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Commit cb46aa34 authored by BIOPZ-Gypas Foivos's avatar BIOPZ-Gypas Foivos
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Remove prepare_annotation directory. Rename process_data to snakemake.

parent c4c2d86e
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configfile: "config.yaml"
localrules: download_genome, assemble_genome, download_annotation, assemble_annotation, finish
#################################################################################
### Final rule
#################################################################################
rule finish:
input:
STAR_index = os.path.join(config["output_dir"], "STAR_index"),
other_RNA_idx = os.path.join(config["output_dir"], "other_RNAs_sequence.idx"),
salmon_index = os.path.join(config["output_dir"], "filtered_transcripts_salmon.idx")
#################################################################################
### Download genome
#################################################################################
rule download_genome:
params:
sequences = expand(config["genome"]),
output:
genome_dir = os.path.join(config["output_dir"], "genome")
singularity:
"docker://zavolab/ubuntu:18.04"
log:
os.path.join(config["local_log"], "download_genome.log")
shell:
"(wget --directory-prefix {output.genome_dir} {params.sequences}) &> {log}"
#################################################################################
### Assemble genome
#################################################################################
rule assemble_genome:
input:
genome_dir = os.path.join(config["output_dir"], "genome")
output:
genome = os.path.join(config["output_dir"], "genome.fa")
params:
genome = os.path.join(config["output_dir"], "genome.fa.gz")
singularity:
"docker://zavolab/ubuntu:18.04"
log:
os.path.join(config["local_log"], "assemble_genome.log")
shell:
"(cat {input.genome_dir}/* > {params.genome}; \
zcat {params.genome} | sed \'s/\s.*//\' > {output.genome}; \
rm {params.genome}; \
) &>{log}"
#################################################################################
### Download annotation
#################################################################################
rule download_annotation:
params:
annotation = expand(config["annotation"]),
output:
annotation_dir = os.path.join(config["output_dir"], "annotation")
singularity:
"docker://zavolab/ubuntu:18.04"
log:
os.path.join(config["local_log"], "download_annotation.log")
shell:
"(wget --directory-prefix {output.annotation_dir} {params.annotation}) &> {log}"
#################################################################################
### Assemble annotation
#################################################################################
