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Commit 609db153 authored by BIOPZ-Gypas Foivos's avatar BIOPZ-Gypas Foivos
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Small changes in the prepare annotation pipeline.

parent 38b6a1e4
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......@@ -3,3 +3,4 @@ Log.out
results
logs
dag.png
nohup.out
......@@ -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}"
......@@ -18,6 +18,6 @@
{
"time": "06:00:00",
"threads":"8",
"mem":"50G"
"mem":"75G"
}
}
......@@ -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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