debug raw_gff3

generate_workflow_snakefile.py

@@ -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"

raw_inputs/raw_gds.yaml

 {
   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",

raw_inputs/raw_gff3.py

@@ -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
     
 

raw_inputs/raw_gff3.yaml

@@ -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"]

tools/htseq_count/htseq_count.rule.snakefile

@@ -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}"