Commit 14182ee0 authored by khalid's avatar khalid
Browse files

debug fastp

parent d80d8daa
......@@ -15,7 +15,7 @@ if config["SeOrPe"] == "PE":
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"],
P = config["<step_name>__fastp_P_PE"],
output_dir = config["<step_name>__fastp_PE_output_dir"],
correction = "--correction " if config["<step_name>__fastp_correction_PE"] == True else "",
low_complexity_filter = "--low_complexity_filter " if config["<step_name>__fastp_low_complexity_filter"] == True else "",
......@@ -59,7 +59,7 @@ elif config["SeOrPe"] == "SE":
complexity_threshold = config["<step_name>__fastp_complexity_threshold"],
report_title = config["<step_name>__fastp_report_title"],
adapter_sequence = config["<step_name>__fastp_adapter_sequence"],
P = config["<step_name>__fastp_P"],
P = config["<step_name>__fastp_P_SE"],
output_dir = config["<step_name>__fastp_SE_output_dir"],
low_complexity_filter = "--low_complexity_filter " if config["<step_name>__fastp_low_complexity_filter"] == True else "",
overrepresentation_analysis = "--overrepresentation_analysis " if config["<step_name>__fastp_overrepresentation_analysis"] == True else "",
......
......@@ -73,7 +73,7 @@
label: "the adapter for read2 (PE data only). This is used if R1/R2 are found not overlapped. If not specified, it will be the same as <adapter_sequence>"
},
{
name: fastp_P,
name: fastp_P_PE,
prefix: -P,
type: numeric,
value: 20,
......@@ -151,14 +151,14 @@
label: "The adapter for read1. For SE data, if not specified, the adapter will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped."
},
{
name: fastp_P,
name: fastp_P_SE,
prefix: -P,
type: numeric,
value: 20,
min: 1,
max: NA,
step: 1,
label: "One in (--overrepresentation_sampling) reads will be computed for overrepresentation analysis (1~10000), smaller is slower.",
label: "For example, if you set -P 100, only 1/100 reads will be used for counting, and if you set -P 1, all reads will be used and slower.",
},
{
name: "fastp_low_complexity_filter",
......
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