rule assemble_annotation:
input:
annotation_dir = os.path.join(config["output_dir"], "annotation")
output:
annotation = os.path.join(config["output_dir"], "annotation.gtf")
params:
annotation = os.path.join(config["output_dir"], "annotation.gtf.gz")
singularity:
"docker://zavolab/ubuntu:18.04"
log:
os.path.join(config["local_log"], "assemble_annotation.log")
shell:
"(cat {input.annotation_dir}/* > {params.annotation}; \
zcat {params.annotation} > {output.annotation}; \
rm {params.annotation}; \
) &>{log}"
#################################################################################
### ToDo: Download other RNA
#################################################################################
#################################################################################
### Generate segemehl index for other RNAs
#################################################################################
rule generate_segemehl_index_other_RNAs:
input:
sequence = config["other_RNA"]
output:
other_RNA_idx = os.path.join(config["output_dir"], "other_RNAs_sequence.idx")
log:
os.path.join(config["local_log"], "generate_segemehl_index_other_RNAs.log")
singularity:
"docker://zavolab/segemehl:0.2.0"
shell:
"(segemehl.x -x {output.other_RNA_idx} -d {input.sequence}) &> {log}"
#################################################################################
### Index genome STAR
#################################################################################
##################################################################################
### Filter protein coding and lncRNA transcripts
##################################################################################
rule filter_transcripts:
input:
script = "scripts/fg_extract_transcripts.py",
annotation = os.path.join(config["output_dir"], "annotation.gtf")
output:
annotation = os.path.join(config["output_dir"], "filtered_transcripts.gtf")
params:
transcript_biotype = "\"protein_coding,lincRNA,antisense_RNA,retained_intron,sense_intronic\""
singularity:
"docker://zavolab/python_htseq:3.6.5_0.10.0"
log:
os.path.join(config["local_log"], "filter_transcripts.log")
shell:
"(python {input.script} \
--gtf {input.annotation} \
--out {output.annotation} \
--transcript_biotype {params.transcript_biotype}) &> {log}"
##################################################################################
### Extract transcript sequences
##################################################################################
rule extract_sequences:
input:
annotation = os.path.join(config["output_dir"], "filtered_transcripts.gtf"),
genome = os.path.join(config["output_dir"], "genome.fa")
output:
