From 609db153e52d2844a02f20d5d8623c3c14c05cac Mon Sep 17 00:00:00 2001
From: BIOPZ-Gypas Foivos <foivos.gypas@unibas.ch>
Date: Tue, 19 Feb 2019 17:47:48 +0100
Subject: [PATCH] Small changes in the prepare annotation pipeline.
---
prepare_annotation/.gitignore | 1 +
prepare_annotation/Snakefile | 7 +++----
prepare_annotation/cluster.json | 2 +-
prepare_annotation/config.yaml | 25 ++++++++++++++++++++++++-
4 files changed, 29 insertions(+), 6 deletions(-)
diff --git a/prepare_annotation/.gitignore b/prepare_annotation/.gitignore
index 6409a94..06cd409 100644
--- a/prepare_annotation/.gitignore
+++ b/prepare_annotation/.gitignore
@@ -3,3 +3,4 @@ Log.out
results
logs
dag.png
+nohup.out
diff --git a/prepare_annotation/Snakefile b/prepare_annotation/Snakefile
index 2916eae..efd220e 100644
--- a/prepare_annotation/Snakefile
+++ b/prepare_annotation/Snakefile
@@ -125,16 +125,15 @@ rule index_genome_STAR:
log:
os.path.join(config["local_log"],"index_genome_STAR.log")
shell:
- "(mkdir -p {output.output}; \
+ "mkdir -p {output.output}; \
chmod -R 777 {output.output}; \
- STAR --runMode genomeGenerate \
+ (STAR --runMode genomeGenerate \
--sjdbOverhang {params.sjdbOverhang} \
--genomeDir {params.outputdir} \
--genomeFastaFiles {input.genome} \
--runThreadN {threads} \
--sjdbGTFfile {input.annotation}) &> {log}"
-
##################################################################################
### Filter protein coding and lncRNA transcripts
##################################################################################
@@ -197,4 +196,4 @@ rule index_salmon:
--transcripts {input.transcripts} \
--index {output.index} \
--kmerLen {params.kmerLen} \
- --threads {threads}) > {log}"
+ --threads {threads}) &> {log}"
diff --git a/prepare_annotation/cluster.json b/prepare_annotation/cluster.json
index 9ac8511..a6bfdd5 100644
--- a/prepare_annotation/cluster.json
+++ b/prepare_annotation/cluster.json
@@ -18,6 +18,6 @@
{
"time": "06:00:00",
"threads":"8",
- "mem":"50G"
+ "mem":"75G"
}
}
diff --git a/prepare_annotation/config.yaml b/prepare_annotation/config.yaml
index 00b9a5d..92249c9 100644
--- a/prepare_annotation/config.yaml
+++ b/prepare_annotation/config.yaml
@@ -3,7 +3,30 @@
### Annotation
##############################################################################
genome: ["ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.1.fa.gz",
- "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa.gz"]
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.3.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.4.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.5.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.6.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.7.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.8.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.9.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.10.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.11.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.12.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.13.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.14.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.15.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.16.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.17.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.18.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.19.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.20.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.21.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.22.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.X.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.Y.fa.gz",
+ "ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.MT.fa.gz"]
annotation: ["ftp://ftp.ensembl.org/pub/release-89/gtf/homo_sapiens/Homo_sapiens.GRCh38.89.chr.gtf.gz"]
other_RNA: "other.fa"
##############################################################################
--
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