If statement 根据config.yaml中的变量（非通配符）命名snakemake中的输入/输出文件

我正在尝试编辑和运行snakemake管道。简而言之，snakemake管道调用默认的基因组比对器（

minimap

），并生成具有此名称的输出文件。我正在尝试向

config.yaml

添加一个变量

aligner

，以指定要调用的对齐器。另外（我实际被卡住的地方），输出文件应该具有

config.yaml

中指定的对齐器名称

我的

config.yaml

如下所示：

# this config.yaml is passed to Snakefile in pipeline-structural-variation subfolder.
# Snakemake is run from this pipeline-structural-variation folder; it is necessary to
# pass an appropriate path to the input-files (the ../ prefix is sufficient for this demo)

aligner: "ngmlr" # THIS IS THE VARIABLE I AM ADDING TO THIS FILE. VALUES COULD BE minimap or ngmlr

# FASTQ file or folder containing FASTQ files
# check if this has to be gzipped
input_fastq: "/nexusb/Gridion/20190917PGD2staal2/PD170815/PD170815_cat_all.fastq.gz" # original is ../RawData/GM24385_nf7_chr20_af.fastq.gz

# FASTA file containing the reference genome
# note that the original reference sequence contains only the sequence of chr20
reference_fasta: "/nexus/bhinckel/19/ONT_projects/PGD_breakpoint/ref_hg19_local/hg19_chr1-y.fasta" # original is ../ReferenceData/human_g1k_v37_chr20_50M.fasta

# Minimum SV length
min_sv_length: 300000 # original value was 40

# Maximum SV length
max_sv_length: 1000000 # original value was 1000000. Note that the value I used to run the pipeline for the sample PD170677 was 100000000000, which will be coerced to NA in the R script (/home/bhinckel/ont_tutorial_sv/ont_tutorial_sv.R)

# Min read length. Shorter reads will be discarded
min_read_length: 1000

# Min mapping quality. Reads will lower mapping quality will be discarded
min_read_mapping_quality: 20

# Minimum read support required to call a SV (auto for auto-detect)
min_read_support: 'auto'

# Sample name
sample_name: "PD170815" # original value was GM24385.nf7.chr20_af. Note that this can be a list

我在下面发布了我的

snakefile

的部分，这些部分生成了扩展名为

\u minimap2.bam

的输出文件，我想用

\u minimap2.bam

或

\u ngmlr.bam

替换这些文件，具体取决于

config.yaml

# INPUT BAM folder
bam = None
if "bam" in config:
    bam = os.path.join(CONFDIR, config["bam"])

# INPUT FASTQ folder
FQ_INPUT_DIRECTORY = []
if not bam:
    if not "input_fastq" in config:
        print("\"input_fastq\" not specified in config file. Exiting...")

    FQ_INPUT_DIRECTORY = os.path.join(CONFDIR, config["input_fastq"])
    if not os.path.exists(FQ_INPUT_DIRECTORY):
        print("Could not find {}".format(FQ_INPUT_DIRECTORY))

    MAPPED_BAM = "{sample}/alignment/{sample}_minimap2.bam" # Original
    #MAPPED_BAM = "{sample}/alignment/{sample}_{alignerName}.bam" # this did not work
    #MAPPED_BAM = f"{sample}/alignment/{sample}_{config['aligner']}.bam" # this did nor work either
else:
    MAPPED_BAM = find_file_in_folder(bam, "*.bam", single=True)

...

if config['aligner'] == 'minimap':
    rule index_minimap2:
        input:
            REF = FA_REF
        output:
            "{sample}/index/minimap2.idx"
        threads: config['threads']
        conda: "env.yml"
        shell:
            "minimap2 -t {threads} -ax map-ont --MD -Y {input.REF} -d {output}"


    rule map_minimap2:
        input:
            FQ = FQ_INPUT_DIRECTORY,
            IDX = rules.index_minimap2.output,
            SETUP = "init"
        output:
            BAM = "{sample}/alignment/{sample}_minimap2.bam",
            BAI = "{sample}/alignment/{sample}_minimap2.bam.bai"

        conda: "env.yml"
        threads: config["threads"]
        shell:
            "cat_fastq {input.FQ} | minimap2 -t {threads} -K 500M -ax map-ont --MD -Y {input.IDX} - | samtools sort -@ {threads} -O BAM -o {output.BAM} - && samtools index -@ {threads} {output.BAM}"

else:
    print(f"Aligner is {config['aligner']} - skipping indexing step for minimap2")

    rule map_ngmlr:
        input:
            REF = FA_REF,
            FQ = FQ_INPUT_DIRECTORY,
            SETUP = "init"
        output:
            BAM = "{sample}/alignment/{sample}_minimap2.bam",
            BAI = "{sample}/alignment/{sample}_minimap2.bam.bai"
        conda: "env.yml"
        threads: config["threads"]
        shell:
            "cat_fastq {input.FQ} | ngmlr -r {input.REF} -t {threads} -x ont - | samtools sort -@ {threads} -O BAM -o {output.BAM} - && samtools index -@ {threads} {output.BAM}"

我最初尝试创建一个

alignerName

参数，类似于

sample

参数，如下所示：

# Parameter: sample_name
sample = "sv_sample01"
if "sample_name" in config:
    sample = config['sample_name']

###############
#
# code below created by me
#
###############
# Parameter: aligner_name
alignerName = "defaultAligner"
if "aligner" in config:
    alignerName = config['aligner']

然后，我尝试在我的输入/输出文件上有

minimap2

的地方输入

{alignerName}

（请参见上面的注释

MAPPED_BAM

变量定义），尽管这会引发错误。我猜snakemake会将

{alignerName}

解释为通配符，尽管我只想将

config['aligner']

中定义的变量名传递给输入/输出文件。我也尝试过使用f-string（

MAPPED_BAM=f“{sample}/alignment/{sample}}{config['aligner']}.BAM”

），不过我猜这也不起作用。

你很接近了

通配符在snakemake中的工作方式是它们被解释为“last”，而f字符串被解释为first。要不解释f字符串中的大括号，可以使用另一个大括号将其转义，如下所示：

print(f"{{keep curly}}")
>>> {keep curly}

所以我们需要做的就是

MAPPED_BAM = f"{{sample}}/alignment/{{sample}}_{config['aligner']}.bam"

---

万分感谢，对snakemake来说是个新手，为了让这段代码正常工作，他尝试了一切，而双花括号正是我想要的。