combine files for makefile lead to make No targets - makefile

Question

I have the following file and directory structure which contains a lot of files and directories:
$ tree
input/
├── C-1-28558666
│ ├── MGRF-C1_S10_L001_R1_001.fastq.gz
│ ├── MGRF-C1_S10_L001_R2_001.fastq.gz
│ ├── MGRF-C1_S10_L002_R1_001.fastq.gz
│ ├── MGRF-C1_S10_L002_R2_001.fastq.gz
│ ├── MGRF-C1_S10_L003_R1_001.fastq.gz
│ ├── MGRF-C1_S10_L003_R2_001.fastq.gz
│ ├── MGRF-C1_S10_L004_R1_001.fastq.gz
│ └── MGRF-C1_S10_L004_R2_001.fastq.gz
├── C-2-28577664
│ ├── MGRF-C2_S11_L001_R1_001.fastq.gz
│ ├── MGRF-C2_S11_L001_R2_001.fastq.gz
│ ├── MGRF-C2_S11_L002_R1_001.fastq.gz
│ ├── MGRF-C2_S11_L002_R2_001.fastq.gz
│ ├── MGRF-C2_S11_L003_R1_001.fastq.gz
│ ├── MGRF-C2_S11_L003_R2_001.fastq.gz
│ ├── MGRF-C2_S11_L004_R1_001.fastq.gz
│ └── MGRF-C2_S11_L004_R2_001.fastq.gz
...
Each file name contain R1 or R2. The files with R1 and R2 belongs together and the below commanand uses the two files and a dm6.fasta.bwt file.
bwa mem ref/dm6.fasta.bwt input/C-1-28558666/MGRF-C1_S10_L001_R1_001.fastq.gz input/C-1-28558666/MGRF-C1_S10_L001_R2_001.fastq.gz | samtools view -Sb - > BAMs/C-1-28558666/MGRF-C1_S10_L001.bam
I have tried to write the following Makefile rule:
BAMs/%.bam: $(addsuffix .bwt,${REFERENCE}) $(foreach SIDE,R1 R2, ../MGRF_NGS_KUMARAN-25071046/*/*${SIDE}*.fq.gz )
bwa mem ${REFERENCE} $(filter %.fq.gz,$^) | samtools view -Sb - > #>
However, I have got:
$ make -n
make: *** No targets. Stop.
How is it possible to fix the above Makefile?

Answer 1

Your first problem comes from the fact that pattern rules do not create targets if they are not explicitly requested. So, you need to explicitly list the targets to make. In the following example they are listed in the BAMS make variable and then used as dependencies of the all target, which is the first of the makefile. all is thus the default goal and typing make or make all will build all bams.
Your second problem is to handle the pair of R1 and R2 dependencies of each bam target. The GNU make static pattern rules are really useful in such situations:
REFERENCE := ref/dm6.fasta
DIRS := $(wildcard input/*)
R1S := $(foreach dir,$(DIRS),$(wildcard $(dir)/*_R1_001.fastq.gz))
RR1S := $(patsubst input/%_R1_001.fastq.gz,%,$(R1S))
BAMS := $(patsubst %,BAMs/%.bam,$(RR1S))
all: $(BAMS)
$(BAMS): BAMs/%.bam: $(REFERENCE).bwt input/%_R1_001.fastq.gz input/%_R2_001.fastq.gz
#mkdir -p $(dir $#); \
bwa mem $^ | samtools view -Sb - > $#
target: target-pattern: prerequisite-pattern is a static pattern rule.
GNU make also has several functions (call, eval, foreach) that can be used in more complex examples:
REFERENCE := ref/dm6.fasta
DIRS := $(wildcard input/*)
R1S := $(foreach dir,$(DIRS),$(wildcard $(dir)/*_R1_001.fastq.gz))
RR1S := $(patsubst input/%_R1_001.fastq.gz,%,$(R1S))
BAMS := $(patsubst %,BAMs/%.bam,$(RR1S))
all: $(BAMS)
define BAM_rule
BAMs/$(1).bam: $(REFERENCE).bwt input/$(1)_R1_001.fastq.gz input/$(1)_R2_001.fastq.gz
#mkdir -p $$(dir $$#); \
bwa mem $$^ | samtools view -Sb - > $$#
endef
$(foreach r,$(RR1S),$(eval $(call BAM_rule,$(r))))
Explanations:
The RR1S variable lists all C-1-28558666/MGRF-C1_S10_L001 stems. It is then used to build the BAMS variable that lists the targets. The BAM_rule variable is a skeleton of the rule that builds a bam target from its corresponding R1 and R2 dependencies. $(1) is the parameter that will be expanded when using the call function: $(call BAM_rule,foo) expands BAM_rule and substitutes all $(1) occurrences by foo. Note that some $ signs must be doubled to be preserved by this first expansion. Finally,
$(foreach r,$(RR1S),$(eval $(call BAM_rule,$(r))))
iterates over all stems and uses the eval function to instantiate one BAM_rule per stem, expanded and specialized by call.
The normal make expansion will then transform each instance of BAM_rule into the rule you would write manually for the given target:
BAMs/C-1-28558666/MGRF-C1_S10_L001.bam: ref/dm6.fasta.bwt input/C-1-28558666/MGRF-C1_S10_L001_R1_001.fastq.gz input/C-1-28558666/MGRF-C1_S10_L001_R2_001.fastq.gz
#mkdir -p BAMs/C-1-28558666; \
bwa mem ref/dm6.fasta.bwt input/C-1-28558666/MGRF-C1_S10_L001_R1_001.fastq.gz input/C-1-28558666/MGRF-C1_S10_L001_R2_001.fastq.gz | samtools view -Sb - > BAMs/C-1-28558666/MGRF-C1_S10_L001.bam