Alternatives to pattern rules with .PHONY targets in a makefile? - makefile

Question

I am writing a pipeline in make to analyse biological data. There are three distinct sections of the pipeline, the first is to check the quality of the data, the second is to clean the data, and third is to align the data. After each section is complete I would like to manually inspect the results before I move on with the next. Therefore, instead of having a single chain of pattern rules, I want to be able to call each section using a phony target (similar to how you call clean). For example:
make analysis.pipeline quality
make analysis.pipeline trim
make analysis.pipeline align
Here is my current makefile:
# analysis pipeline
include analysis.pipeline.config
# align data
all: $(sorted_bam)
$(results)/%.sorted.bam: $(results)/%.bam
samtools sort $^ $(basename $#)
$(results)/%.bam: $(results)/%.sam
samtools view -bS $^ > $#
$(results)/%.sam: $(results)/%.adaprm.fastq
bowtie2 -x $(genome) -U $^ -S $#
# clean data
.PHONY: trim
trim: $(qc_processed) $(trimmed_fastq)
$(results)/%.adaprm_fastqc.html: $(results)/%.adaprm.fastq
fastqc -o $(#D) $^
$(results)/%.adaprm.fastq: $(data)/%.fastq
cutadapt -a AACCGGTT $^ > $#
# check data
.PHONY: quality
quality: $(qc_raw)
$(results)/%_fastqc.html: $(data)/%.fastq
mkdir -p $(#D) && fastqc -o $(#D) $^
The makefile is written to run in a src directory, which is separate to where the targets and dependencies are built, namely data and results directories. Is it possible to call each section of my pipeline the way I intend to, will there be any issue if I run it in parallel, and is this the right way to get around not being able to use implicit pattern rules in phony targets?
Updated makefile
# objects = A.fastq B.fastq
.PHONY: quality
quality: A_fastqc.html B_fastqc.html C_fastqc.html
.PHONY: trim
trim: A.trimmed_fastqc.html B.trimmed_fastqc.html
.PHONY: align
align: A.sorted.bam.bai B.sorted.bam.bai
# ALIGN DATA SECTION
%.sorted.bam.bai: %.sorted.bam
samtools index $^
%.sorted.bam: %.bam
samtools sort $^ $#
%.bam: %.sam
samtools view -bS $^ > $#
%.sam: %.trimmed.fastq %.trimmed_fastqc.html
bowtie2 -x $(genome) -U $< -S $#
# TRIM DATA SECTION
%.trimmed_fastqc.html: %.trimmed.fastq
fastqc $^
%.trimmed.fastq: %.adaprm.fastq
seqtk trimfq $^ > $#
%.adaprm.fastq: %.fastq %_fastqc.html
cutadapt -a AACCGGTT $< > $#
# CHECK QUALITY SECTION
%_fastqc.html: %.fastq
fastqc $^