read_qc = "fastq_scan" # options: fastq_scan, fastqc
String fastp_args = "-g -5 20 -3 20"
Expand Down Expand Up @@ -101,14 +101,14 @@ workflow read_QC_trim_se {
samplename = samplename,
read1 = read1,
target_organism = target_organism,
kraken2_db = select_first([kraken_db])
kraken2_db = select_first([kraken2_db])
}
call kraken.kraken2_standalone as kraken2_theiacov_dehosted {
input:
samplename = samplename,
read1 = select_first([ncbi_scrub_se.read1_dehosted]),
target_organism = target_organism,
kraken2_db = select_first([kraken_db])
kraken2_db = select_first([kraken2_db])
}
}
if ("~{workflow_series}" == "theiaprok") {
Expand All @@ -122,18 +122,18 @@ workflow read_QC_trim_se {
}
}
if ("~{workflow_series}" == "theiaprok") {
if ((call_kraken) && defined(kraken_db)) {
if ((call_kraken2) && defined(kraken2_db)) {
call kraken.kraken2_standalone as kraken2_theiaprok {
input:
samplename = samplename,
read1 = read1,
kraken2_db = select_first([kraken_db]),
disk_size = kraken_disk_size,
memory = kraken_memory,
cpu = kraken_cpu
kraken2_db = select_first([kraken2_db]),
disk_size = kraken2_disk_size,
memory = kraken2_memory,
cpu = kraken2_cpu
}
} if ((call_kraken) && ! defined(kraken_db)) {
String kraken_db_warning = "Kraken database not defined"
} if ((call_kraken2) && ! defined(kraken2_db)) {
String kraken2_db_warning = "Kraken database not defined"
}
}
output {
Expand Down Expand Up @@ -172,7 +172,7 @@ workflow read_QC_trim_se {
String? kraken2_target_organism_name = target_organism
File? kraken2_report_dehosted = kraken2_theiacov_dehosted.kraken2_report
String kraken2_docker = select_first([kraken2_theiacov_raw.kraken2_docker, kraken2_theiaprok.kraken2_docker, ""])
String kraken2_database = select_first([kraken2_theiacov_raw.kraken2_database, kraken2_theiaprok.kraken2_database, kraken_db_warning, ""])
String kraken2_database = select_first([kraken2_theiacov_raw.kraken2_database, kraken2_theiaprok.kraken2_database, kraken2_db_warning, ""])

# trimming versioning
String? trimmomatic_version = trimmomatic_se.version
Expand Down

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