final tweaks

.gitignore

 /.snakemake
 /logs/*
-/resources/*
+/benchmarks/*
 /results/*
 /tools/

config/config.yaml

 output_name_prefix:
-  "Homo_sapiens_4"
+#  "Homo_sapiens_4"
 
 input_HiFi_reads:
-  "test_datasets/dataset3_sim_hChr19.fastq"
+#  "dataset3_sim_hChr19.fastq"
 
 input_reference:
-  "test_datasets/Homo_sapiens_ch19.fasta"
+#  "Homo_sapiens_ch19.fasta"
 
   
 

resources/.gitignore

+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore
\ No newline at end of file

run_snakemake.sh

 #!/bin/bash
-#cd "$(dirname "$0")"
+cd "$(dirname "$0")"
 
 snakemake --cores 10 --use-conda
 

workflow/rules/gffcompare.smk

@@ -8,7 +8,7 @@ rule convert_bed_gtf:
     conda:
         "../envs/py27tama.yaml"
     shell:
-        "python tools/tama/tama_go/format_converter/tama_convert_bed_gtf_ensembl_no_cds.py {input} {output} 2>{log}"
+        "python tools/tama/tama_go/format_converter/tama_convert_bed_gtf_ensembl_no_cds.py {input} {output} 1>&2>{log}"
 
 
 def get_output_files(wildcards):
@@ -16,13 +16,13 @@ def get_output_files(wildcards):
     
     if config["RUN_TAMA_COLLAPSE"] and config["TAMA_split_input"]:
         input_list.append("results/structural_annotation/TAMA_collapse_merged_{output_name}/{output_name}.gtf") 
-    if config["RUN_TAMA_COLLAPSE"] and not config["TAMA_split_input"]:
-        input_list.append("results/structural_annotation/TAMA_collapse_unmerged_{output_name}/{output_name}.gtf")
+    # if config["RUN_TAMA_COLLAPSE"] and not config["TAMA_split_input"]:    # bugs with wildcards
+    #     input_list.append("results/structural_annotation/TAMA_collapse_unmerged_{output_name}/{output_name}.gtf")
     if config["RUN_ISO_SEQ_COLLAPSE"]:
         input_list.extend(rules.iso_seq_collapse.output)
     if config["RUN_STRINGTIE"]:
         input_list.extend(rules.stringtie.output) 
-    #print(input_list)
+
     return input_list
 
 rule compare_gtf:
@@ -37,4 +37,4 @@ rule compare_gtf:
     conda:
         "../envs/gffcompare.yaml"
     shell: 
-        "gffcompare {input} -o {output}"
+        "gffcompare {input} -o {output} 1>&2>{log}"
\ No newline at end of file