From 3b21e4045d002aa021bc7655e7aec12ed16d4400 Mon Sep 17 00:00:00 2001
From: burri0000 <dominik.burri@unibas.ch>
Date: Fri, 21 Feb 2020 19:40:29 +0100
Subject: [PATCH] corrected alfa_index
---
Snakefile | 20 ++++++++++----------
scripts/labkey_to_snakemake.py | 1 +
2 files changed, 11 insertions(+), 10 deletions(-)
diff --git a/Snakefile b/Snakefile
index 9de3243..4db8543 100644
--- a/Snakefile
+++ b/Snakefile
@@ -334,22 +334,22 @@ rename_expr = {"fr-firststrand": ("out.plus", "out.minus"),
rule generate_alfa_index:
''' Generate ALFA index files from sorted GTF file '''
input:
- gtf =lambda wildcards: samples_table["gtf"][samples_table["organism"]==wildcards.organism][0]
- output:
- index_stranded = os.path.join(config["alfa_indexes"], "{organism}",
- "{index_size}", "ALFA", "sorted_genes.stranded.ALFA_index"),
- index_unstranded = os.path.join(config["alfa_indexes"], "{organism}",
- "{index_size}", "ALFA", "sorted_genes.unstranded.ALFA_index")
- params:
+ gtf = lambda wildcards: samples_table["gtf"][samples_table["organism"]==wildcards.organism][0],
chr_len = os.path.join(
config["star_indexes"],
"{organism}",
"{index_size}",
"STAR_index",
"chrNameLength.txt"),
+ output:
+ index_stranded = os.path.join(config["alfa_indexes"], "{organism}",
+ "{index_size}", "ALFA", "sorted_genes.stranded.ALFA_index"),
+ index_unstranded = os.path.join(config["alfa_indexes"], "{organism}",
+ "{index_size}", "ALFA", "sorted_genes.unstranded.ALFA_index")
+ params:
genome_index = "sorted_genes",
- out_dir = directory(os.path.join(config["alfa_indexes"], "{organism}", "{index_size}", "ALFA"))
- threads: 4
+ out_dir = lambda wildcards, output: os.path.basename(output.index_stranded)
+ threads: 4
singularity:
"docker://zavolab/alfa:1.1.1"
log:
@@ -357,7 +357,7 @@ rule generate_alfa_index:
shell:
"alfa -a {input.gtf} \
-g {params.genome_index} \
- --chr_len {params.chr_len} \
+ --chr_len {input.chr_len} \
-p {threads} \
-o {params.out_dir} &> {log}"
diff --git a/scripts/labkey_to_snakemake.py b/scripts/labkey_to_snakemake.py
index b6b9569..86ecf78 100755
--- a/scripts/labkey_to_snakemake.py
+++ b/scripts/labkey_to_snakemake.py
@@ -311,6 +311,7 @@ def main():
kallisto_indexes: "results/kallisto_indexes/"
salmon_indexes: "results/salmon_indexes/"
star_indexes: "results/star_indexes/"
+ alfa_indexes: "results/alfa_indexes/"
...''')
sys.stdout.write('Create snakemake table finished successfully...\n')
--
GitLab