CBIbigA/hicstuff_pipeline
hicstuff_pipeline
Overview
Topics:
Latest release: None, Last update: 2022-02-17
Linting: linting: failed, Formatting: formatting: failed
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/CBIbigA/hicstuff_pipeline . --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.
Linting and formatting
Linting results
1Lints for snakefile /tmp/tmp27xhe6tc/workflow/Snakefile:
2 * Path composition with '+' in line 21:
3 This becomes quickly unreadable. Usually, it is better to endure some
4 redundancy against having a more readable workflow. Hence, just repeat
5 common prefixes. If path composition is unavoidable, use pathlib or
6 (python >= 3.6) string formatting with f"...".
7 Also see:
8
9
10Lints for snakefile /tmp/tmp27xhe6tc/workflow/rules/cooler.smk:
11 * Path composition with '+' in line 3:
12 This becomes quickly unreadable. Usually, it is better to endure some
13 redundancy against having a more readable workflow. Hence, just repeat
14 common prefixes. If path composition is unavoidable, use pathlib or
15 (python >= 3.6) string formatting with f"...".
16 Also see:
17
18 * Path composition with '+' in line 6:
19 This becomes quickly unreadable. Usually, it is better to endure some
20 redundancy against having a more readable workflow. Hence, just repeat
21 common prefixes. If path composition is unavoidable, use pathlib or
22 (python >= 3.6) string formatting with f"...".
23 Also see:
24
25 * Path composition with '+' in line 8:
26 This becomes quickly unreadable. Usually, it is better to endure some
27 redundancy against having a more readable workflow. Hence, just repeat
28 common prefixes. If path composition is unavoidable, use pathlib or
29 (python >= 3.6) string formatting with f"...".
30 Also see:
31
32 * Path composition with '+' in line 10:
33 This becomes quickly unreadable. Usually, it is better to endure some
34 redundancy against having a more readable workflow. Hence, just repeat
35 common prefixes. If path composition is unavoidable, use pathlib or
36 (python >= 3.6) string formatting with f"...".
37 Also see:
38
39 * Path composition with '+' in line 20:
40 This becomes quickly unreadable. Usually, it is better to endure some
41 redundancy against having a more readable workflow. Hence, just repeat
42 common prefixes. If path composition is unavoidable, use pathlib or
43 (python >= 3.6) string formatting with f"...".
44 Also see:
45
46 * Path composition with '+' in line 22:
47 This becomes quickly unreadable. Usually, it is better to endure some
48 redundancy against having a more readable workflow. Hence, just repeat
49 common prefixes. If path composition is unavoidable, use pathlib or
50 (python >= 3.6) string formatting with f"...".
51 Also see:
52
53 * Path composition with '+' in line 24:
54 This becomes quickly unreadable. Usually, it is better to endure some
55 redundancy against having a more readable workflow. Hence, just repeat
56 common prefixes. If path composition is unavoidable, use pathlib or
57 (python >= 3.6) string formatting with f"...".
58 Also see:
59
60 * Path composition with '+' in line 26:
61 This becomes quickly unreadable. Usually, it is better to endure some
62 redundancy against having a more readable workflow. Hence, just repeat
63 common prefixes. If path composition is unavoidable, use pathlib or
64 (python >= 3.6) string formatting with f"...".
65 Also see:
66
67
68Lints for snakefile /tmp/tmp27xhe6tc/workflow/rules/cutadapt.smk:
69 * Path composition with '+' in line 8:
70 This becomes quickly unreadable. Usually, it is better to endure some
71 redundancy against having a more readable workflow. Hence, just repeat
72 common prefixes. If path composition is unavoidable, use pathlib or
73 (python >= 3.6) string formatting with f"...".
74 Also see:
75
76 * Path composition with '+' in line 15:
77 This becomes quickly unreadable. Usually, it is better to endure some
78 redundancy against having a more readable workflow. Hence, just repeat
79 common prefixes. If path composition is unavoidable, use pathlib or
80 (python >= 3.6) string formatting with f"...".
81 Also see:
82
83
84Lints for snakefile /tmp/tmp27xhe6tc/workflow/rules/hicstuff.smk:
85 * Path composition with '+' in line 21:
86 This becomes quickly unreadable. Usually, it is better to endure some
87 redundancy against having a more readable workflow. Hence, just repeat
88 common prefixes. If path composition is unavoidable, use pathlib or
89 (python >= 3.6) string formatting with f"...".
90 Also see:
91
92 * Path composition with '+' in line 25:
93 This becomes quickly unreadable. Usually, it is better to endure some
94 redundancy against having a more readable workflow. Hence, just repeat
95 common prefixes. If path composition is unavoidable, use pathlib or
96 (python >= 3.6) string formatting with f"...".
97 Also see:
98
99 * Path composition with '+' in line 27:
100 This becomes quickly unreadable. Usually, it is better to endure some
101 redundancy against having a more readable workflow. Hence, just repeat
102 common prefixes. If path composition is unavoidable, use pathlib or
103 (python >= 3.6) string formatting with f"...".
