snakemake

问题 This question follows on from a question I asked previously and it regards understanding how to access config files correctly using Snakemake. I have a specific problem I need to address which I'll ask first and a general problem understanding how indexing works which I'll ask second. I'm using snakemake to run and ATAC-seq pipeline from Alignment/QC through to motif analysis. A: Specific Question I'm trying to add a rule called trim_galore_pe to trim adapters from my fastq files before

问题 I'm building an SQL script out of text data. The (part of) script shall consist of a CREATE TABLE statement and an optional INSERT INTO statement. The values for INSERT INTO statement are taken from the list of files, each one may exist or may not; all values of existing files are merged. The crucial part is that the INSERT INTO statement shall be skipped whenever no one data file exists. I've created a script in Snakemake that does that. There are two ambiguous rules that create a script:

问题 I'm building an SQL script out of text data. The (part of) script shall consist of a CREATE TABLE statement and an optional INSERT INTO statement. The values for INSERT INTO statement are taken from the list of files, each one may exist or may not; all values of existing files are merged. The crucial part is that the INSERT INTO statement shall be skipped whenever no one data file exists. I've created a script in Snakemake that does that. There are two ambiguous rules that create a script:

问题 Say I'm following the best practise workflow suggested for snakemake. Now I'd like to know how (i.e. which version) a given file, say plots/myplot.pdf , was generated. I found this surprisingly hard if not impossible only having the result folder at hand. In more detail, say I was generated the results using. snakemake --use-conda --conda-prefix ~/.conda/myenvs which will resolve and download the conda-environments specified in the rule below (copied from the documentation): rule NAME: input:

问题 I know three working ways to define a wrapper-based rule in a Snakefile: rule way1_wrapper_repository: wrapper: "0.0.8/bio/samtools_sort" rule way2_local_relative_directory: wrapper: "local_wrappers/dir/samtools_sort" rule way3_local_absolute_directory: wrapper: "file:///absolute/path/to/wrapper/samtools_sort" The documentation states: Alternatively, e.g., for development, the wrapper directive can also point to full URLs, including URLs to local files with absolute paths file:// or relative

问题 I know three working ways to define a wrapper-based rule in a Snakefile: rule way1_wrapper_repository: wrapper: "0.0.8/bio/samtools_sort" rule way2_local_relative_directory: wrapper: "local_wrappers/dir/samtools_sort" rule way3_local_absolute_directory: wrapper: "file:///absolute/path/to/wrapper/samtools_sort" The documentation states: Alternatively, e.g., for development, the wrapper directive can also point to full URLs, including URLs to local files with absolute paths file:// or relative

问题 This is a very strange problem. When my {input} specified in the rule section is a list of <200 files, snakemake worked all right. But when {input} has more than 500 files, snakemake just quitted with messages (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) . The complete log did not provide any error messages. For the log, please see: https://github.com/snakemake/snakemake/files/5285271/2020-09-25T151835.613199.snakemake.log The rule that

问题 I am using snakemake to design a RNAseq-data analysis pipeline. While I've managed to do that, I want to make my pipeline to be as adaptable as possible and make it able to deal with single-reads (SE) data or paired-end (PE) data within the same run of analyses, instead of analysing SE data in one run and PE data in another. My pipeline is supposed to be designed like this : dataset download that gives 1 file (SE data) or 2 files (PE data) --> set of rules A specific to 1 file OR set of rules

问题 I am trying to combine Snakemake with Singularity, and I noticed that a simple awk command no longer works when using singularity. The $1 in the last line gets replaced by bash instead of being used as the first field by awk . Here is a minimal working example ( Snakefile ): singularity: "docker://debian:stretch" rule all: input: "test.txt" rule test: output: "test.txt" shell: "cat /etc/passwd | awk -F':' '{{print $1}}' > {output}" When I run snakemake without singularity, the output test.txt

问题 I am trying to combine Snakemake with Singularity, and I noticed that a simple awk command no longer works when using singularity. The $1 in the last line gets replaced by bash instead of being used as the first field by awk . Here is a minimal working example ( Snakefile ): singularity: "docker://debian:stretch" rule all: input: "test.txt" rule test: output: "test.txt" shell: "cat /etc/passwd | awk -F':' '{{print $1}}' > {output}" When I run snakemake without singularity, the output test.txt