From ca611ec78d4f2f7546646b2c59a71faa9eca4ec7 Mon Sep 17 00:00:00 2001
From: petkoa97 <petkoa97@mi.fu-berlin.de>
Date: Fri, 28 Apr 2023 16:59:44 +0200
Subject: [PATCH] final tweaks
---
.gitignore | 2 +-
config/config.yaml | 6 +++---
resources/.gitignore | 4 ++++
run_snakemake.sh | 2 +-
workflow/rules/gffcompare.smk | 10 +++++-----
5 files changed, 14 insertions(+), 10 deletions(-)
create mode 100644 resources/.gitignore
diff --git a/.gitignore b/.gitignore
index 90c5555..b4aab95 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,5 @@
/.snakemake
/logs/*
-/resources/*
+/benchmarks/*
/results/*
/tools/
diff --git a/config/config.yaml b/config/config.yaml
index 90b249f..4cbf648 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -1,11 +1,11 @@
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"
diff --git a/resources/.gitignore b/resources/.gitignore
new file mode 100644
index 0000000..86d0cb2
--- /dev/null
+++ b/resources/.gitignore
@@ -0,0 +1,4 @@
+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore
\ No newline at end of file
diff --git a/run_snakemake.sh b/run_snakemake.sh
index ce727c8..e3530b3 100644
--- a/run_snakemake.sh
+++ b/run_snakemake.sh
@@ -1,5 +1,5 @@
#!/bin/bash
-#cd "$(dirname "$0")"
+cd "$(dirname "$0")"
snakemake --cores 10 --use-conda
diff --git a/workflow/rules/gffcompare.smk b/workflow/rules/gffcompare.smk
index bae396b..2ae008e 100644
--- a/workflow/rules/gffcompare.smk
+++ b/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}"
\ No newline at end of file
+ "gffcompare {input} -o {output} 1>&2>{log}"
\ No newline at end of file
--
GitLab