Я знаю, что это распространенная ошибка, и я уже проверил другие сообщения, но это не решило мою проблему. Я хотел бы использовать имя базы данных, которую я использую для правила SortMeRNA (rRNAdb=config["rRNA_database"]), так же, как я использую version=config["genome_version"]. Но, очевидно, я не могу.
SyntaxError:
Not all output, log and benchmark files of rule SortMeRNA contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file
......
import glob
import os
configfile : "config.json"
#################### GLOBAL VARIABLES #######################
OUTDIR = os.path.abspath(config["outdir"])
# ID NGS
idNGS = config["idNGS"]
# Fichiers FASTQ
DIR_FASTQ = config["dir_fastq"]
## PARAMETERS TRIMMOMATIC
w = config["w"]
Q = config["Q"]
m = config["m"]
## Bowtie2 database
BWT2_DB = config["BWT2_DB"]
## Templates multiQC
DIR_TPL = config["DIR_TPL"]
#### VERSIONS genomes and database ####
version = config["genome_version"]
rRNAdb = config["rRNA_database"]
####################### FASTQ FILES #########################
def list_samples(DIR_FASTQ): # create list with all sample names from fastq directory
SAMPLES=[]
for file in glob.glob(DIR_FASTQ+"/*.fastq.gz"):
base=os.path.basename(file)
sample=(base.replace('.fastq.gz', ''))
SAMPLES.append(sample)
return(SAMPLES)
SAMPLES = list_samples(DIR_FASTQ)
########################## RULES ############################
rule all:
input:
OUTDIR+"/multiQC/multiQC-PL09_"+idNGS+".html",
OUTDIR+"/multiQC/multiQC-PL21_"+idNGS+".html"
rule fastQC:
input:
DIR_FASTQ+"/{sample}.fastq.gz"
output:
"{OUTDIR}/FastQC/{sample}_fastqc.zip",
"{OUTDIR}/FastQC/{sample}_fastqc.html"
threads:
16
shell:
"""
fastqc {input} -o {OUTDIR}/FastQC/
"""
rule trimmomatic:
input:
DIR_FASTQ+"/{sample}.fastq.gz"
output:
trim_out="{OUTDIR}/Trimmomatic/{sample}_SL-{w}-{Q}_Min-{m}.fastq.gz",
trim1_out="{OUTDIR}/Trimmomatic/{sample}_SL-{w}-{Q}_Min-{m}.stdout",
trim1_err="{OUTDIR}/Trimmomatic/{sample}_SL-{w}-{Q}_Min-{m}.stderr"
threads:
16
shell:
"trimmomatic SE -phred33 {input} {output.trim_out} SLIDINGWINDOW:{w}:{Q} MINLEN:{m} > {output.trim1_out} 2> {output.trim1_err}"
rule Bowtie2:
input:
fasta_trim="{OUTDIR}/Trimmomatic/{sample}_SL-"+str(w)+"-"+str(Q)+"_Min-"+str(m)+".fastq.gz"
output:
BWT2_ERR="{OUTDIR}/Bowtie2/{sample}_SL-{w}-{Q}_Min-{m}_bowtie2_{version}.stderr",
BWT2_SAM=temp("{OUTDIR}/Bowtie2/{sample}_SL-{w}-{Q}_Min-{m}_bowtie2_{version}.sam"),
BWT2_BAM=temp("{OUTDIR}/Bowtie2/{sample}_SL-{w}-{Q}_Min-{m}_bowtie2_{version}.bam"),
BWT2_BAM_SORTED="{OUTDIR}/Bowtie2/{sample}_SL-{w}-{Q}_Min-{m}_bowtie2_{version}.sorted.bam"
threads:
16
shell:
"""
bowtie2 -x {BWT2_DB} -U {input} 2> {output.BWT2_ERR} > {output.BWT2_SAM}
