Commit e7dd4dff authored by khalid's avatar khalid
Browse files

debug raw_gff3

parent a18cc47b
......@@ -79,7 +79,7 @@ def generate(name, path_yaml = "", path_input = DEFAULT_PATH_INPUT, path_output
result += "config.update("+raw_input+")\n"
# !!! possibilité de définir samples plusieurs fois si il y a raw_reads et raw_vcf ... !!!
# il faut vérifier que les samples sont les mêmes ?
if not raw_input.endswith("_index") and not raw_input.endswith("_popmap") and not raw_input.endswith("_vcfFile"):
if not raw_input.endswith("_index") and not raw_input.endswith("_popmap") and not raw_input.endswith("_vcfFile") and not raw_input.endswith("_gff3"):
result += "SAMPLES = "+raw_input+"['samples']\n"
result += "\n"
......
{
name: raw_gds,
function_call: "raw_gds(config['results_dir'], config['gds_file'])",
function_call: "raw_gds(config['results_dir'], config['sample_dir'])",
options: [
{
name: "gds_file",
......
......@@ -2,10 +2,10 @@ import os
import re
import sys
def raw_vcf(results_dir, sample_dir):
def raw_gff3(results_dir, input_dir):
samples = list()
out = dict()
out["gds"] = input_dir
out["gff3"] = input_dir
return out
......
......@@ -3,8 +3,8 @@
function_call: "raw_gff3(config['results_dir'], config['sample_dir'])",
options: [
{
name: "sample_dir",
type: "input_dir",
name: "gff_file",
type: "input_file",
value: "/Data",
label: "gff3 file: ",
volumes: [Data: "/Data", Results: "/Results"]
......
......@@ -7,8 +7,8 @@ rule <step_name>__htseq_count:
config["results_dir"]+'/logs/' + config["<step_name>__htseq_count_output_dir"] + '/{sample}_htseq_count_log.txt'
params:
command = config["<step_name>__htseq_count_command"],
htseq_count_minaqual = config["htseq_count_minaqual"],
htseq_stranded = config["htseq_stranded"],
htseq_count_minaqual = config["<step_name>__htseq_count_minaqual"],
htseq_stranded = config["<step_name>__htseq_stranded"],
output_dir = config["results_dir"]+'/'+config["<step_name>__htseq_count_output_dir"]
shell:
"{params.command} -f bam -a {params.htseq_count_minaqual} -s {params.htseq_stranded} -r {params.htseq_orientation} {input.bam} {input.gff_file} 2> {log} > {output.stats}"
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