From da795e6947a7d53012772f6bc1f7c787e844b9d8 Mon Sep 17 00:00:00 2001
From: rlegendr <rachel.legendre@pasteur.fr>
Date: Fri, 17 Sep 2021 14:14:46 +0200
Subject: [PATCH] fixe maestro path
---
Snakefile | 8 ++++----
config/config.yaml | 24 +++++++++++++-----------
workflow/rules/cutadapt.rules | 2 +-
workflow/rules/sortmerna.rules | 6 +++++-
4 files changed, 23 insertions(+), 17 deletions(-)
diff --git a/Snakefile b/Snakefile
index f57d18c..9a3899f 100755
--- a/Snakefile
+++ b/Snakefile
@@ -182,8 +182,8 @@ if config["bowtie2_mapping"]["do"]:
# indexing for bowtie2
bowtie2_index_fasta = unpack(mapping_index)
bowtie2_index_log = "02-Mapping/{REF}/bowtie2/logs/bowtie2_{REF}_indexing.log"
- bowtie2_index_output_done = os.path.join(config["genome"]["genome_directory"]+"{REF}/bowtie2/{REF}.1.bt2")
- bowtie2_index_output_prefix = os.path.join(config["genome"]["genome_directory"]+"{REF}/bowtie2/{REF}")
+ bowtie2_index_output_done = os.path.join(config["genome"]["genome_directory"], "{REF}/bowtie2/{REF}.1.bt2")
+ bowtie2_index_output_prefix = os.path.join(config["genome"]["genome_directory"], "{REF}/bowtie2/{REF}")
include: os.path.join(RULES, "bowtie2_index.rules")
@@ -212,8 +212,8 @@ if config["star_mapping"]["do"]:
star_index_fasta = unpack(mapping_index)
star_mapping_splice_file = unpack(annot_index)
star_index_log = "02-Mapping/{REF}/STAR/logs/STAR_{REF}_indexing.log"
- star_index_output_done = os.path.join(config["genome"]["genome_directory"], "/{REF}/STAR/SAindex")
- star_index_output_dir = os.path.join(config["genome"]["genome_directory"], "/{REF}/STAR/")
+ star_index_output_done = os.path.join(config["genome"]["genome_directory"], "{REF}/STAR/SAindex")
+ star_index_output_dir = os.path.join(config["genome"]["genome_directory"], "{REF}/STAR/")
include: os.path.join(RULES, "star_index.rules")
diff --git a/config/config.yaml b/config/config.yaml
index 1bbad1d..439a315 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -53,17 +53,18 @@ tmpdir: "/pasteur/sonic/scratch/public/"
# - rRNA_mapping: Mapping on ribosomal RNA
#===============================================================================
+
genome:
- genome_directory: ../genome/
- name: saccer3
- fasta_file: ../genome/saccer3/saccer3.fa
- gff_file: ../genome/saccer3/saccer3.gff
+ genome_directory: /pasteur/zeus/projets/p01/BioIT/Genomes
+ name: Rabies
+ fasta_file: /pasteur/zeus/projets/p01/BioIT/Genomes/Rabies/Rabies.fa
+ gff_file: /pasteur/zeus/projets/p01/BioIT/Genomes/Rabies/Rabies.gff
host_mapping: true
host_name: hg38
- host_fasta_file: ../genome/hg38/hg38.fa
- host_gff_file: ../genome/hg38/hg38.gff
+ host_fasta_file: /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.fa
+ host_gff_file: /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.gff
rRNA_mapping: true
- ribo_fasta_file: ../genome/hg38/hg38_rRNA.fa
+ ribo_fasta_file: /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_rRNA.fa
#===============================================================================
# FastQC section
@@ -156,11 +157,12 @@ star_mapping:
pseudomapping:
do: yes
- fasta: ../genome/hg38/hg38.fa
- gtf: ../genome/hg38/hg38.gff
- options: ""
+ fasta: /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38_cDNA.fa
+ gtf: /pasteur/zeus/projets/p01/BioIT/Genomes/hg38/hg38.gtf
+ options: "--single"
kmer: 31
- threads: 4
+ threads: 12
+
#############################################################################
# feature_counts used to count reads against features
diff --git a/workflow/rules/cutadapt.rules b/workflow/rules/cutadapt.rules
index cc6ebec..d9f95d5 100755
--- a/workflow/rules/cutadapt.rules
+++ b/workflow/rules/cutadapt.rules
@@ -55,7 +55,7 @@ rule cutadapt:
outfiles=($tmp)
# add mode and adapter sequences
- cmd+=" cutadapt -{params.mode} {params.adapters} -m {params.min} -q {params.qual} {params.options} "
+ cmd+=" cutadapt -{params.mode} {params.adapters} -m {params.min} -q {params.qual} {params.options} -j {threads} "
# paired end or single end
if [[ ${{#infiles[@]}} -eq 2 ]];
then
diff --git a/workflow/rules/sortmerna.rules b/workflow/rules/sortmerna.rules
index 8b05fdd..2128bb8 100755
--- a/workflow/rules/sortmerna.rules
+++ b/workflow/rules/sortmerna.rules
@@ -32,6 +32,7 @@ rule sortmerna:
no_rRNA = temp(sortmerna_outfile_no_rRNA)
singularity:
"rnaflow.img"
+ shadow: "shallow"
log:
err = sortmerna_logs_err,
out = sortmerna_logs_out
@@ -52,7 +53,10 @@ rule sortmerna:
fi
- sortmerna --ref ${{fasta}},${{index}} -a {threads} --reads {input.fastq} --aligned {output.rRNA} --fastx --sam --num_alignments 1 --other {output.no_rRNA} --log -v > {log.out} 2> {log.err}
+ sortmerna --ref ${{fasta}},${{index}} -a {threads} --reads {input.fastq} --aligned {output.rRNA} --fastx --other {output.no_rRNA} --log -v > {log.out} 2> {log.err}
+ mv {output.no_rRNA}.fastq {output.no_rRNA}
+ mv {output.rRNA}.fastq {output.rRNA}
+
"""
--
GitLab