Remove get_samples and add raw_inputs system

generate_sag_yaml.py

@@ -124,6 +124,12 @@ def generate_workflow_params(pipeline):
     template["title"] = "Global parameters :"
     for option in workflow["options"]:
         template["content"].append(option)
+
+    if "input" in workflow:
+        raw_input = read_yaml("raw_inputs/" + workflow["input"] + ".yaml")
+        for option in raw_input["options"]:
+            template["content"].append(option)
+
     template["content"].append(
         yaml.load("{name: memo, type: textArea, value: '', label: 'Text area for the user'}")
     )

generate_workflow.py

@@ -128,6 +128,9 @@ def generate_snakefile(pipeline, out_file):
     else:
         params_equals = list()
 
+    if "input" in params:
+        res += "from "+params["input"]+" import "+params["input"]+"\n"
+
     path = "workflows/" + pipeline + "/" + pipeline + ".snakefile"
     with open(path, "r") as mainrule:
         res += mainrule.read()
@@ -327,6 +330,9 @@ def generate_pipeline_files(workflow, out_dir, local_config="default"):
                 out_dir + "/files/scripts",
             )
 
+    if "input" in workflow_yaml:
+        shutil.copy("./raw_inputs/"+workflow_yaml["input"]+".py", out_dir+"/files")
+
     shutil.copy("./get_samples.py", out_dir+"/files")
     shutil.copy("./generate_multiqc_config.py", out_dir+"/files")
     shutil.copy("./tools.py", out_dir+"/files")

generate_workflow_snakefile.py

@@ -33,7 +33,7 @@ def generate(name):
 
     result += "\n"
 
-    result += "SAMPLES = config[\"samples\"]\n"
+    #result += "SAMPLES = config[\"samples\"]\n"
     result += "STEPS = config[\"steps\"]\n"
     result += "PREPARE_REPORT_OUTPUTS = config[\"prepare_report_outputs\"]\n"
     result += "PREPARE_REPORT_SCRIPTS = config[\"prepare_report_scripts\"]\n"
@@ -51,16 +51,23 @@ def generate(name):
 
     result += "\n"
 
-    result += "# Generic input functions\n"
-    result += "## get raw_reads\n"
-    result += "def raw_reads():\n"
-    result += "\tinputs = dict()\n"
-    result += "\tif (config[\"SeOrPe\"] == \"PE\"):\n"
-    result += "\t\tinputs[\"read\"] = config['sample_dir']+'/{sample}_R1'+config[\"sample_suffix\"]\n"
-    result += "\t\tinputs[\"read2\"] = config['sample_dir']+'/{sample}_R2'+config[\"sample_suffix\"]\n"
-    result += "\telse:\n"
-    result += "\t\tinputs[\"read\"] = config['sample_dir']+'/{sample}'+config[\"sample_suffix\"]\n"
-    result += "\treturn inputs\n"
+    if "input" in yaml:
+        raw_inputs_yaml = read_yaml("./raw_inputs/"+yaml["input"]+".yaml")
+        result += "# raw_inputs function call\n"
+        result += yaml["input"]+" = "+raw_inputs_yaml["function_call"]+"\n"
+        result += "SAMPLES = "+yaml["input"]+"['samples']\n"
+    #else : # OLD (to replace for all workflows with input raw_reads)
+    #    result += "# Generic input functions\n"
+    #    result += "## get raw_reads\n"
+    #    result += "def raw_reads():\n"
+    #    result += "\tinputs = dict()\n"
+    #    result += "\tif (config[\"SeOrPe\"] == \"PE\"):\n"
+    #    result += "\t\tinputs[\"read\"] = config['sample_dir']+'/{sample}_R1'+config[\"sample_suffix\"]\n"
+    #    result += "\t\tinputs[\"read2\"] = config['sample_dir']+'/{sample}_R2'+config[\"sample_suffix\"]\n"
+    #    result += "\telse:\n"
+    #    result += "\t\tinputs[\"read\"] = config['sample_dir']+'/{sample}'+config[\"sample_suffix\"]\n"
+    #    result += "\treturn inputs\n"
+    #    result += "raw_reads = raw_reads()\n"
 
     result += "\n"
 
@@ -81,7 +88,7 @@ def generate(name):
 
                         if param["origin_command"] == "raw_reads":
 
