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SHELL := /bin/bash
MAKEFLAGS += --no-builtin-rules
MAKEFLAGS += --no-builtin-variables
.SUFFIXES:
.DELETE_ON_ERROR:
.SECONDARY:
.ONESHELL:
.DEFAULT: all
CPUS = 2
RAM = 2
SNIPPY = ../bin/snippy --cpus $(CPUS) --ram $(RAM)
SNIPPYCORE = ../bin/snippy-core
R1 = reads_R1.fastq.gz
R2 = reads_R2.fastq.gz
WGSIM = wgsim
GBK=example.gbk
REF=example.fna
BED=example.bed
all: core.txt
wc -l S?/snps.tab
core.txt : S1/snps.tab S2/snps.tab S3/snps.tab S4/snps.tab
$(SNIPPYCORE) --prefix core --ref $(REF) S1 S2 S3 S4
$(SNIPPYCORE) --prefix core-mask --ref $(REF) --mask $(BED) S1 S2 S3 S4
%/snps.tab : %/R1.fq %/R2.fq
$(SNIPPY) --force --ref $(REF) --outdir $(@D) --R1 $(word 1,$^) --R2 $(word 2,$^)
%/R1.fq %/R2.fq : $(REF)
mkdir -p $(@D)
$(WGSIM) -S $(shell echo $(@D) | sed 's/[^0-9]//g') \
-h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \
$< $(@D)/R1.fq $(@D)/R2.fq > $(@D)/dwgsim.tab
%.fna : %.gbk
any2fasta -n -u $< > $@
bigtest/snps.tab : genome.fa reads_R1.fq.gz reads_R2.fq.gz
$(SNIPPY) --force --cpus 36 --outdir bigtest --ref $(word 1,$^) --R1 $(word 2,$^) --R2 $(word 3,$^)
genome.fa :
curl http://ftp.ebi.ac.uk/pub/databases/ena/wgs/public/cv/CVOW01.fasta.gz \
| gunzip | sed -e 's/ENA|CVOW01000001|//' > $@
reads_R1.fq.gz :
curl ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/006/SRR1157476/SRR1157476_1.fastq.gz \
| gunzip | seqtk sample 0.2 - | pigz -9 > $@
reads_R2.fq.gz :
curl ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/006/SRR1157476/SRR1157476_2.fastq.gz \
| gzip -d -c | seqtk sample 0.2 - | pigz -9 > $@
clean :
rm -fr ./bigtest core*.* ./S{1,2,3,4}
|
