updated input preparation rules

Snakefile

@@ -46,25 +46,16 @@ INPUT_SR = config["data"]["sr"]
 INPUT_METAT = config["data"]["metat"]
 
 # Data from input
-DATA_FAST5 = [os.path.join(RESULTS_DIR, "input", os.path.basename(f)) for f in INPUT_FAST5]
+DATA_FAST5 = [os.path.join(RESULTS_DIR, "input_ont", os.path.basename(f)) for f in INPUT_FAST5]
 assert len(DATA_FAST5) == len(set(DATA_FAST5)), "Created link names for FAST5 files are NOT unique: {}".format(DATA_FAST5)
-# DATA_SR    = [os.path.join(RESULTS_DIR, "input", os.path.basename(f)) for f in INPUT_SR]
-# assert len(DATA_SR) == len(set(DATA_SR)), "Created link names for SR files are NOT unique: {}".format(DATA_FAST5)
-
-# # Input
-# BARCODES = config["barcodes"]
-# RUNS = [
-#     config["runs"]["first"],
-#     config["runs"]["second"],
-# #    config["runs"]["third"]
-# ]
-# SAMPLES = config["samples"]
-# BINNING_SAMPLES = config["binning_samples"]
-
-# # References
-# IGC_URI = config["igc"]["uri"]
-# HG38_URI = config["hg38"]["uri"]
-# REFERENCES = ["igc", "hg38"]
+DATA_SR = {
+    "r1": os.path.join(RESULTS_DIR, "input_sr", os.path.basename(INPUT_SR["r1"])),
+    "r2": os.path.join(RESULTS_DIR, "input_sr", os.path.basename(INPUT_SR["r2"]))
+}
+DATA_METAT = {
+    "r1": os.path.join(RESULTS_DIR, "input_metat", os.path.basename(INPUT_METAT["r1"])),
+    "r2": os.path.join(RESULTS_DIR, "input_metat", os.path.basename(INPUT_METAT["r2"]))
+}
 
 # # Tools
 # ASSEMBLERS = config["assemblers"]

workflow/rules/prepare_input.smk

@@ -4,12 +4,13 @@ localrules: link_input_files
 
 rule link_input_files:
     input:
-        INPUT_FAST5 #+ INPUT_SR + INPUT_METAT
+        INPUT_FAST5 + list(INPUT_SR.values()) + list(INPUT_METAT.values())
     output:
-        DATA_FAST5 #+ DATA_SR + DATA_METAT
+        DATA_FAST5 + list(DATA_SR.values()) + list(DATA_METAT.values())
     message:
         "Link input files"
     run:
         assert len(input) == len(output), "Input and output lists have different length"
         for ifname, ofname in zip(input, output):
-            os.symlink(ifname, ofname, target_is_directory=False)
\ No newline at end of file
+            # print("{} ==> {}".format(ifname, ofname))
+            os.symlink(os.path.abspath(ifname), ofname, target_is_directory=False)

workflow/steps/prepare_input.smk

@@ -5,7 +5,7 @@ include:
 
 rule PREPARE_INPUT:
     input:
-        DATA_FAST5 #+ DATA_SR + DATA_METAT
+        DATA_FAST5 + list(DATA_SR.values()) + list(DATA_METAT.values())
     output:
         "status/prepare_input.done"
     shell: