rochevin/RNA-seq-from-SRR-single
None
Overview
Topics:
Latest release: None, Last update: 2022-02-15
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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/rochevin/RNA-seq-from-SRR-single . --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
.
Describe how to configure the workflow (using config.yaml and maybe additional files). All of them need to be present with example entries inside of the config folder.
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Linting results
1Lints for snakefile /tmp/tmp2dbexe33/workflow/Snakefile:
2 * Absolute path "/mapping/bam/{sample}.sorted.bai" in line 40:
3 Do not define absolute paths inside of the workflow, since this renders
4 your workflow irreproducible on other machines. Use path relative to the
5 working directory instead, or make the path configurable via a config
6 file.
7 Also see:
8 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
9 * Absolute path "/mapping/counts/STAR/{sample}_counts.tsv" in line 41:
10 Do not define absolute paths inside of the workflow, since this renders
11 your workflow irreproducible on other machines. Use path relative to the
12 working directory instead, or make the path configurable via a config
13 file.
14 Also see:
15 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
16 * Path composition with '+' in line 40:
17 This becomes quickly unreadable. Usually, it is better to endure some
18 redundancy against having a more readable workflow. Hence, just repeat
19 common prefixes. If path composition is unavoidable, use pathlib or
20 (python >= 3.6) string formatting with f"...".
21 Also see:
22
23 * Path composition with '+' in line 41:
24 This becomes quickly unreadable. Usually, it is better to endure some
25 redundancy against having a more readable workflow. Hence, just repeat
26 common prefixes. If path composition is unavoidable, use pathlib or
27 (python >= 3.6) string formatting with f"...".
28 Also see:
29
30
31Lints for snakefile /tmp/tmp2dbexe33/workflow/rules/SRR.smk:
32 * Absolute path "/{prefix}_1" in line 14:
33 Do not define absolute paths inside of the workflow, since this renders
34 your workflow irreproducible on other machines. Use path relative to the
35 working directory instead, or make the path configurable via a config
36 file.
37 Also see:
38 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
39 * Absolute path "/benchmarks/fastqdump/{prefix}.benchmark.txt" in line 15:
40 Do not define absolute paths inside of the workflow, since this renders
41 your workflow irreproducible on other machines. Use path relative to the
42 working directory instead, or make the path configurable via a config
43 file.
44 Also see:
45 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
46 * Absolute path "/benchmarks/mergefastq/{sample}.benchmark.txt" in line 32:
47 Do not define absolute paths inside of the workflow, since this renders
48 your workflow irreproducible on other machines. Use path relative to the
49 working directory instead, or make the path configurable via a config
50 file.
51 Also see:
52 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
53 * Mixed rules and functions in same snakefile.:
54 Small one-liner functions used only once should be defined as lambda
55 expressions. Other functions should be collected in a common module, e.g.
56 'rules/common.smk'. This makes the workflow steps more readable.
57 Also see:
58 https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes
59 * Path composition with '+' in line 15:
60 This becomes quickly unreadable. Usually, it is better to endure some
61 redundancy against having a more readable workflow. Hence, just repeat
62 common prefixes. If path composition is unavoidable, use pathlib or
63 (python >= 3.6) string formatting with f"...".
64 Also see:
65
66 * Path composition with '+' in line 32:
67 This becomes quickly unreadable. Usually, it is better to endure some
68 redundancy against having a more readable workflow. Hence, just repeat
69 common prefixes. If path composition is unavoidable, use pathlib or
70 (python >= 3.6) string formatting with f"...".
71 Also see:
72
73 * Path composition with '+' in line 3:
74 This becomes quickly unreadable. Usually, it is better to endure some
75 redundancy against having a more readable workflow. Hence, just repeat
76 common prefixes. If path composition is unavoidable, use pathlib or
77 (python >= 3.6) string formatting with f"...".
78 Also see:
79
80 * Path composition with '+' in line 9:
81 This becomes quickly unreadable. Usually, it is better to endure some
82 redundancy against having a more readable workflow. Hence, just repeat
83 common prefixes. If path composition is unavoidable, use pathlib or
84 (python >= 3.6) string formatting with f"...".
85 Also see:
86
87 * Path composition with '+' in line 11:
88 This becomes quickly unreadable. Usually, it is better to endure some
89 redundancy against having a more readable workflow. Hence, just repeat
90 common prefixes. If path composition is unavoidable, use pathlib or
91 (python >= 3.6) string formatting with f"...".
92 Also see:
93
94 * Path composition with '+' in line 15:
95 This becomes quickly unreadable. Usually, it is better to endure some
96 redundancy against having a more readable workflow. Hence, just repeat
97 common prefixes. If path composition is unavoidable, use pathlib or
98 (python >= 3.6) string formatting with f"...".
