Snakemake 规则从输入变量写入一个新的文本文件（Snakemake 语法）

Question

我有一个功能齐全的 Snakemake 工作流程，但我想添加一个规则，将输入变量作为新行写出到新生成的输出文本文件中。简要总结一下，我在下面包含了相关代码：

OUTPUTDIR = config["outputDIR"] 
SAMPLEID = list(SAMPLE_TABLE.Sample_Name)
# Above 2 lines are functional in other parts of script.

rule all:
  input:
    manifest = OUTPUTDIR + "/manifest.txt"

rule write_manifest:
  input:
    sampleid = SAMPLEID,
    loc_r1 = expand("{base}/trimmed/{sample}_1.trimmed.fastq.gz", base = OUTPUTDIR, sample = SAMPLELIST),
    loc_r2 = expand("{base}/trimmed/{sample}_2.trimmed.fastq.gz", base = OUTPUTDIR, sample = SAMPLELIST)
  output:
    OUTPUTDIR + "/manifest.txt"
  shell:
    """
    echo "{input.sampleid},{input.loc_r1},forward" >> {output}
    echo "{input.sampleid},{input.loc_r2},reverse" >> {output}
    """

我的问题是 Snakemake 正在读取文件，我需要它来打印它检测到的文件路径或样本 ID。帮助语法？

所需的输出文件需要如下所示：

depth1,$PWD/raw_seqs_dir/Test01_full_L001_R1_001.fastq.gz,forward
depth1,$PWD/raw_seqs_dir/Test01_full_L001_R2_001.fastq.gz,reverse
depth2,$PWD/raw_seqs_dir/Test02_full_L001_R1_001.fastq.gz,forward
depth2,$PWD/raw_seqs_dir/Test02_full_L001_R2_001.fastq.gz,reverse

正在尝试使用 echo 写入。

错误信息：

Building DAG of jobs...
MissingInputException in [write_manifest]:
Missing input files for rule write_manifest:
sample1
sample2
sample3

更新：通过将 sampleid 添加到 params:

rule write_manifest:
  input:
    loc_r1 = expand("{base}/trimmed/{sample}_{suf}_1.trimmed.fastq.gz", base = SCRATCHDIR, sample = SAMPLE$
    loc_r2 = expand("{base}/trimmed/{sample}_{suf}_2.trimmed.fastq.gz", base = SCRATCHDIR, sample = SAMPLE$
  output:
    OUTPUTDIR + "/manifest.txt"
  params:
    sampleid = SAMPLEID
  shell:
    """
    echo "{params.sampleid},{input.loc_r1},forward" >> {output}
    echo "{params.sampleid},{input.loc_r2},reverse" >> {output}
    """

我的输出看起来像这样（这是不正确的）

sample1 sample2 sample3,$PWD/tmp/dir/sample1.fastq $PWD/tmp/dir/sample2.fastq $PWD/tmp/dir/sample3.fastq,forward
sample1 sample2 sample3,$PWD/tmp/dir/sample1.fastq $PWD/tmp/dir/sample2.fastq $PWD/tmp/dir/sample3.fastq,reverse

这仍然不是我想要的，我需要它看起来像下面期望的输出。我可以把它写成让 Snakemake 循环遍历每个 sample/input/params 吗？所需的输出文件需要如下所示：

depth1,$PWD/raw_seqs_dir/Test01_full_L001_R1_001.fastq.gz,forward
depth1,$PWD/raw_seqs_dir/Test01_full_L001_R2_001.fastq.gz,reverse
depth2,$PWD/raw_seqs_dir/Test02_full_L001_R1_001.fastq.gz,forward
depth2,$PWD/raw_seqs_dir/Test02_full_L001_R2_001.fastq.gz,reverse

Answer 1

您需要在参数中使用通配符 sample 而不是变量 SAMPLEID。这将在执行时使用特定于该规则的正确样本 ID。

params:
    sample = '{sample}'
shell:
    """
    echo "{params.sample},{input.loc_r1},forward" >> {output}
    echo "{params.sample},{input.loc_r2},reverse" >> {output}
    """

Snakemake 规则从输入变量写入一个新的文本文件（Snakemake 语法）

Snakemake rule to write a new text file from input variables (Snakemake syntax)

shell

snakemake