jsquaredosquared/novocraft-sv-benchmarking

Comparing performance of SV callers when using NovoAlign vs other aligners.

Overview

Latest release: None, Last update: 2024-11-29

Linting: linting: failed, Formatting: formatting: failed

Topics: sv-calling novoalign

Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Mamba package manager (a drop-in replacement for conda). If you have neither Conda nor Mamba, it is recommended to install Miniforge. More details regarding Mamba can be found here.

When using Mamba, run

mamba create -c conda-forge -c bioconda --name snakemake snakemake snakedeploy

to install both Snakemake and Snakedeploy in an isolated environment. For all following commands ensure that this environment is activated via

conda activate snakemake

Step 2: Deploy workflow

With Snakemake and Snakedeploy installed, the workflow can be deployed as follows. First, create an appropriate project working directory on your system and enter it:

mkdir -p path/to/project-workdir
cd path/to/project-workdir

In all following steps, we will assume that you are inside of that directory. Then run

snakedeploy deploy-workflow https://github.com/jsquaredosquared/novocraft-sv-benchmarking . --tag None

Snakedeploy will create two folders, workflow and config. The former contains the deployment of the chosen workflow as a Snakemake module, the latter contains configuration files which will be modified in the next step in order to configure the workflow to your needs.

Step 3: Configure workflow

To configure the workflow, adapt config/config.yml to your needs following the instructions below.

Step 4: Run workflow

The deployment method is controlled using the --software-deployment-method (short --sdm) argument.

To run the workflow with automatic deployment of all required software via conda/mamba, use

snakemake --cores all --sdm conda

Snakemake will automatically detect the main Snakefile in the workflow subfolder and execute the workflow module that has been defined by the deployment in step 2.

For further options such as cluster and cloud execution, see the docs.

Step 5: Generate report

After finalizing your data analysis, you can automatically generate an interactive visual HTML report for inspection of results together with parameters and code inside of the browser using

snakemake --report report.zip

Configuration

The following section is imported from the workflow’s config/README.md.

Configuration

Please see the "Usage" section of the main README.md file for more information on configuring the workflow.