-                            result += "\tinputs[\"" + param["input_name"] + "\"] = raw_reads()[\"read\"]\n"
+                            result += "\tinputs[\"" + param["input_name"] + "\"] = raw_reads[\""+param["origin_name"]+"\"]\n"
                         else:
 
                             result += "\tinputs[\"" + param["input_name"] + "\"] = rules." + param["origin_command"] + ".output." + param["origin_name"] + "\n"
@@ -110,10 +117,14 @@ def generate(name):
 
         for step in yaml["steps_in"]:
 
-            if ("step_name" in step) and ("tool_name" in step):
-
-                result += "\tif (step == \"" + step["step_name"] + "\"):\n"
-                result += "\t\toutputs = rules." + step["tool_name"] + ".output\n"
+            if ("step_name" in step) and ("rule_name" in step):
+                add = ""
+                if ("_SE" in step["rule_name"]):
+                    add = "and config['SeOrPe'] == 'SE'"
+                if ("_PE" in step["rule_name"]):
+                    add = "and config['SeOrPe'] == 'PE'"
+                result += "\tif (step == \"" + step["step_name"] + "\" " + add + " ):\n"
+                result += "\t\toutputs = rules." + step["rule_name"] + ".output\n"
                 result += "\t\t\n"
 
 

raw_inputs/raw_reads.py

+import os
+import re
+import sys
+
+def raw_reads(results_dir, sample_dir, SeOrPe):
+    samples = list()
+    PE_mark = "" # _R or _
+    suffixes = list()
+    dicoSamples = dict() # sample_name: file(s)
+    files = os.listdir(sample_dir)
+    if SeOrPe == "PE":
+        regex = re.compile(r"^(.+)(_R1|_R2|_1|_2)(.+)")
+    else:
+        regex = re.compile(r"^(.+?)(\..*)")
+    for file in files:
+        res = re.match(regex, file)
+        if res:
+            if res.group(1) not in samples:
+                samples.append(res.group(1))
+                if SeOrPe == "PE":
+                    suffixes.append(res.group(3))
+                    if len(res.group(2)) == 3:
+                        PE_mark = "_R"
+                    else:
+                        PE_mark = "_"
+                else:
+                    suffixes.append(res.group(2))
+
+            if res.group(1) not in dicoSamples.keys():
+                dicoSamples[res.group(1)] = list()
+
+            dicoSamples[res.group(1)].append(file)
+
+    if (len(set(suffixes)) == 1 ):
+        suffix = list(set(suffixes))[0]
+        with open(results_dir+"/samples.tsv","w") as sampleTab:
+            if SeOrPe == "PE":
+                sampleTab.write("sample\tfile_read_1\tfile_read_2")
+            else:
+                sampleTab.write("sample\tfile_read_1")
+            for sample in sorted(samples):
+                sampleTab.write("\n"+sample+"\t"+"\t".join(sorted(dicoSamples[sample])))
+
+        out = {'samples': sorted(samples), 'suffix': suffix, 'dico': dicoSamples}
+
+        if SeOrPe == "SE":
+            out ["read"] = os.path.join(sample_dir,"{sample}"+suffix)
+        else:
+            out ["read"] = os.path.join(sample_dir,"{sample}"+PE_mark+"1"+suffix)
+            out ["read2"] = os.path.join(sample_dir,"{sample}"+PE_mark+"2"+suffix)
+
+        return out
+    else:
+        exit("Files have different suffixes:" + ','.join(suffixes))
+
+#print(raw_reads(sys.argv[1],sys.argv[2],sys.argv[3]))
\ No newline at end of file

raw_inputs/raw_reads.yaml

+{
+  name: raw_reads,
+  function_call: "raw_reads(config['results_dir'], config['sample_dir'], config['SeOrPe'])",
+  options: [
+    {
+      name: "sample_dir",
+      type: "input_dir",
+      value: "/Data",
+      label: "Directory containing the fastq files: ",
+      volumes:  [Data: "/Data", Results: "/Results"]
+    },
+    {
+      name: "SeOrPe",
+      type: "radio",
+      value: "SE",
+      choices: [Single end: SE, Paired end: PE],
+      label: "Single end reads (SE) or Paired end reads (PE): "
+    }
+  ]
+}
\ No newline at end of file

workflows/Genome_Profile/Genome_Profile.snakefile

@@ -7,7 +7,6 @@ import csv
 # Wildcards #
 #############
 
-SAMPLES = config["samples"]
 STEPS = config["steps"]
 PREPARE_REPORT_OUTPUTS = config["prepare_report_outputs"]
 PREPARE_REPORT_SCRIPTS = config["prepare_report_scripts"]
@@ -19,28 +18,14 @@ config = config["params"]
 # Inputs #
 ##########
 