transcripts = os.path.join(config["output_dir"], "filtered_transcripts.fa")
singularity:
"docker://zavolab/cufflinks:2.2.1"
log:
os.path.join(config["local_log"],"extract_sequences.log")
shell:
"(gffread {input.annotation} \
-g {input.genome} \
-w {output.transcripts}) &> {log}"
##################################################################################
### Index salmon
##################################################################################
rule index_salmon:
input:
transcripts = os.path.join(config["output_dir"], "filtered_transcripts.fa")
output:
index = os.path.join(config["output_dir"], "filtered_transcripts_salmon.idx")
params:
kmerLen = config["kmerLen"],
singularity:
"docker://zavolab/salmon:0.11.0"
log:
os.path.join(config["local_log"],"index_salmon.log")
threads: 8
shell:
"(salmon index \
--transcripts {input.transcripts} \
--index {output.index} \
--kmerLen {params.kmerLen} \
--threads {threads}) &> {log}"
{
"__default__" :
{
"queue": "6hours",
"time": "05:00:00",
"threads": "1",
"mem": "4G",
"name": "{rule}.{wildcards}",
"out": "$PWD/logs/cluster_log/{rule}.{wildcards}-%j-%N.out"
},
"generate_segemehl_index_other_RNAs":
{
"time": "06:00:00",
"threads":"8",
"mem":"50G"
},
"index_genome_STAR":
{
"time": "06:00:00",
"threads":"8",
"mem":"75G"
}
}
---
##############################################################################
### 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.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"
##############################################################################
### Output and log directories
##############################################################################
output_dir: "results"
local_log: "logs/local_log"
cluster_log: "logs/cluster_log"
##############################################################################
### Options
##############################################################################
sjdbOverhang: 100
kmerLen: 31
...
>RNA45SN1
GCTGACACGCTGTCCTCTGGCGACCTGTCGCTGGAGAGGTTGGGCCTCCGGATGCGCGCGGGGCTCTGGC
CTACCGGTGACCCGGCTAGCCGGCCGCGCTCCTGCTTGAGCCGCCTGCCGGGGCCCGCGGGCCTGCTGTT
CTCTCGCGCGTCCGAGCGTCCCGACTCCCGGTGCCGGCCCGGGTCCGGGTCTCTGACCCACCCGGGGGCG
GCGGGGAAGGCGGCGAGGGCCACCGTGCCCCCGTGCGCTCTCCGCTGCGGGCGCCCGGGGCGGCCGCGAC
AACCCCACCCCGCTGGCTCCGTGCCGTGCGTGTCAGGCGTTCTCGTCTCCGCGGGGTTGTCCGCCGCCCC
TTCCCCGGAGTGGGGGGTTGGCCGGAGCCGATCGGCTCGCTGGCCGGCCGGCCGGCCTCCGCTCCCGGGG
GGCTCTTCGTGATCGATGTGGTGACGTCGTGCTCTCCCGGGCCGGGTCCGAGCCGCGACGGGCGAGGGGC
GGACGTTCGTGGCGAACGGGACCGTCCTTCTCGCTCCGCCCCGCGGGGGTCCCCTCGTCTCTCCTCTCCC
CGCCCGCCGGCGGTGCGTGTGGGAAGGCGTGGGGTGCGGACCCCGGCCCGACCTCGCCGTCCCGCCCGCC
GCCTTCTGCGTCGCGGGGCGGGCCGGCGGGGTCCTCTGACGCGGCAGACAGCCCTCGCTGTCGCCTCCAG
