Commit c580f2fb authored by Midoux Cedric's avatar Midoux Cedric
Browse files

underscores allowed in sample names

parent 07f329ef
......@@ -17,9 +17,9 @@ rule mapping:
R2 = "DATA/trim/{reads}_R2.fastq.gz",
i = expand("work/index/{{contigs}}.{ext}.bt2l", ext=["1", "2", "3", "4", "rev.1", "rev.2"])
output:
sam = temp("work/bowtie/align_{contigs}_{reads}.sam"),
bam = "work/bowtie/align_{contigs}_{reads}.bam",
bai = "work/bowtie/align_{contigs}_{reads}.bam.bai"
sam = temp("work/bowtie/align-{contigs}-{reads}.sam"),
bam = "work/bowtie/align-{contigs}-{reads}.bam",
bai = "work/bowtie/align-{contigs}-{reads}.bam.bai"
params:
index = "work/index/{contigs}"
threads:
......@@ -48,10 +48,10 @@ rule mapping:
rule count_contig:
input:
bam = "work/bowtie/align_{contigs}_{reads}.bam",
bai = "work/bowtie/align_{contigs}_{reads}.bam.bai"
bam = "work/bowtie/align-{contigs}-{reads}.bam",
bai = "work/bowtie/align-{contigs}-{reads}.bam.bai"
output:
"report/count-contigs_{contigs}_{reads}.tsv"
"report/count-contigs-{contigs}-{reads}.tsv"
shell:
"samtools idxstats "
"{input.bam} "
......@@ -61,10 +61,10 @@ rule count_contig:
rule count_gene:
input:
unpack(gff_input),
bam = "work/bowtie/align_{contigs}_{reads}.bam",
bai = "work/bowtie/align_{contigs}_{reads}.bam.bai"
bam = "work/bowtie/align-{contigs}-{reads}.bam",
bai = "work/bowtie/align-{contigs}-{reads}.bam.bai"
output:
"report/count-genes_{contigs}_{reads}.tsv"
"report/count-genes-{contigs}-{reads}.tsv"
shell:
"htseq-count "
"--format bam "
......
......@@ -9,9 +9,9 @@ rule all:
"report/multiqc_report.html",
expand("report/reads_{sample}-krona.html", sample=config["SAMPLES"]),
"report/quast_coassembly/report.html",
expand("report/count-contigs_coassembly_{sample}.tsv", sample=config["SAMPLES"]),
expand("report/count-contigs-coassembly-{sample}.tsv", sample=config["SAMPLES"]),
"report/contigs_coassembly-taxNames.tsv",
expand("report/count-contigs_coassembly_{sample}.tsv", sample=config["SAMPLES"]),
expand("report/count-contigs-coassembly-{sample}.tsv", sample=config["SAMPLES"]),
"report/genes_coassembly-taxNames.tsv",
"report/diamond_nr_coassembly.tsv",
"work/prokka/coassembly_prokka.tsv",
......
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