-# Generic input functions
-## get raw_reads
-def raw_reads():
-    inputs = dict()
-    if (config["SeOrPe"] == "PE"):
-        inputs["read"] = config['sample_dir']+'/{sample}_R1'+config["sample_suffix"]
-        inputs["read2"] = config['sample_dir']+'/{sample}_R2'+config["sample_suffix"]
-    elif (config["SeOrPe"] == "SE"):
-        inputs["read"] = config['sample_dir']+'/{sample}'+config["sample_suffix"]
-    else:
-        sys.exit("SeOrPe should be SE or PE")
-    return inputs
-
-## get reads (trimmed or raw)
-def reads():
-    return raw_reads()
-
+# raw_inputs function call
+raw_reads = raw_reads(config['results_dir'], config['sample_dir'], config['SeOrPe'])
+SAMPLES = raw_reads['samples']
 
 # Tools inputs functions
 
 def fastp_inputs():
-    return raw_reads()
+    return raw_reads
 
 def jellyfish_count_inputs():
     inputs = dict()
@@ -51,9 +36,9 @@ def jellyfish_count_inputs():
         else:
             inputs["read"] = expand(rules.fastp_SE.output.read,sample=SAMPLES)
     else:
-        inputs["read"] = expand(raw_reads()["read"],sample=SAMPLES)
+        inputs["read"] = expand(raw_reads["read"],sample=SAMPLES)
         if (config["SeOrPe"] == "PE"):
-            inputs["read2"] = expand(raw_reads()["read2"],sample=SAMPLES)
+            inputs["read2"] = expand(raw_reads["read2"],sample=SAMPLES)
     return inputs
 
 {import global_functions}

workflows/Genome_Profile/Genome_Profile.yaml

@@ -4,6 +4,7 @@
   description: "",
   version: "0.0.1",
   author: "MBB",
+  input: raw_reads,
   steps:
     [
       { title: Preprocessing, name: preprocessing, tools: [fastp,"null"], default: "null" },
@@ -18,19 +19,5 @@
         label: "Results directory: ",
         volumes:  [Results: "/Results"]
       },
-      {
-        name: "sample_dir",
-        type: "input_dir",
-        value: "/Data",
-        label: "Data directory: ",
-        volumes:  [Data: "/Data", Results: "/Results"]
-      },
-      {
-        name: "SeOrPe",
-        type: "radio",
-        value: "PE",
-        choices: [Single end: SE, Paired end: PE],
-        label: "Single end reads (SE) or Paired end reads (PE): ",
-      },
     ],
 }
\ No newline at end of file

workflows/Metabarcoding/Metabarcoding.snakefile

@@ -7,7 +7,6 @@ import csv
 # Wildcards #
 #############
 
-SAMPLES = config["samples"]
 STEPS = config["steps"]
 PREPARE_REPORT_OUTPUTS = config["prepare_report_outputs"]
 PREPARE_REPORT_SCRIPTS = config["prepare_report_scripts"]
@@ -19,28 +18,21 @@ config = config["params"]
 # Inputs #
 ##########
 
-# Generic input functions
-## get raw_reads
-def raw_reads():
-    inputs = dict()
-    if (config["SeOrPe"] == "PE"):
-        inputs["read"] = config['sample_dir']+'/{sample}_R1'+config["sample_suffix"]
-        inputs["read2"] = config['sample_dir']+'/{sample}_R2'+config["sample_suffix"]
-    else:
-        inputs["read"] = config['sample_dir']+'/{sample}'+config["sample_suffix"]
-    return inputs
+# raw_inputs function call
+raw_reads = raw_reads(config['results_dir'], config['sample_dir'], config['SeOrPe'])
+SAMPLES = raw_reads['samples']
 