TGGTTGTCGACTTGCGGGCGGCCCCCCTCCGCGGCGGTGGGGGTGCCGTCCCGCCGGCCCGTCGTGCTGC
CCTCTCGGGGGGTTTGCGCGAGCGTCGGCTCCGCCTGGGCCCTTGCGGTGCTCCTGGAGCGCTCCGGGTT
GTCCCTCAGGTGCCCGAGGCCGAACGGTGGTGTGTCGTTCCCGCCCCCGGCGCCCCCTCCTCCGGTCGCC
GCCGCGGTGTCCGCGCGTGGGTCCTGAGGGAGCTCGTCGGTGTGGGGTTCGAGGCGGTTTGAGTGAGACG
AGACGAGACGCGCCCCTCCCACGCGGGGAAGGGCGCCCGCCTGCTCTCGGTGAGCGCACGTCCCGTGCTC
CCCTCTGGCGGGTGCGCGCGGGCCGTGTGAGCGATCGCGGTGGGTTCGGGCCGGTGTGACGCGTGCGCCG
GCCGGCCGCCGAGGGGCTGCCGTTCTGCCTCCGACCGGTCGTGTGTGGGTTGACTTCGGAGGCGCTCTGC
CTCGGAAGGAAGGAGGTGGGTGGACGGGGGGGCCTGGTGGGGTTGCGCGCACGCGCGCACCGGCCGGGCC
CCCGCCCTGAACGCGAACGCTCGAGGTGGCCGCGCGCAGGTGTTTCCTCGTACCGCAGGGCCCCCTCCCT
TCCCCAGGCGTCCCTCGGCGCCTCTGCGGGCCCGAGGAGGAGCGGCTGGCGGGTGGGGGGAGTGTGACCC
ACCCTCGGTGAGAAAAGCCTTCTCTAGCGATCTGAGAGGCGTGCCTTGGGGGTACCGGATCCCCCGGGCC
GCCGCCTCTGTCTCTGCCTCCGTTATGGTAGCGCTGCCGTAGCGACCCGCTCGCAGAGGACCCTCCTCCG
CTTCCCCCTCGACGGGGTTGGGGGGGAGAAGCGAGGGTTCCGCCGGCCACCGCGGTGGTGGCCGAGTGCG
GCTCGTCGCCTACTGTGGCCCGCGCCTCCCCCTTCCGAGTCGGGGGAGGATCCCGCCGGGCCGGGCCCGG
CGTTCCCAGCGGGTTGGGACGCGGCGGCCGGCGGGCGGTGGGTGTGCGCGCCCGGCGCTCTGTCCGGCGC
GTGACCCCCTCCGCCGCGAGTCGGCTCTCCGCCCGCTCCCGTGCCGAGTCGTGACCGGTGCCGACGACCG
CGTTTGCGTGGCACGGGGTCGGGCCCGCCTGGCCCTGGGAAAGCGTCCCACGGTGGGGGCGCGCCGGTCT
CCCGGAGCGGGACCGGGTCGGAGGATGGACGAGAATCACGAGCGACGGTGGTGCGGGCGTGTCGGGTTCG
TGGCTGCGGTCGCTCCGGGGCCCCCGGTGGCGGGGCCCCGGGGCTCGCGAGGCGGTTCTCGGTGGGGGCC
GAGGGCCGTCCGGCGTCCCAGGCGGGGCGCCGCGGGACCGCCCTCGTGTCTGTGGCGGTGGGATCCCGCG
GCCGTGTTTTCCTGGTGGCCCGGCCGTGCCTGAGGTTTCTCCCCGAGCCGCCGCCTCTGCGGGCTCCCGG
GTGCCCTTGCCCTCGCGGTCCCCGGCCCTCGCCCGTCTGTGCCCTCTTCCCCGCCCGCCGCCCGCCGATC
CTCTTCTTCCCCCCGAGCGGCTCACCGGCTTCACGTCCGTTGGTGGCCCCGCCTGGGACCGAACCCGGCA
CCGCCTCGTGGGGCGCCGCCGCCGGCCACTGATCGGCCCGGCGTCCGCGTCCCCCGGCGCGCGCCTTGGG
GACCGGGTCGGTGGCGCCCCGCGTGGGGCCCGGTGGGCTTCCCGGAGGGTTCCGGGGGTCGGCCTGCGGC
GCGTGCGGGGGAGGAGACGGTTCCGGGGGACCGGCCGCGACTGCGGCGGCGGTGGTGGGGGCAGCCGCGG
GGATCGCCGAGGGCCGGTCGGCCGCCCCGGGTGCCGCGCGGTGCCGCCGGCGGCGGTGAGGCCCCGCGCG
TGTGTCCCGGCCGCGGTCGGCCGCGCTCGAGGGGTCCCCGTGGCGTCCCCTTCCCCGCCGGCCGCCTTTC
TCGCGCCTTCCCCGTCGCCCCGGCCTCGCCCGTGGTCTCTCGTCTTCTCCCGGCCCGCTCTTCCGAACCG
GGTCGGCGCGTCCCCCGGGTGCGCCTCGCTTCCCGGGCCTGCCGCGGCCCTTCCCCGAGGCGTCCGTCCC
GGGCGTCGGCGTCGGGGAGAGCCCGTCCTCCCCGCGTGGCGTCGCCCCGTTCGGCGCGCGCGTGCGCCCG
AGCGCGGCCCGGTGGTCCCTGCCGGACAGGCGTTCGTGCGACGTGTGGCGTGGGTCGACCTCCGCCTTGC
CGGTCGCTCGCCCTTTCCCCGGGTCGGGGGGTGGGGCCCGGGCCGGGGCCTCGGCCCCGGTCGCGGTCCC
CCGTCCCGGGCGGGGGCGGGCGCGCCGGCCGGCCTCGGTCGGCCCTCCCTTGGCCGTCGTGTGGCGTGTG
CCACCCCTGCGCCCGCGCCCGCCGGCGGGGCTCGGAGCCGGGCTTCGGCCGGGCCCCGGGCCCTCGACCG
GACCGGTGCGCGGGCGCTGCGGCCGCACGGCGCGACTGTCCCCGGGCCGGGCACCGCGGTCCGCCTCTCG
CTCGCCGCCCGGACGTCGGGGCCGCCCCGCGGGGCGGGCGGAGCGCCGTCCCCGCCTCGCCGCCGCCCGC
GGGCGCCGGCCGCGCGCGCGCGCGCGTGGCCGCCGGTCCCTCCCGGCCGCCGGGCGCGGGTCGGGCCGTC
CGCCTCCTCGCGGGCGGGCGCGACGAAGAAGCGTCGCGGGTCTGTGGCGCGGGGCCCCGGTGGTCGTGTC
