different wildcards you can do like: wildcards.sample = "s002" # print that value: wildcards.sample..., "fastq2"] # here we use it on our spoofed wildcards object fq2_from_sample(wildcards) 因为snakemake...(wildcards): return samples_table.loc[wildcards.sample, "fastq2"] rule trim_awesome: input:...[wildcards.sample, "fastq2"] } # make sure our spoofed wildcards variable is set: wildcards.sample...= "s003" # Now see what that function returns on that wildcards input: fq_dict_from_sample(wildcards
/rnaseq/01.clean.reads/{sample}_clean_1.fq") GENOMES, = glob_wildcards("{genome}.fa.masked") GENOMES...' is not defined 然后又换成下面的写法 def getGenomes(wildcards): return wildcards.genome rule samtools_merge...这里面提到 'wildcards' is not "directly" defined in the input of a rule....安装这个思路我写我自己的 def getGenome01(wildcards): return expand(rules.samtools_sort.output.bam,genome=wildcards.genome...,sample=SAMPLES) def getGenome02(wildcards): return expand(rules.samtools_index.output,genome=wildcards.genome
: config["samples"][wildcards.sample] output: "mapped_reads/{sample}.bam" threads: 8...: config["samples"][wildcards.sample] 我们可以像字典一样去访问它,比如当我们传入A 时,即传给了通配符对应的{sample},并可以获得对应的值data/samples...rule bwa_map: input: "data/genome.fa", lambda wildcards: config["samples"][wildcards.sample...5-临时与保护文件 比如在下面流程中: rule bwa_map: input: "data/genome.fa", lambda wildcards: config...["samples"][wildcards.sample] output: temp("mapped_reads/{sample}.bam") params:
3 [Tue Apr 2 21:09:19 2019] rule adda: input: 3.txt output: 3_add_a.txt jobid: 2 wildcards...done [Tue Apr 2 21:11:09 2019] rule adda: input: 1.txt output: 1_add_a.txt jobid: 1 wildcards...2 21:13:57 2019] rule addb: input: 2_add_a.txt output: 2_add_a_add_b.txt jobid: 0 wildcards...2 21:13:57 2019] rule addb: input: 1_add_a.txt output: 1_add_a_add_b.txt jobid: 1 wildcards...2 21:13:57 2019] rule addb: input: 3_add_a.txt output: 3_add_a_add_b.txt jobid: 2 wildcards
caused_by"=>{"type"=>"illegal_state_exception", "reason"=>"There are no external requests known to support wildcards...caused_by"=>{"type"=>"illegal_state_exception", "reason"=>"There are no external requests known to support wildcards...caused_by"=>{"type"=>"illegal_state_exception", "reason"=>"There are no external requests known to support wildcards...caused_by"=>{"type"=>"illegal_state_exception", "reason"=>"There are no external requests known to support wildcards...caused_by"=>{"type"=>"illegal_state_exception", "reason"=>"There are no external requests known to support wildcards
Wildcards can be used : sonar.java.test.libraries=path/to/specific/Library.jar,path/to/libs/*.jar,directory...Wildcards can be used : sonar.java.libraries=path/to/specific/Library.jar,path/to/libs/*.jar,directory...Wildcards can be used : sonar.libraries=path/to/specific/Library.jar,path/to/libs/*.jar,directory/**/
samples/" output_folder = "/home/myan/scratch/private/practice_data/RNAseq/20220511/" SRR,FRR = glob_wildcards...}_%j.out -e logs_errors/{rule}/{rule}_{wildcards}_%j.err --mail-type=ALL --mail-user=mingyan24@126.com...)] print(fq_list) inputs = [(dir,file) for dir,files in fq_list.items() for file in files] #glob_wildcards...pomeRTD/00.raw.fastq/" output_folder = "/home/myan/scratch/private/pomeRTD/" #Folder,SRR,FRR = glob_wildcards...print(list_fastq) inputs = [(dir,file) for dir,files in list_fastq.items() for file in files] #glob_wildcards
WorkflowError: Target rules may not contain wildcards....Please specify concrete files or a rule without wildcards at the command line, or have a rule without...wildcards at the very top of your workflow (e.g. the typical "rule all" which just collects all results...data/raw/002_R2.fq output: results/awesome/002_R1.fq, results/awesome/002_R2.fq jobid: 2 wildcards...data/raw/003_R2.fq output: results/awesome/003_R1.fq, results/awesome/003_R2.fq jobid: 0 wildcards
