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Commit ca611ec7 authored by petkoa97's avatar petkoa97
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final tweaks

parent 649cad53
Branches dev
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/.snakemake /.snakemake
/logs/* /logs/*
/resources/* /benchmarks/*
/results/* /results/*
/tools/ /tools/
output_name_prefix: output_name_prefix:
"Homo_sapiens_4" # "Homo_sapiens_4"
input_HiFi_reads: input_HiFi_reads:
"test_datasets/dataset3_sim_hChr19.fastq" # "dataset3_sim_hChr19.fastq"
input_reference: input_reference:
"test_datasets/Homo_sapiens_ch19.fasta" # "Homo_sapiens_ch19.fasta"
......
# Ignore everything in this directory
*
# Except this file
!.gitignore
\ No newline at end of file
#!/bin/bash #!/bin/bash
#cd "$(dirname "$0")" cd "$(dirname "$0")"
snakemake --cores 10 --use-conda snakemake --cores 10 --use-conda
...@@ -8,7 +8,7 @@ rule convert_bed_gtf: ...@@ -8,7 +8,7 @@ rule convert_bed_gtf:
conda: conda:
"../envs/py27tama.yaml" "../envs/py27tama.yaml"
shell: 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): def get_output_files(wildcards):
...@@ -16,13 +16,13 @@ def get_output_files(wildcards): ...@@ -16,13 +16,13 @@ def get_output_files(wildcards):
if config["RUN_TAMA_COLLAPSE"] and config["TAMA_split_input"]: if config["RUN_TAMA_COLLAPSE"] and config["TAMA_split_input"]:
input_list.append("results/structural_annotation/TAMA_collapse_merged_{output_name}/{output_name}.gtf") 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"]: # 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") # input_list.append("results/structural_annotation/TAMA_collapse_unmerged_{output_name}/{output_name}.gtf")
if config["RUN_ISO_SEQ_COLLAPSE"]: if config["RUN_ISO_SEQ_COLLAPSE"]:
input_list.extend(rules.iso_seq_collapse.output) input_list.extend(rules.iso_seq_collapse.output)
if config["RUN_STRINGTIE"]: if config["RUN_STRINGTIE"]:
input_list.extend(rules.stringtie.output) input_list.extend(rules.stringtie.output)
#print(input_list)
return input_list return input_list
rule compare_gtf: rule compare_gtf:
...@@ -37,4 +37,4 @@ rule compare_gtf: ...@@ -37,4 +37,4 @@ rule compare_gtf:
conda: conda:
"../envs/gffcompare.yaml" "../envs/gffcompare.yaml"
shell: shell:
"gffcompare {input} -o {output}" "gffcompare {input} -o {output} 1>&2>{log}"
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