GCGTGGGGGGCGGGTGGTTGGGGCGTCCGGTTCGCCGCGCCCCGCCCCGGCCCCACCGGTCCCGGCCGCC
GCCCCCGCGCCCGCTCGCTCCCTCCCGTCCGCCCGTCCGCGGCCCGTCCGTCCGTCCGTCGTCCTCCTCG
CTTGCGGGGCGCCGGGCCCGTCCTCGCGAGGCCCCCCGGCCGGCCGTCCGGCCGCGTCGGGGCCTCGCCG
CGCTCTACCTTACCTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATG
TCTGAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCG
CTCGCTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCCGACGGGCGCTGACCCCC
TTCGCGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTCAGCCCCTCTCCGGCCCCGGCCGG
GGGGCGGGCGCCGGCGGCTTTGGTGACTCTAGATAACCTCGGGCCGATCGCACGCCCCCCGTGGCGGCGA
CGACCCATTCGAACGTCTGCCCTATCAACTTTCGATGGTAGTCGCCGTGCCTACCATGGTGACCACGGGT
GACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCA
GGCGCGCAAATTACCCACTCCCGACCCGGGGAGGTAGTGACGAAAAATAACAATACAGGACTCTTTCGAG
GCCCTGTAATTGGAATGAGTCCACTTTAAATCCTTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCA
GCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGAT
CTTGGGAGCGGGCGGGCGGTCCGCCGCGAGGCGAGCCACCGCCCGTCCCCGCCCCTTGCCTCTCGGCGCC
CCCTCGATGCTCTTAGCTGAGTGTCCCGCGGGGCCCGAAGCGTTTACTTTGAAAAAATTAGAGTGTTCAA
AGCAGGCCCGAGCCGCCTGGATACCGCAGCTAGGAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGT
TTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAAATT
CTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAA
GTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGTTCCGACCATAAACGATGCCGACCGGCGATGCGGC
GGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGGGGGGAGTATGG
TTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGA
CTCAACACGGGAAACCTCACCCGGCCCGGACACGGACAGGATTGACAGATTGATAGCTCTTTCTCGATTC
CGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGATAACGAACGA
GACTCTGGCATGCTAACTAGTTACGCGACCCCCGAGCGGTCGGCGTCCCCCAACTTCTTAGAGGGACAAG
TGGCGTTCAGCCACCCGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCG
CGCTACACTGACTGGCTCAGCGTGTGCCTACCCTACGCCGGCAGGCGCGGGTAACCCGTTGAACCCCATT
CGTGATGGGGATCGGGGATTGCAATTATTCCCCATGAACGAGGAATTCCCAGTAAGTGCGGGTCATAAGC
TTGCGTTGATTAAGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGGATGGTTTAGTGAG
GCCCTCGGATCGGCCCCGCCGGGGTCGGCCCACGGCCCTGGCGGAGCGCTGAGAAGACGGTCGAACTTGA
CTATCTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTAACGGAGC
CCGGAGGGCGAGGCCCGCGGCGGCGCCGCCGCCGCCGCGCGCTTCCCTCCGCACACCCACCCCCCCACCG
CGACGCGGCGCGTGCGCGGGCGGGGCCCGCGTGCCCGTTCGTTCGCTCGCTCGTTCGTTCGCCGCCCGGC
CCCGCCGGCCGCGAGAGCCGGAGAACTCGGGAGGGAGACGGGGGAGAGAGAGAGAGAGAGAGAAAGAGAA
AGAAGGGCGTGTCGTTGGTGTGCGCGTGTCGTGGGGCCGGCGGGCGGCGGGGAGCGGTCCCCGGCCGCGG
CCCCGACGACGTGGGTGTCGGCGGGCGCGGGGGCGGTTCTCGGCGGCGTCGCGGCGGGTCTGGGGGGGTC
TCGGTGCCCTCCTCCCCGCCGGGGCCCGTCGTCCGGCCCCGCCGCGCCGGCTCCCCGTCTTCGGGGCCGG
CCGGATTCCCGTCGCCTCCGCCGCGCCGCTCCGCGCCGCCGGGCACGGCCCCGCTCGCTCTCCCCGGCCT
TCCCGCTAGGGCGTCTCGAGGGTCGGGGGCCGGACGCCGGTCCCCTCCCCCGCCTCCTCGTCCGCCCCCC
