Commit 81756677 authored by khalid's avatar khalid
Browse files

Add fastp PE adapter detection and change json file name to allow MultiQC detection

parent edfc3cd5
......@@ -5,13 +5,14 @@ if config["SeOrPe"] == "PE":
**<step_name>__fastp_PE_inputs()
output:
report_html = config["results_dir"]+"/"+config["<step_name>__fastp_PE_output_dir"]+"/fastp_report_{sample}.html",
report_json = config["results_dir"]+"/"+config["<step_name>__fastp_PE_output_dir"]+"/fastp_report_{sample}.json",
report_json = config["results_dir"]+"/"+config["<step_name>__fastp_PE_output_dir"]+"/fastp_report_{sample}fastp.json",
read_preprocessed = config["results_dir"]+"/"+config["<step_name>__fastp_PE_output_dir"]+"/{sample}_R1.fq.gz",
read2_preprocessed = config["results_dir"]+"/"+config["<step_name>__fastp_PE_output_dir"]+"/{sample}_R2.fq.gz"
params:
command = config["<step_name>__fastp_PE_command"],
complexity_threshold = config["<step_name>__fastp_complexity_threshold"],
report_title = config["<step_name>__fastp_report_title"],
detect_adapter_for_pe = "--detect_adapter_for_pe" if config["<step_name>__fastp_adapter_detection_PE"] == True else "",
adapter_sequence = config["<step_name>__fastp_adapter_sequence"],
adapter_sequence_R2 = config["<step_name>__fastp_adapter_sequence_R2_PE"],
P = config["<step_name>__fastp_P"],
......@@ -36,6 +37,7 @@ if config["SeOrPe"] == "PE":
"--html {output.report_html} "
"--json {output.report_json} "
"--report_title {params.report_title} "
"{params.detect_adapter_for_pe} "
"--adapter_sequence '{params.adapter_sequence}' "
"--adapter_sequence_r2 '{params.adapter_sequence_R2}' "
"{params.overrepresentation_analysis} "
......@@ -50,7 +52,7 @@ elif config["SeOrPe"] == "SE":
**<step_name>__fastp_SE_inputs()
output:
report_html = config["results_dir"]+"/"+config["<step_name>__fastp_SE_output_dir"]+"/fastp_report_{sample}.html",
report_json = config["results_dir"]+"/"+config["<step_name>__fastp_SE_output_dir"]+"/fastp_report_{sample}.json",
report_json = config["results_dir"]+"/"+config["<step_name>__fastp_SE_output_dir"]+"/fastp_report_{sample}fastp.json",
read_preprocessed = config["results_dir"]+"/"+config["<step_name>__fastp_SE_output_dir"]+"/{sample}.fq.gz",
params:
command = config["<step_name>__fastp_SE_command"],
......
......@@ -19,9 +19,9 @@
inputs: [{ name: read, type: "reads" }, { name: read2, type: "reads" }],
outputs: [
{ name: report_html, type: "html", file: "fastp_report_{sample}.html", description: "Rapport HTML du préprocessing effectué" },
{ name: report_json, type: "json", file: "fastp_report_{sample}.json", description: "Rapport JSON du préprocessing effectué" },
{ name: read_preprocessed, type: "reads", file: "{sample}_R1.fq.gz", description: "Reads R1 préprocessés" },
{ name: read2_preprocessed, type: "reads", file: "{sample}_R2.fq.gz", description: "Reads R2 préprocessés" },
{ name: report_json, type: "json", file: "fastp_report_{sample}fastp.json", description: "Rapport JSON du préprocessing effectué" },
{ name: read_preprocessed, type: "reads", file: "{sample}_<R>1.fq.gz", description: "Reads R1 préprocessés" },
{ name: read2_preprocessed, type: "reads", file: "{sample}_<R>2.fq.gz", description: "Reads R2 préprocessés" },
],
options:
[
......@@ -105,7 +105,7 @@
inputs: [{ name: read, type: "reads" }],
outputs: [
{ name: report_html, type: "html", file: "fastp_report_{sample}.html", description: "Rapport HTML du préprocessing effectué" },
{ name: report_json, type: "json", file: "fastp_report_{sample}.json", description: "Rapport JSON du préprocessing effectué" },
{ name: report_json, type: "json", file: "fastp_report_{sample}fastp.json", description: "Rapport JSON du préprocessing effectué" },
{ name: read_preprocessed, type: "reads", file: "{sample}.fq.gz", description: "Reads préprocessés" },
],
options:
......@@ -137,6 +137,12 @@
value: "fastp report",
label: "fastp report title",
},
{
name: "fastp_adapter_detection_PE",
type: "checkbox",
value: TRUE,
label: "adapter sequence auto-detection is disabled by default since the adapters can be trimmed by overlap analysis. However, you can specify --detect_adapter_for_pe to enable it",
},
{
name: fastp_adapter_sequence,
prefix: --adapter_sequence,
......
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