 # Tools inputs functions
 
 def cutadapt_inputs():
-    return raw_reads()
+    return raw_reads
 
 def dada2_inputs():
     inputs = dict()
     if config["trimming"] == 'null':
-        inputs["read"] = expand(raw_reads()["read"],sample=SAMPLES)
+        inputs["read"] = expand(raw_reads["read"],sample=SAMPLES)
         if (config["SeOrPe"] == "PE"):
-            inputs["read2"] = expand(raw_reads()["read2"],sample=SAMPLES)
+            inputs["read2"] = expand(raw_reads["read2"],sample=SAMPLES)
     if config["trimming"] == 'cutadapt':
         if (config["SeOrPe"] == "SE"):
             inputs["read"] = expand(rules.cutadapt_SE.output[0],sample=SAMPLES)
@@ -65,9 +57,9 @@ def dada2_learn_errors_inputs():
             inputs["filtRs"] = expand(rules.cutadapt_PE.output.read2_trimmed,sample=SAMPLES)
             inputs["cutadapt_stats"] = config["results_dir"]+"/"+config["cutadapt_PE_output_dir"]+"/cutadapt_stats.tsv"
     else: # no trimming
-        inputs["filtFs"] = expand(raw_reads()["read"],sample=SAMPLES)
+        inputs["filtFs"] = expand(raw_reads["read"],sample=SAMPLES)
         if (config["SeOrPe"] == "PE"):
-            inputs["filtRs"] = expand(raw_reads()["read2"],sample=SAMPLES)
+            inputs["filtRs"] = expand(raw_reads["read2"],sample=SAMPLES)
     return inputs
 
 {import global_functions}

workflows/Metabarcoding/Metabarcoding.yaml

@@ -4,6 +4,7 @@
   description: ,
   version: "0.0.1",
   author: "MBB",
+  input: raw_reads,
   steps:
     [
       { title: Trimming, name: trimming, tools: [cutadapt, "null"], default: "null" },
@@ -18,25 +19,5 @@
         label: "Results directory: ",
         volumes:  [Results: "/Results"]
       },
-      {
-        name: "sample_dir",
-        type: "input_dir",
-        value: "/Data",
-        label: "Data directory: ",
-        volumes:  [Data: "/Data", Results: "/Results"]
-      },
-      #{
-      #  name: "sample_suffix",
-      #  type: "text",
-      #  value: ".fastq.gz",
-      #  label: "Samples suffix: ",
-      #},
-      {
-        name: "SeOrPe",
-        type: "radio",
-        value: "PE",
-        choices: [Single end: SE, Paired end: PE],
-        label: "Single end reads (SE) or Paired end reads (PE): ",
-      },
     ],
 }
\ No newline at end of file

workflows/MitoZ/MitoZ.snakefile

@@ -7,7 +7,6 @@ import csv
 # Wildcards #
 #############
 
-SAMPLES = config["samples"]
 STEPS = config["steps"]
 PREPARE_REPORT_OUTPUTS = config["prepare_report_outputs"]
 PREPARE_REPORT_SCRIPTS = config["prepare_report_scripts"]
@@ -19,28 +18,21 @@ config = config["params"]
 # Inputs #
 ##########
 
-# Generic input functions
-## get raw_reads
-def raw_reads():
-    inputs = dict()
-    if (config["SeOrPe"] == "PE"):
-        inputs["read"] = config['sample_dir']+'/{sample}_R1'+config["sample_suffix"]
-        inputs["read2"] = config['sample_dir']+'/{sample}_R2'+config["sample_suffix"]
-    else:
-        inputs["read"] = config['sample_dir']+'/{sample}'+config["sample_suffix"]
-    return inputs
+# raw_inputs function call
+raw_reads = raw_reads(config['results_dir'], config['sample_dir'], config['SeOrPe'])
+SAMPLES = raw_reads['samples']
 
 # Tools inputs functions
 
 def cutadapt_inputs():
-    return raw_reads()
+    return raw_reads
 
 def mitoz_filter_inputs():
     inputs = dict()
     if config["trimming"] == 'null':
-        inputs["read"] = expand(raw_reads()["read"],sample=SAMPLES)
+        inputs["read"] = expand(raw_reads["read"],sample=SAMPLES)
         if (config["SeOrPe"] == "PE"):
-            inputs["read2"] = expand(raw_reads()["read2"],sample=SAMPLES)
+            inputs["read2"] = expand(raw_reads["read2"],sample=SAMPLES)
     if config["trimming"] == 'cutadapt':
         if (config["SeOrPe"] == "SE"):
             inputs["read"] = expand(rules.cutadapt_SE.output.read,sample=SAMPLES)