CGCCGTCCAGGTACCTAGCGCGTTCCGGCGCGGAGGTTTAAAGACCCCTTGGGGGGATCGCCCGTCCGCC
CGTGGGTCGGGGGCGGTGGTGGGCCCGCGGGGGAGTCCCGTCGGGAGGGGCCCGGCCCCTCCCGCGCCTC
CACCGCGGACTCCGCTCCCCGGCCGGGGCCGCGCCGCCGCCGCCGCCGCGGCGGCCGTCGGGTGGGGGCT
TTACCCGGCGGCCGTCGCGCGCCTGCCGCGCGTGTGGCGTGCGCCCCGCGCCGTGGGGGCGGGAACCCCC
GGGCGCCTGTGGGGTGGTGTCCGCGCTCGCCCCCGCGTGGGCGGCGCGCGCCTCCCCGTGGTGTGAAACC
TTCCGACCCCTCTCCGGAGTCCGGTCCCGTTTGCTGTCTCGTCTGGCCGGCCTGAGGCAACCCCCTCTCC
TCTTGGGCGGGGGGGGGGGGGACGTGCCGCGCCAGGAAGGGCCTCCTCCCGGTGCGTCGTCGGGAGCGCC
CTCGCCAAATCGACCTCGTACGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC
TAGCTGCGAGAATTAATGTGAATTGCAGGACACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCG
GGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGCCGATCAATCGCCCCCGGGGGTGCCTCCGGGC
TCCTCGGGGTGCGCGGCTGGGGGTTCCCTCGCAGGGCCCGCCGGGGGCCCTCCGTCCCCCTAAGCGCAGA
CCCGGCGGCGTCCGCCCTCCTCTTGCCGCCGCGCCCGCCCCTTCCCCCTCCCCCCGCGGGCCCTGCGTGG
TCACGCGTCGGGTGGCGGGGGGGAGAGGGGGGCGCGCCCGGCTGAGAGAGACGGGGAGGGCGGCGCCGCC
GCCGCCCGCGAAGACGGAGAGGGAAAGAGAGAGCCGGCTCGGGCCGAGTTCCCGTGGCCGCCGCCTGCGG
TCCGGGTTCCTCCCTCGGGGGGCTCCCTCGCGCCGCGCGCGGCTCGGGGTTCGGGGTTCGTCGGCCCCGG
CCGGGTGGAAGGTCCCGTGCCCGTCGTCGTCGTCGTCGTCGCGCGTCGTCGGCGGTGGGGGCGTGTTGCG
TGCGGTGTGGTGGTGGGGGAGGAGGAAGGCGGGTCCGGAAGGGGAAGGGTGCCGGCGGGGAGAGAGGGTC
GGGGGAGCGCGTCCCGGTCGCCGCGGTTCGCCGCCCGCCCCCGGTGGCGGCCCGGCGTCCGGCCGACCGC
CGCTCCCGCGCCCCTCCTCCTCCCCGCCGCCCCTCCTCCGAGGCCCCGCCCGTCCTCCTCGCCCTCCCCG
CGCGTACGCGCGCCCGCCCGCCCGGCTCGCCTCGCGGCGCGTCGGCCGGGGCCGGGAGCCCGCCCCGCGG
CCCGCCCGGCCGCGCCCGTGGCCGCGGCGCCGGGGTTCGCGTGTCCCCGGCGGCGACCCGCGGGACGCCG
CGGTGTCGTCCGCCGTCGCGCGCCCGCCTCCGGCTCGCGGCCGCGCCGCGCCGCGCCGGGGCCCCGTCCC
GAGCTTCCGCGTCGGGGCGGGGCGGCTCCGCCGCCGCGTCCTCGGACCCGTCCCCCCGACCTCCGCGGGG
GAGACGGGTCGGGGCGTGCGGCGCCCGTCCCGCCCCCGGCCCGTGCCCCTCCCTCCGGTCGTCCCGCTCC
GGCGGGGCGGCGCGGGGGTGCCGCCGGCCGCGCGCTCTCTCTCCCGTCGCCTCTCCCCCTCGCCGGGCCC
GTCTCCCGACGGAGCGTCGGGCGGGCGGTCGGGCCGGCGCGATTCCGTCCGTCCGTCCGCCGAGCGGCCC
GTCCCCCTCCGAGACGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCAGCGGA
GGAGAAGAAACTAACCAGGATTCCCTCAGTAACGGCGAGTGAACAGGGAAGAGCCCAGCGCCGAATCCCC
GCCCCGCGGCGGGGCGCGGGACATGTGGCGTACGGAAGACCCGCTCCCCGGCGCCGCTCGTGGGGGGCCC
AAGTCCTTCTGATCGAGGCCCAGCCCGTGGACGGTGTGAGGCCGGTAGCGGCCCCCGGCGCGCCGGGCCC
GGGTCTTCCCGGAGTCGGGTTGCTTGGGAATGCAGCCCAAAGCGGGTGGTAAACTCCATCTAAGGCTAAA
TACCGGCACGAGACCGATAGTCAACAAGTACCGTAAGGGAAAGTTGAAAAGAACTTTGAAGAGAGAGTTC
AAGAGGGCGTGAAACCGTTAAGAGGTAAACGGGTGGGGTCCGCGCAGTCCGCCCGGAGGATTCAACCCGG
CGGCGGGTCCGGCCGTGTCGGCGGCCCGGCGGATCTTTCCCGCCCCCCGTTCCTCCCGACCCCTCCACCC
GCCCTCCCTTCCCCCGCCGCCCCTCCTCCTCCTCCCCGGAGGGGGCGGGCTCCGGCGGGTGCGGGGGTGG
GCGGGCGGGGCCGGGGGTGGGGTCGGCGGGGGACCGTCCCCCGACCGGCGACCGGCCGCCGCCGGGCGCA
TTTCCACCGCGGCGGTGCGCCGCGACCGGCTCCGGGACGGCTGGGAAGGCCCGGCGGGGAAGGTGGCTCG
