Following my previous question:Snakemake: HISAT2 alignment of many RNAseq reads against many genomes UPDATED.
I wanted to run the hisat2 alignment using touch in snakemake.
I have several genome files with suffix .1.ht2l to .8.ht2l
bob.1.ht2l
...
bob.8.ht2l
steve.1.ht2l
...
steve.8.ht2l
and sereval RNAseq samples
flower_kevin_1.fastq.gz
flower_kevin_2.fastq.gz
flower_daniel_1.fastq.gz
flower_daniel_2.fastq.gz
I need to align all rnaseq reads against each genome.
workdir: "/path/to/dir/"
(HISAT2_INDEX_PREFIX,)=glob_wildcards('/path/to/dir/{prefix}.fasta')
(SAMPLES,)=glob_wildcards("/path/to/dir/{sample}_1.fastq.gz")
rule all:
input:
expand("{prefix}.{sample}.bam", zip, prefix=HISAT2_INDEX_PREFIX, sample=SAMPLES)
rule hisat2_build:
input:
database="/path/to/dir/{prefix}.fasta"
output:
done = touch("{prefix}")
threads: 2
shell:
("/Tools/hisat2-2.1.0/hisat2-build -p {threads} {input.database} {wildcards.prefix}")
rule hisat2:
input:
hisat2_prefix_done = "{prefix}",
fastq1="/path/to/dir/{sample}_1.fastq.gz",
fastq2="/path/to/dir/{sample}_2.fastq.gz"
output:
bam = "{prefix}.{sample}.bam",
txt = "{prefix}.{sample}.txt",
log: "{prefix}.{sample}.snakemake_log.txt"
threads: 50
shell:
"/Tools/hisat2-2.1.0/hisat2 -p {threads} -x {wildcards.prefix}"
" -1 {input.fastq1} -2 {input.fastq2} --summary-file {output.txt} |"
"/Tools/samtools-1.9/samtools sort -@ {threads} -o {output.bam}"
The output gives me bob and steve aligned ONLY against ONE rna-seq sample (i.e. flower_kevin). I don't know how to solve. Any suggestions would be helpful.