workflows/MitoZ/MitoZ.yaml

@@ -4,6 +4,7 @@
   description: ,
   version: "0.0.1",
   author: "MBB",
+  input: raw_reads,
   steps:
     [
       { title: Trimming, name: trimming, tools: [cutadapt, "null"], default: "null" },
@@ -42,22 +43,9 @@
         choices: [Single end: SE, Paired end: PE],
         label: "Single end reads (SE) or Paired end reads (PE): ",
       },
-      {
-        name: "clade",
-        type: "radio",
-        value: "Arthropoda",
-        choices: [
-          Arthropoda: Arthropoda,
-          Chordata: Chordata, 
-          Echinodermata: Echinodermata,
-          Annelida-segmented-worms: Annelida-segmented-worms,
-          Bryozoa: Bryozoa,
-          Mollusca: Mollusca,
-          Nematoda: Nematoda,
-          Nemertea-ribbon-worms: Nemertea-ribbon-worms,
-          Porifera-sponges: Porifera-sponges
-        ],
-        label: "Taxa group for MitoZ : ",
-      },
     ],
+    params_equals: [
+      { param_A: mitoz_filter_clade, param_B: mitoz_assemble_clade },
+      { param_A: mitoz_filter_clade, param_B: mitoz_annotate_clade },
+    ]
 }
\ No newline at end of file

workflows/Mito_Assembler_Megahit/Mito_Assembler_Megahit.snakefile

@@ -7,7 +7,6 @@ import csv
 # Wildcards #
 #############
 
-SAMPLES = config["samples"]
 STEPS = config["steps"]
 PREPARE_REPORT_OUTPUTS = config["prepare_report_outputs"]
 PREPARE_REPORT_SCRIPTS = config["prepare_report_scripts"]
@@ -19,38 +18,24 @@ config = config["params"]
 # Inputs #
 ##########
 
-# Generic input functions
-## get raw_reads
-def raw_reads():
-    inputs = dict()
-    if (config["SeOrPe"] == "PE"):
-        inputs["read"] = config['sample_dir']+'/{sample}_R1'+config["sample_suffix"]
-        inputs["read2"] = config['sample_dir']+'/{sample}_R2'+config["sample_suffix"]
-    elif (config["SeOrPe"] == "SE"):
-        inputs["read"] = config['sample_dir']+'/{sample}'+config["sample_suffix"]
-    else:
-        sys.exit("SeOrPe should be SE or PE")
-    return inputs
-
-## get reads (trimmed or raw)
-def reads():
-    return raw_reads()
-
+# raw_inputs function call
+raw_reads = raw_reads(config['results_dir'], config['sample_dir'], config['SeOrPe'])
+SAMPLES = raw_reads['samples']
 
 # Tools inputs functions
 
 def fastqc_inputs():
     inputs = dict()
-    inputs["read"] = expand(raw_reads()["read"],sample=SAMPLES)
+    inputs["read"] = expand(raw_reads["read"],sample=SAMPLES)
     if (config["SeOrPe"] == "PE"):
-        inputs["read2"] = expand(raw_reads()["read2"],sample=SAMPLES)
+        inputs["read2"] = expand(raw_reads["read2"],sample=SAMPLES)
     return inputs
 
 def megahit_inputs():
     inputs = dict()
-    inputs["read"] = expand(raw_reads()["read"],sample=SAMPLES)
+    inputs["read"] = expand(raw_reads["read"],sample=SAMPLES)
     if (config["SeOrPe"] == "PE"):
-        inputs["read2"] = expand(raw_reads()["read2"],sample=SAMPLES)
+        inputs["read2"] = expand(raw_reads["read2"],sample=SAMPLES)
     return inputs
 
 def mitoz_findmitoscaf_inputs():
@@ -64,9 +49,9 @@ def mitoz_findmitoscaf_inputs():
 def mitoz_annotate_inputs():
     inputs = dict()
     inputs["fastafile"] = rules.mitoz_findmitoscaf.output.mitogenome
-    inputs["read"] = expand(raw_reads()["read"],sample=SAMPLES)
+    inputs["read"] = expand(raw_reads["read"],sample=SAMPLES)
     if (config["SeOrPe"] == "PE"):
-        inputs["read2"] = expand(raw_reads()["read2"],sample=SAMPLES)
+        inputs["read2"] = expand(raw_reads["read2"],sample=SAMPLES)
     return inputs
 
