I know this is a common error and I already checked other posts but it didn't resolved my issue. I would like to use the name of the database I use for SortMeRNA rule (rRNAdb=config["rRNA_database"]) the same way I use version=config["genome_version"]. But obviously, I can't.
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")
Is it because I use it in params and output in SortMeRNA rule and not in inputs of this rule ? Because for version in Bowtie rule, it doesn't seem to be problem to use it in outputs of the rule and not in input...
All output files need to have same wildcards, or else it would cause conflict in resolving job dependencies. Not all files in output: have {rRNAdb} wildcard, which is causing this problem. For example, if you have two {rRNAdb} values, both would write to file "{OUTDIR}/temp/{sample}.fastq", which snakemake correctly doesn't allow.
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"
"""
PS - It appears you are mixing variable OUTDIR with wildcards, which will cause some other errors.