samtools view -bS -o {output.BWT2_BAM} {output.BWT2_SAM}
samtools sort {output.BWT2_BAM} -o {output.BWT2_BAM_SORTED}
samtools index {output.BWT2_BAM_SORTED}
"""
rule copy_to_pigz: # we just copy fastq files to gunzip them and use them in sortMeRNA, this way we don't touch the original ones
input:
DIR_FASTQ+"/{sample}.fastq.gz"
output:
"{OUTDIR}/temp/{sample}.fastq.gz" # this temp directory will be deleted at the end of the pipeline in multiQC rule
shell:
"cp {input} {output}"
rule SortMeRNA:
input:
"OUTDIR/temp/{sample}.fastq.gz"
output:
fasta_pigz=temp("{OUTDIR}/temp/{sample}.fastq"),
blast="{OUTDIR}/SortMeRNA/{sample}.fastq_SortMeRNA_{rRNAdb}.blast",
log="{OUTDIR}/SortMeRNA/{sample}.fastq_SortMeRNA_{rRNAdb}.log"
params:
prefixSortMeRNA="{OUTDIR}/SortMeRNA/{sample}.fastq_SortMeRNA_{rRNAdb}",
sortmerna_DB=config["SORTMERNA_DB"]
shell:
"""
pigz -d -k {input}
sortmerna --ref {params.sortmerna_DB} --reads {output.fasta_pigz} --aligned {params.prefixSortMeRNA} --blast '1' --log TRUE
"""
rule multiQC:
input:
expand(OUTDIR+"/FastQC/{sample}_fastqc.zip", sample=SAMPLES),
expand(OUTDIR+"/Trimmomatic/{sample}_SL-"+str(w)+"-"+str(Q)+"_Min-"+str(m)+".fastq.gz", sample=SAMPLES),
expand(OUTDIR+"/Trimmomatic/{sample}_SL-"+str(w)+"-"+str(Q)+"_Min-"+str(m)+".stdout", sample=SAMPLES),
expand(OUTDIR+"/Trimmomatic/{sample}_SL-"+str(w)+"-"+str(Q)+"_Min-"+str(m)+".stderr", sample=SAMPLES),
expand(OUTDIR+"/Bowtie2/{sample}_SL-"+str(w)+"-"+str(Q)+"_Min-"+str(m)+"_bowtie2_"+version+".stderr", sample=SAMPLES),
expand(OUTDIR+"/SortMeRNA/{sample}.fastq_SortMeRNA_"+rRNAdb+".blast", sample=SAMPLES),
expand(OUTDIR+"/SortMeRNA/{sample}.fastq_SortMeRNA_"+rRNAdb+".log", sample=SAMPLES),
tpl_plNGS=DIR_TPL+"/template-PL-NGS_multiqc_config.yaml",
tpl_plBioinfo=DIR_TPL+"/template-PL-Bioinfo_multiqc_config.yaml"
output:
rap_plNGS="{OUTDIR}/multiQC/multiQC-PL09_{idNGS}.html",
rap_plBioinfo="{OUTDIR}/multiQC/multiQC-PL21_{idNGS}.html"
shell:
"""
sed -e "s/ID_NGS_HERE/{idNGS}/g" < {input.tpl_plNGS} > {OUTDIR}/multiQC/PL-NGS_multiqc_config.yaml
sed -e "s/ID_NGS_HERE/{idNGS}/g" < {input.tpl_plBioinfo} > {OUTDIR}/multiQC/PL-Bioinfo_multiqc_config.yaml
multiqc -c {OUTDIR}/multiQC/PL-NGS_multiqc_config.yaml -n {output.rap_plNGS} {OUTDIR}/
multiqc -c {OUTDIR}/multiQC/PL-Bioinfo_multiqc_config.yaml -n {output.rap_plBioinfo} {OUTDIR}/
rm -r {OUTDIR}/temp
"""
onsuccess:
shell("date '+%d/%m/%Y %H:%M:%S' > time_end_RNAseq.txt")
Это потому, что я использую его в params и output в SortMeRNA правиле, а не в inputs этого правила? Поскольку для version в Bowtie правиле, кажется, нет проблем использовать его в outputs правила, а не в input ...