Wildcards in the regular expression can only be ‘’ for any character(s) or ‘|’ for a choice....显示所有的数据库 通配符只有两种: * 和 | * 表示所有 | 表示或 SHOW DATABASES [LIKE 'identifier_with_wildcards']; Show Tables/...Wildcards in the regular expression can only be ‘*’ for any character(s) or ‘|’ for a choice....SHOW TABLES [IN database_name] ['identifier_with_wildcards']; Show Views SHOW VIEWS;...显示的信息更全面 SHOW TABLE EXTENDED [IN|FROM database_name] LIKE 'identifier_with_wildcards' [PARTITION(partition_spec
): return config["sample"][wildcards.sample][wildcards.end] rule rename: input: get_fq...): return config["diffGroup"][wildcards.dgroup]["control"] def get_diff_case_sn(wildcards):...return config["diffGroup"][wildcards.dgroup]["case"] def get_diff_control_bam(wildcards): sn =...get_diff_case_bam(wildcards): sn = get_diff_case_sn(wildcards) bams = [f"03align/{i}.filter.bam..." for i in sn] return bams def get_diff_control_peak(wildcards): sn = get_diff_control_sn(wildcards
output: "sorted_reads/{sample}.bam" shell: "samtools sort -T sorted_reads/{wildcards.sample...output: mapped_reads/B.bam jobid: 6 reason: Missing output files: mapped_reads/B.bam wildcards...output: mapped_reads/A.bam jobid: 4 reason: Missing output files: mapped_reads/A.bam wildcards...Missing output files: sorted_reads/B.bam; Input files updated by another job: mapped_reads/B.bam wildcards...Missing output files: sorted_reads/A.bam; Input files updated by another job: mapped_reads/A.bam wildcards
exclusion) --no-ignore-case case sensitive matching (default) --no-wildcards...verbatim string matching --no-wildcards-match-slash wildcards do not match '/'...--wildcards use wildcards (default for exclusion) --wildcards-match-slash wildcards
output: "sorted_reads/{sample}.bam" shell: "samtools sort -T sorted_reads/{wildcards.sample...我们在snakemake 中使用的{sample},实际上是创建的wildcards 对象的一个属性。因此在shell 中需要写为{wildcards.sample}。...output: "sorted_reads/{sample}.bam" shell: "samtools sort -T sorted_reads/{wildcards.sample...output: "sorted_reads/{sample}.bam" shell: "samtools sort -T sorted_reads/{wildcards.sample...https://archive.fastgit.org/snakemake/snakemake-tutorial-data/archive/refs/tags/v7.4.2.tar.gz tar --wildcards
(这包括_all字符串或未指定索引时)| |expand_wildcards | 是否将通配符表达式扩展为打开,关闭或两者的具体索引。...(这包括_all字符串或未指定索引时)| |expand_wildcards | 是否将通配符表达式扩展为打开,关闭或两者的具体索引。...(这包括_all字符串或未指定索引时)| |expand_wildcards | 是否将通配符表达式扩展为打开,关闭或两者的具体索引。...(这包括_all字符串或未指定索引时)| |expand_wildcards | 是否将通配符表达式扩展为打开,关闭或两者的具体索引。...(这包括_all字符串或未指定索引时) expand_wildcards - 是否将通配符表达式扩展为打开,关闭或两者的具体索引。
expand_wildcards expand_wildcards表示查询索引的范围,open表示查询所有匹配并open的索引,closed则表示查询所有匹配的索引,如下: 假设bank关闭,bank2...pretty&expand_wildcards=open" 此时,只会展示open的索引信息,如下: ?...pretty&expand_wildcards=closed" 结果如下: ?
= os.path.join(*args) return os.path.normpath(path) def find_data_files(self, srcdir, *wildcards...也可以加进来 if '.svn' in dirname: return names = [] lst, wildcards...= arg for wc in wildcards: wc_name = self.opj(dirname, wc)...('recursive', True) if recursive: os.path.walk(srcdir, walk_helper, (file_list, wildcards...)) else: walk_helper((file_list, wildcards), srcdir,
SYNOPSIS amalgamate [-s] [-w {wildcards}] [-f {file|macro}]......-w {wildcards} Specify a comma separated list of file name patterns to match
super T> 是Java泛型中的“通配符(Wildcards)” 和 “边界(Bounds)”的概念 是指 “上界通配符(Upper Bounds Wildcards)” 是指 “下界通配符(Lower Bounds Wildcards)” 1....下面代码就是“上界通配符(Upper Bounds Wildcards)”: Plate 翻译成人话就是:一个能放水果以及一切是水果派生类的盘子。...相对应的,“下界通配符(Lower Bounds Wildcards)”: Plate 表达的就是相反的概念:一个能放水果以及一切是水果基类的盘子。Plate<?
target specified: Specify SQL_ID (eg: from V$SQL.SQL_ID) report target: Defaults to NULL: (% and _ wildcards...specified: Specify MODULE name (eg: from V$SESSION.MODULE) report target: Defaults to NULL: (% and _ wildcards...specified: Specify ACTION name (eg: from V$SESSION.ACTION) report target: Defaults to NULL: (% and _ wildcards...Specify CLIENT_ID (eg: from V$SESSION.CLIENT_IDENTIFIER) report target: Defaults to NULL: (% and _ wildcards...specified: Specify PLSQL_ENTRY name (eg: "SYS.DBMS_LOB.*") report target: Defaults to NULL: (% and _ wildcards
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