 def igv_visualize_inputs():

workflows/Mito_Assembler_Megahit/Mito_Assembler_Megahit.yaml

@@ -4,6 +4,7 @@
   description: ,
   version: "0.0.1",
   author: "MBB",
+  input: raw_reads,
   steps:
     [
         { title: Quality check, name: quality_check, tools: [fastqc,"null"], default: fastqc },
@@ -21,47 +22,8 @@
         label: "Results directory: ",
         volumes:  [Results: "/Results"]
       },
-      {
-        name: "help_sample",
-        type: "help",
-        label: "The Data directory must only contain the reads files (fastq). In case of paired end reads, the files names must contain '_R1' or '_R2'",
-      },
-      {
-        name: "sample_dir",
-        type: "input_dir",
-        value: "/Data",
-        label: "Data directory: ",
-        volumes:  [Data: "/Data", Results: "/Results"]
-      },
-      #{
-      #  name: "sample_suffix",
-      #  type: "text",
-      #  value: ".fastq.gz",
-      #  label: "Samples suffix: ",
-      #},
-      {
-        name: "SeOrPe",
-        type: "radio",
-        value: "PE",
-        choices: [Single end: SE, Paired end: PE],
-        label: "Single end reads (SE) or Paired end reads (PE): ",
-      },
-      {
-        name: "clade",
-        type: "radio",
-        value: "Arthropoda",
-        choices: [
-          Arthropoda: Arthropoda,
-          Chordata: Chordata, 
-          Echinodermata: Echinodermata,
-          Annelida-segmented-worms: Annelida-segmented-worms,
-          Bryozoa: Bryozoa,
-          Mollusca: Mollusca,
-          Nematoda: Nematoda,
-          Nemertea-ribbon-worms: Nemertea-ribbon-worms,
-          Porifera-sponges: Porifera-sponges
-        ],
-        label: "Taxa group for MitoZ : ",
-      },
     ],
+    params_equals: [
+      { param_A: find_mitoscaf_clade, param_B: mitoz_annotate_clade },
+    ]
 }
\ No newline at end of file

workflows/RADseq_denovo/RADseq_denovo.snakefile

@@ -7,7 +7,6 @@ import csv
 # Wildcards #
 #############
 
-SAMPLES = config["samples"]
 STEPS = config["steps"]
 PREPARE_REPORT_OUTPUTS = config["prepare_report_outputs"]
 PREPARE_REPORT_SCRIPTS = config["prepare_report_scripts"]
@@ -29,24 +28,15 @@ individus = get_individus()
 # Inputs #
 ##########
 
-# Generic input functions
-## get raw_reads
-def raw_reads():
-    inputs = dict()
-    if (config["SeOrPe"] == "PE"):
-        inputs["read"] = config['sample_dir']+'/{sample}_R1'+config["sample_suffix"]
-        inputs["read2"] = config['sample_dir']+'/{sample}_R2'+config["sample_suffix"]
-    elif (config["SeOrPe"] == "SE"):
-        inputs["read"] = config['sample_dir']+'/{sample}'+config["sample_suffix"]
-    else:
-        sys.exit("SeOrPe should be SE or PE")
-    return inputs
+# raw_inputs function call
+raw_reads = raw_reads(config['results_dir'], config['sample_dir'], config['SeOrPe'])
+SAMPLES = raw_reads['samples']
 
 ## get reads (trimmed or raw)
 def reads():
     inputs = dict()
     if (config["trimming"] == "null"):
-        return raw_reads()
+        return raw_reads
     elif (config["trimming"] == "trimmomatic"):
         if (config["SeOrPe"] == "SE"):
             inputs["read"] = rules.trimmomatic_SE.output.read
@@ -58,14 +48,14 @@ def reads():
 # Tools inputs functions
 
 def fastqc_inputs():
-    return raw_reads()
+    return raw_reads
 
 def process_radtags_inputs():
-    return raw_reads()
+    return raw_reads
 
 def ustacks_inputs():
     if (config["demultiplexing"] == "null"):
-        return raw_reads()
+        return raw_reads
     else:
         inputs = dict()
         if (config["SeOrPe"] == "PE"):

workflows/RADseq_denovo/RADseq_denovo.yaml

@@ -4,6 +4,7 @@
   description: RADseq analysis of data without reference genome,
   version: "0.0.1",
   author: "MBB",