GGGGGCCCCGTCCGTCCGTCCGTCCGTCCTCCTCCTCCCCCGTCTCCGCCCCCCGGCCCCGCGTCCTCCC
TCGGGAGGGCGCGCGGGTCGGGGCGGCGGCGGCGGCGGCGGTGGCGGCGGCGGCGGCGGCGGCGGGACCG
AAACCCCCCCCGAGTGTTACAGCCCCCCCGGCAGCAGCACTCGCCGAATCCCGGGGCCGAGGGAGCGAGA
CCCGTCGCCGCGCTCTCCCCCCTCCCGGCGCCCACCCCCGCGGGGAATCCCCCGCGAGGGGGGTCTCCCC
CGCGGGGGCGCGCCGGCGTCTCCTCGTGGGGGGGCCGGGCCACCCCTCCCACGGCGCGACCGCTCTCCCA
CCCCTCCTCCCCGCGCCCCCGCCCCGGCGACGGGGGGGGTGCCGCGCGCGGGTCGGGGGGCGGGGCGGAC
TGTCCCCAGTGCGCCCCGGGCGGGTCGCGCCGTCGGGCCCGGGGGAGGTTCTCTCGGGGCCACGCGCGCG
TCCCCCGAAGAGGGGGACGGCGGAGCGAGCGCACGGGGTCGGCGGCGACGTCGGCTACCCACCCGACCCG
TCTTGAAACACGGACCAAGGAGTCTAACACGTGCGCGAGTCGGGGGCTCGCACGAAAGCCGCCGTGGCGC
AATGAAGGTGAAGGCCGGCGCGCTCGCCGGCCGAGGTGGGATCCCGAGGCCTCTCCAGTCCGCCGAGGGC
GCACCACCGGCCCGTCTCGCCCGCCGCGCCGGGGAGGTGGAGCACGAGCGCACGTGTTAGGACCCGAAAG
ATGGTGAACTATGCCTGGGCAGGGCGAAGCCAGAGGAAACTCTGGTGGAGGTCCGTAGCGGTCCTGACGT
GCAAATCGGTCGTCCGACCTGGGTATAGGGGCGAAAGACTAATCGAACCATCTAGTAGCTGGTTCCCTCC
GAAGTTTCCCTCAGGATAGCTGGCGCTCTCGCAGACCCGACGCACCCCCGCCACGCAGTTTTATCCGGTA
AAGCGAATGATTAGAGGTCTTGGGGCCGAAACGATCTCAACCTATTCTCAAACTTTAAATGGGTAAGAAG
CCCGGCTCGCTGGCGTGGAGCCGGGCGTGGAATGCGAGTGCCTAGTGGGCCACTTTTGGTAAGCAGAACT
GGCGCTGCGGGATGAACCGAACGCCGGGTTAAGGCGCCCGATGCCGACGCTCATCAGACCCCAGAAAAGG
TGTTGGTTGATATAGACAGCAGGACGGTGGCCATGGAAGTCGGAATCCGCTAAGGAGTGTGTAACAACTC
ACCTGCCGAATCAACTAGCCCTGAAAATGGATGGCGCTGGAGCGTCGGGCCCATACCCGGCCGTCGCCGG
CAGTCGAGAGTGGACGGGAGCGGCGGGGGCGGCGCGCGCGCGCGCGCGTGTGGTGTGCGTCGGAGGGCGG
CGGCGGCGGCGGCGGCGGGGGTGTGGGGTCCTTCCCCCGCCCCCCCCCCCACGCCTCCTCCCCTCCTCCC
GCCCACGCCCCGCTCCCCGCCCCCGGAGCCCCGCGGACGCTACGCCGCGACGAGTAGGAGGGCCGCTGCG
GTGAGCCTTGAAGCCTAGGGCGCGGGCCCGGGTGGAGCCGCCGCAGGTGCAGATCTTGGTGGTAGTAGCA
AATATTCAAACGAGAACTTTGAAGGCCGAAGTGGAGAAGGGTTCCATGTGAACAGCAGTTGAACATGGGT
CAGTCGGTCCTGAGAGATGGGCGAGCGCCGTTCCGAAGGGACGGGCGATGGCCTCCGTTGCCCTCGGCCG
ATCGAAAGGGAGTCGGGTTCAGATCCCCGAATCCGGAGTGGCGGAGATGGGCGCCGCGAGGCGTCCAGTG
CGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGAGCCCCGGGGAGAGTTCTCTTTTCTTTGTGAAGGGC
AGGGCGCCCTGGAATGGGTTCGCCCCGAGAGAGGGGCCCGTGCCTTGGAAAGCGTCGCGGTTCCGGCGGC
GTCCGGTGAGCTCTCGCTGGCCCTTGAAAATCCGGGGGAGAGGGTGTAAATCTCGCGCCGGGCCGTACCC
ATATCCGCAGCAGGTCTCCAAGGTGAACAGCCTCTGGCATGTTGGAACAATGTAGGTAAGGGAAGTCGGC
AAGCCGGATCCGTAACTTCGGGATAAGGATTGGCTCTAAGGGCTGGGTCGGTCGGGCTGGGGCGCGAAGC
GGGGCTGGGCGCGCGCCGCGGCTGGACGAGGCGCCGCCGCCCCCCCCACGCCCGGGGCACCCCCCTCGCG
GCCCTCCCCCGCCCCACCCCGCGCGCGCCGCTCGCTCCCTCCCCGCCCCGCGCCCTCTCTCTCTCTCTCT
CCCCCGCTCCCCGTCCTCCCCCCTCCCCGGGGGAGCGCCGCGTGGGGGCGGCGGCGGGGGGAGAAGGGTC
GGGGCGGCAGGGGCCGGCGGCGGCCCGCCGCGGGGCCCCGGCGGCGGGGGCACGGTCCCCCGCGAGGGGG
GCCCGGGCACCCGGGGGGCCGGCGGCGGCGGCGACTCTGGACGCGAGCCGGGCCCTTCCCGTGGATCGCC
CCAGCTGCGGCGGGCGTCGCGGCCGCCCCCGGGGAGCCCGGCGGGCGCCGGCGCGCCCCCCCCCCCACCC
CACGTCTCGTCGCGCGCGCGTCCGCTGGGGGCGGGGAGCGGTCGGGCGGCGGCGGTCGGCGGGCGGCGGG