Linting and formatting

Linting results

  1Lints for snakefile /tmp/tmp5ctl5twu/workflow/rules/01_align.smk:
  2    * Mixed rules and functions in same snakefile.:
  3      Small one-liner functions used only once should be defined as lambda
  4      expressions. Other functions should be collected in a common module, e.g.
  5      'rules/common.smk'. This makes the workflow steps more readable.
  6      Also see:
  7      https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes
  8
  9Lints for snakefile /tmp/tmp5ctl5twu/workflow/rules/03_benchmark.smk:
 10    * Mixed rules and functions in same snakefile.:
 11      Small one-liner functions used only once should be defined as lambda
 12      expressions. Other functions should be collected in a common module, e.g.
 13      'rules/common.smk'. This makes the workflow steps more readable.
 14      Also see:
 15      https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes
 16
 17Lints for rule download_reference (line 1, /tmp/tmp5ctl5twu/workflow/rules/00_prepare.smk):
 18    * Specify a conda environment or container for each rule.:
 19      This way, the used software for each specific step is documented, and the
 20      workflow can be executed on any machine without prerequisites.
 21      Also see:
 22      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 23      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 24
 25Lints for rule novoindex_reference (line 12, /tmp/tmp5ctl5twu/workflow/rules/00_prepare.smk):
 26    * Specify a conda environment or container for each rule.:
 27      This way, the used software for each specific step is documented, and the
 28      workflow can be executed on any machine without prerequisites.
 29      Also see:
 30      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 31      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 32    * Shell command directly uses variable config from outside of the rule:
 33      It is recommended to pass all files as input and output, and non-file
 34      parameters via the params directive. Otherwise, provenance tracking is
 35      less accurate.
 36      Also see:
 37      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
 38
 39Lints for rule download_hg002_fastqs (line 56, /tmp/tmp5ctl5twu/workflow/rules/00_prepare.smk):
 40    * Do not access input and output files individually by index in shell commands:
 41      When individual access to input or output files is needed (i.e., just
 42      writing '{input}' is impossible), use names ('{input.somename}') instead
 43      of index based access.
 44      Also see:
 45      https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules
 46    * Specify a conda environment or container for each rule.:
 47      This way, the used software for each specific step is documented, and the
 48      workflow can be executed on any machine without prerequisites.
 49      Also see:
 50      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 51      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 52
 53Lints for rule download_hg002_tier1_sv_truth_set (line 68, /tmp/tmp5ctl5twu/workflow/rules/00_prepare.smk):
 54    * Do not access input and output files individually by index in shell commands:
 55      When individual access to input or output files is needed (i.e., just
 56      writing '{input}' is impossible), use names ('{input.somename}') instead
 57      of index based access.
 58      Also see:
 59      https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules
 60    * Specify a conda environment or container for each rule.:
 61      This way, the used software for each specific step is documented, and the
 62      workflow can be executed on any machine without prerequisites.
 63      Also see:
 64      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 65      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 66
 67Lints for rule download_delly_exclude (line 85, /tmp/tmp5ctl5twu/workflow/rules/00_prepare.smk):
 68    * Specify a conda environment or container for each rule.:
 69      This way, the used software for each specific step is documented, and the
 70      workflow can be executed on any machine without prerequisites.
 71      Also see:
 72      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 73      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 74
 75Lints for rule align_with_novoalign (line 40, /tmp/tmp5ctl5twu/workflow/rules/01_align.smk):
 76    * Shell command directly uses variable config from outside of the rule:
 77      It is recommended to pass all files as input and output, and non-file
 78      parameters via the params directive. Otherwise, provenance tracking is
 79      less accurate.
 80      Also see:
 81      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
 82
 83Lints for rule configure_manta (line 1, /tmp/tmp5ctl5twu/workflow/rules/02_call.smk):
 84    * Do not access input and output files individually by index in shell commands:
 85      When individual access to input or output files is needed (i.e., just
 86      writing '{input}' is impossible), use names ('{input.somename}') instead
 87      of index based access.
 88      Also see:
 89      https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules
 90    * Shell command directly uses variable config from outside of the rule:
 91      It is recommended to pass all files as input and output, and non-file
 92      parameters via the params directive. Otherwise, provenance tracking is
 93      less accurate.
 94      Also see:
 95      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
 96
 97Lints for rule run_dysgu (line 38, /tmp/tmp5ctl5twu/workflow/rules/02_call.smk):
 98    * Do not access input and output files individually by index in shell commands:
 99      When individual access to input or output files is needed (i.e., just
100      writing '{input}' is impossible), use names ('{input.somename}') instead
101      of index based access.
102      Also see:
103      https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules
104    * Shell command directly uses variable config from outside of the rule:
105      It is recommended to pass all files as input and output, and non-file
106      parameters via the params directive. Otherwise, provenance tracking is
107      less accurate.
108      Also see:
109      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
110
111Lints for rule run_delly (line 60, /tmp/tmp5ctl5twu/workflow/rules/02_call.smk):
112    * Do not access input and output files individually by index in shell commands:
113      When individual access to input or output files is needed (i.e., just
114      writing '{input}' is impossible), use names ('{input.somename}') instead
115      of index based access.
116      Also see:
117      https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules
118    * Shell command directly uses variable config from outside of the rule:
119      It is recommended to pass all files as input and output, and non-file
120      parameters via the params directive. Otherwise, provenance tracking is
121      less accurate.
122      Also see:
123      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
124
125Lints for rule run_smoove (line 79, /tmp/tmp5ctl5twu/workflow/rules/02_call.smk):
126    * Do not access input and output files individually by index in shell commands:
127      When individual access to input or output files is needed (i.e., just
128      writing '{input}' is impossible), use names ('{input.somename}') instead
129      of index based access.
130      Also see:
131      https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules
132    * Shell command directly uses variable config from outside of the rule:
133      It is recommended to pass all files as input and output, and non-file
134      parameters via the params directive. Otherwise, provenance tracking is
135      less accurate.
136      Also see:
137      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
138
139Lints for rule run_tiddit (line 107, /tmp/tmp5ctl5twu/workflow/rules/02_call.smk):
140    * Do not access input and output files individually by index in shell commands:
141      When individual access to input or output files is needed (i.e., just
142      writing '{input}' is impossible), use names ('{input.somename}') instead
143      of index based access.
144      Also see:
145      https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules
146    * Shell command directly uses variable config from outside of the rule:
147      It is recommended to pass all files as input and output, and non-file
148      parameters via the params directive. Otherwise, provenance tracking is
149      less accurate.
150      Also see:
151      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
152
153Lints for rule run_insurveyor (line 125, /tmp/tmp5ctl5twu/workflow/rules/02_call.smk):
154    * Do not access input and output files individually by index in shell commands:
155      When individual access to input or output files is needed (i.e., just
156      writing '{input}' is impossible), use names ('{input.somename}') instead
157      of index based access.
158      Also see:
159      https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules
160    * Shell command directly uses variable config from outside of the rule:
161      It is recommended to pass all files as input and output, and non-file
162      parameters via the params directive. Otherwise, provenance tracking is
163      less accurate.
164      Also see:
165      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
166    * Shell command directly uses variable config from outside of the rule:
167      It is recommended to pass all files as input and output, and non-file
168      parameters via the params directive. Otherwise, provenance tracking is
169      less accurate.
170      Also see:
171      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
172
173Lints for rule bgzip_and_index_sv_vcf (line 151, /tmp/tmp5ctl5twu/workflow/rules/02_call.smk):
174    * Do not access input and output files individually by index in shell commands:
175      When individual access to input or output files is needed (i.e., just
176      writing '{input}' is impossible), use names ('{input.somename}') instead
177      of index based access.
178      Also see:
179      https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules
180
181Lints for rule split_truth_set_by_svtype (line 9, /tmp/tmp5ctl5twu/workflow/rules/03_benchmark.smk):
182    * Do not access input and output files individually by index in shell commands:
183      When individual access to input or output files is needed (i.e., just
184      writing '{input}' is impossible), use names ('{input.somename}') instead
185      of index based access.
186      Also see:
187      https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules
188
189Lints for rule generate_plots (line 1, /tmp/tmp5ctl5twu/workflow/rules/04_compare.smk):
190    * No log directive defined:
191      Without a log directive, all output will be printed to the terminal. In
192      distributed environments, this means that errors are harder to discover.
193      In local environments, output of concurrent jobs will be mixed and become
194      unreadable.
195      Also see:
196      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files

Formatting results

 1[DEBUG] 
 2[DEBUG] In file "/tmp/tmp5ctl5twu/workflow/rules/02_call.smk":  Formatted content is different from original
 3[DEBUG] 
 4[DEBUG] In file "/tmp/tmp5ctl5twu/workflow/rules/01_align.smk":  Formatted content is different from original
 5[DEBUG] 
 6[DEBUG] 
 7[DEBUG] 
 8[DEBUG] 
 9[DEBUG] In file "/tmp/tmp5ctl5twu/workflow/rules/03_benchmark.smk":  Formatted content is different from original
10[INFO] 3 file(s) would be changed 😬
11[INFO] 3 file(s) would be left unchanged 🎉
12
13snakefmt version: 0.10.2