99 Also see:
100
101
102Lints for snakefile /tmp/tmp2dbexe33/workflow/rules/STAR_quant.smk:
103 * Absolute path "/benchmarks/star_index_gtf/{input.fasta}.benchmark.txt" in line 14:
104 Do not define absolute paths inside of the workflow, since this renders
105 your workflow irreproducible on other machines. Use path relative to the
106 working directory instead, or make the path configurable via a config
107 file.
108 Also see:
109 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
110 * Absolute path "/mapping/sam/{sample}/{sample}_Aligned.out.sam" in line 30:
111 Do not define absolute paths inside of the workflow, since this renders
112 your workflow irreproducible on other machines. Use path relative to the
113 working directory instead, or make the path configurable via a config
114 file.
115 Also see:
116 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
117 * Absolute path "/mapping/sam/{sample}/{sample}_ReadsPerGene.out.tab" in line 31:
118 Do not define absolute paths inside of the workflow, since this renders
119 your workflow irreproducible on other machines. Use path relative to the
120 working directory instead, or make the path configurable via a config
121 file.
122 Also see:
123 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
124 * Absolute path "/mapping/sam/{sample}/{sample}_" in line 38:
125 Do not define absolute paths inside of the workflow, since this renders
126 your workflow irreproducible on other machines. Use path relative to the
127 working directory instead, or make the path configurable via a config
128 file.
129 Also see:
130 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
131 * Absolute path "/benchmarks/star_aln/{sample}.benchmark.txt" in line 44:
132 Do not define absolute paths inside of the workflow, since this renders
133 your workflow irreproducible on other machines. Use path relative to the
134 working directory instead, or make the path configurable via a config
135 file.
136 Also see:
137 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
138 * Absolute path "/mapping/sam/{sample}/{sample}_ReadsPerGene.out.tab" in line 60:
139 Do not define absolute paths inside of the workflow, since this renders
140 your workflow irreproducible on other machines. Use path relative to the
141 working directory instead, or make the path configurable via a config
142 file.
143 Also see:
144 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
145 * Absolute path "/mapping/counts/STAR/{sample}_counts.tsv" in line 61:
146 Do not define absolute paths inside of the workflow, since this renders
147 your workflow irreproducible on other machines. Use path relative to the
148 working directory instead, or make the path configurable via a config
149 file.
150 Also see:
151 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
152 * Absolute path "/benchmarks/cp_STAR_quant_to_counts/{sample}.benchmark.txt" in line 64:
153 Do not define absolute paths inside of the workflow, since this renders
154 your workflow irreproducible on other machines. Use path relative to the
155 working directory instead, or make the path configurable via a config
156 file.
157 Also see:
158 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
159 * Path composition with '+' in line 4:
160 This becomes quickly unreadable. Usually, it is better to endure some
161 redundancy against having a more readable workflow. Hence, just repeat
162 common prefixes. If path composition is unavoidable, use pathlib or
163 (python >= 3.6) string formatting with f"...".
164 Also see:
165
166 * Path composition with '+' in line 30:
167 This becomes quickly unreadable. Usually, it is better to endure some
168 redundancy against having a more readable workflow. Hence, just repeat
169 common prefixes. If path composition is unavoidable, use pathlib or
170 (python >= 3.6) string formatting with f"...".
171 Also see:
172
173 * Path composition with '+' in line 31:
174 This becomes quickly unreadable. Usually, it is better to endure some
175 redundancy against having a more readable workflow. Hence, just repeat
176 common prefixes. If path composition is unavoidable, use pathlib or
177 (python >= 3.6) string formatting with f"...".
178 Also see:
179
180 * Path composition with '+' in line 34:
181 This becomes quickly unreadable. Usually, it is better to endure some
182 redundancy against having a more readable workflow. Hence, just repeat
183 common prefixes. If path composition is unavoidable, use pathlib or
184 (python >= 3.6) string formatting with f"...".
185 Also see:
186
187 * Path composition with '+' in line 44:
188 This becomes quickly unreadable. Usually, it is better to endure some
189 redundancy against having a more readable workflow. Hence, just repeat
190 common prefixes. If path composition is unavoidable, use pathlib or
191 (python >= 3.6) string formatting with f"...".
192 Also see:
193
194 * Path composition with '+' in line 60:
195 This becomes quickly unreadable. Usually, it is better to endure some
196 redundancy against having a more readable workflow. Hence, just repeat
197 common prefixes. If path composition is unavoidable, use pathlib or
198 (python >= 3.6) string formatting with f"...".
199 Also see:
200
201
202... (truncated)
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1TypeError: cannot unpack non-iterable PosixPath object
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3snakefmt version: 0.5.0