GCGGGGCGGTTCGTCCCCCCGCCCTACCCCCCCGGCCCCGTCCGCCCCCCGTTCCCCCCTCCTCCTCGGC
GCGCGGCGGCGGCGGCGGGCGGCGGAGGGGCCGCGGGCCGGTCCCCCCCGCCGGGTCCGCCCCCGGGGCC
GCGGTTCCGCGCGGCGCCTCGCCTCGGCCGGCGCCTAGCAGCCGACTTAGAACTGGTGCGGACCAGGGGA
ATCCGACTGTTTAATTAAAACAAAGCATCGCGAAGGCCCGCGGCGGGTGTTGACGCGATGTGATTTCTGC
CCAGTGCTCTGAATGTCAAAGTGAAGAAATTCAATGAAGCGCGGGTAAACGGCGGGAGTAACTATGACTC
TCTTAAGGTAGCCAAATGCCTCGTCATCTAATTAGTGACGCGCATGAATGGATGAACGAGATTCCCACTG
TCCCTACCTACTATCCAGCGAAACCACAGCCAAGGGAACGGGCTTGGCGGAATCAGCGGGGAAAGAAGAC
CCTGTTGAGCTTGACTCTAGTCTGGCACGGTGAAGAGACATGAGAGGTGTAGAATAAGTGGGAGGCCCCC
GGCGCCCCCCCGGTGTCCCCGCGAGGGGCCCGGGGCGGGGTCCGCCGGCCCTGCGGGCCGCCGGTGAAAT
ACCACTACTCTGATCGTTTTTTCACTGACCCGGTGAGGCGGGGGGGCGAGCCCCGAGGGGCTCTCGCTTC
TGGCGCCAAGCGCCCGGCCGCGCGCCGGCCGGGCGCGACCCGCTCCGGGGACAGTGCCAGGTGGGGAGTT
TGACTGGGGCGGTACACCTGTCAAACGGTAACGCAGGTGTCCTAAGGCGAGCTCAGGGAGGACAGAAACC
TCCCGTGGAGCAGAAGGGCAAAAGCTCGCTTGATCTTGATTTTCAGTACGAATACAGACCGTGAAAGCGG
GGCCTCACGATCCTTCTGACCTTTTGGGTTTTAAGCAGGAGGTGTCAGAAAAGTTACCACAGGGATAACT
GGCTTGTGGCGGCCAAGCGTTCATAGCGACGTCGCTTTTTGATCCTTCGATGTCGGCTCTTCCTATCATT
GTGAAGCAGAATTCACCAAGCGTTGGATTGTTCACCCACTAATAGGGAACGTGAGCTGGGTTTAGACCGT
CGTGAGACAGGTTAGTTTTACCCTACTGATGATGTGTTGTTGCCATGGTAATCCTGCTCAGTACGAGAGG
AACCGCAGGTTCAGACATTTGGTGTATGTGCTTGGCTGAGGAGCCAATGGGGCGAAGCTACCATCTGTGG
GATTATGACTGAACGCCTCTAAGTCAGAATCCCGCCCAGGCGGAACGATACGGCAGCGCCGCGGAGCCTC
GGTTGGCCTCGGATAGCCGGTCCCCCGCCTGTCCCCGCCGGCGGGCCGCCCCCCCCTCCACGCGCCCCGC
GCGCGCGGGAGGGCGCGTGCCCCGCCGCGCGCCGGGACCGGGGTCCGGTGCGGAGTGCCCTTCGTCCTGG
GAAACGGGGCGCGGCTGGAAAGGCGGCCGCCCCCTCGCCCGTCACGCACCGCACGTTCGTGGGGAACCTG
GCGCTAAACCATTCGTAGACGACCTGCTTCTGGGTCGGGGTTTCGTACGTAGCAGAGCAGCTCCCTCGCT
GCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTCCGCGCGCGCGCGCGCGCGTGCGTGCGGGGG
GCCCGGCGGGGCGTGCGCGTCCGGCGCCGTCCGTCCTTCCGTTCGTCTTCCTCCCTCCCGGCCTCTCCCG
CCGACCGCGGGCGTGGTGGTGGGGGTGGGGGGGAGGGCGCGCGACCCCGGTCGGCGCGCCCCGCTTCTTC
GGTTCCCGCCTCCTCCCCGTTCACCGCCGGGGCGGCTCGTCCGCTCCGGGCCGGGACGGGGTCCGGGGAG
CGTGGTTTGGGAGCCGCGGAGGCGGCCGCGCCGAGCCGGGCCCGTGGCCCGCCGGTCCCCGTCCCGGGGG
TTGGCCGCGCGGGCCCCGGTGGGGCGGCCACCCGGGGTCCCGGCCCTCGCG
>RNA5S1
GTCTACGGCCATACCACCCTGAACGCGCCCGATCTCGTCTGATCTCGGAAGCTAAGCAGGGTCGGGCCTG
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTTT
.*
Log.out
results
logs
dag.png
nohup.out
samples
snakemake --dag -np | dot -Tpng > dag.png
# set -e
mkdir -p logs/cluster_log
mkdir -p logs/local_log
snakemake \
--cluster-config cluster.json \
--cluster "sbatch --cpus-per-task={cluster.threads} --mem={cluster.mem} --qos={cluster.queue} --time={cluster.time} --job-name={cluster.name} -o {cluster.out} -p scicore" \
--cores 256 \
-p \
--rerun-incomplete \
--use-singularity \
--singularity-args "--bind ${PWD}"
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