104 Also see:
105
106 * Path composition with '+' in line 37:
107 This becomes quickly unreadable. Usually, it is better to endure some
108 redundancy against having a more readable workflow. Hence, just repeat
109 common prefixes. If path composition is unavoidable, use pathlib or
110 (python >= 3.6) string formatting with f"...".
111 Also see:
112
113 * Path composition with '+' in line 2:
114 This becomes quickly unreadable. Usually, it is better to endure some
115 redundancy against having a more readable workflow. Hence, just repeat
116 common prefixes. If path composition is unavoidable, use pathlib or
117 (python >= 3.6) string formatting with f"...".
118 Also see:
119
120 * Path composition with '+' in line 25:
121 This becomes quickly unreadable. Usually, it is better to endure some
122 redundancy against having a more readable workflow. Hence, just repeat
123 common prefixes. If path composition is unavoidable, use pathlib or
124 (python >= 3.6) string formatting with f"...".
125 Also see:
126
127
128Lints for snakefile /tmp/tmp27xhe6tc/workflow/rules/juicertools.smk:
129 * Path composition with '+' in line 25:
130 This becomes quickly unreadable. Usually, it is better to endure some
131 redundancy against having a more readable workflow. Hence, just repeat
132 common prefixes. If path composition is unavoidable, use pathlib or
133 (python >= 3.6) string formatting with f"...".
134 Also see:
135
136 * Path composition with '+' in line 29:
137 This becomes quickly unreadable. Usually, it is better to endure some
138 redundancy against having a more readable workflow. Hence, just repeat
139 common prefixes. If path composition is unavoidable, use pathlib or
140 (python >= 3.6) string formatting with f"...".
141 Also see:
142
143 * Path composition with '+' in line 31:
144 This becomes quickly unreadable. Usually, it is better to endure some
145 redundancy against having a more readable workflow. Hence, just repeat
146 common prefixes. If path composition is unavoidable, use pathlib or
147 (python >= 3.6) string formatting with f"...".
148 Also see:
149
150 * Path composition with '+' in line 33:
151 This becomes quickly unreadable. Usually, it is better to endure some
152 redundancy against having a more readable workflow. Hence, just repeat
153 common prefixes. If path composition is unavoidable, use pathlib or
154 (python >= 3.6) string formatting with f"...".
155 Also see:
156
157 * Path composition with '+' in line 6:
158 This becomes quickly unreadable. Usually, it is better to endure some
159 redundancy against having a more readable workflow. Hence, just repeat
160 common prefixes. If path composition is unavoidable, use pathlib or
161 (python >= 3.6) string formatting with f"...".
162 Also see:
163
164
165Lints for snakefile /tmp/tmp27xhe6tc/workflow/rules/makeChromSize.smk:
166 * Path composition with '+' in line 7:
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
174Lints for snakefile /tmp/tmp27xhe6tc/workflow/rules/pairtools.smk:
175 * Path composition with '+' in line 3:
176 This becomes quickly unreadable. Usually, it is better to endure some
177 redundancy against having a more readable workflow. Hence, just repeat
178 common prefixes. If path composition is unavoidable, use pathlib or
179 (python >= 3.6) string formatting with f"...".
180 Also see:
181
182 * Path composition with '+' in line 5:
183 This becomes quickly unreadable. Usually, it is better to endure some
184 redundancy against having a more readable workflow. Hence, just repeat
185 common prefixes. If path composition is unavoidable, use pathlib or
186 (python >= 3.6) string formatting with f"...".
187 Also see:
188
189 * Path composition with '+' in line 7:
190 This becomes quickly unreadable. Usually, it is better to endure some
191 redundancy against having a more readable workflow. Hence, just repeat
192 common prefixes. If path composition is unavoidable, use pathlib or
193 (python >= 3.6) string formatting with f"...".
194 Also see:
195
196 * Path composition with '+' in line 9:
197 This becomes quickly unreadable. Usually, it is better to endure some
198 redundancy against having a more readable workflow. Hence, just repeat
199 common prefixes. If path composition is unavoidable, use pathlib or
200 (python >= 3.6) string formatting with f"...".
201
202... (truncated)
Formatting results
1[DEBUG]
2[DEBUG] In file "/tmp/tmp27xhe6tc/workflow/rules/pairtools.smk": Formatted content is different from original
3[DEBUG]
4[DEBUG] In file "/tmp/tmp27xhe6tc/workflow/rules/hicstuff.smk": Formatted content is different from original
5[DEBUG]
6[DEBUG] In file "/tmp/tmp27xhe6tc/workflow/Snakefile": Formatted content is different from original
7[DEBUG]
8[DEBUG] In file "/tmp/tmp27xhe6tc/workflow/rules/juicertools.smk": Formatted content is different from original
9[DEBUG]
10[DEBUG] In file "/tmp/tmp27xhe6tc/workflow/rules/makeChromSize.smk": Formatted content is different from original
11[DEBUG]
12[DEBUG] In file "/tmp/tmp27xhe6tc/workflow/rules/cutadapt.smk": Formatted content is different from original
13[DEBUG]
14[DEBUG] In file "/tmp/tmp27xhe6tc/workflow/rules/cooler.smk": Formatted content is different from original
15[INFO] 7 file(s) would be changed 😬
16
17snakefmt version: 0.5.0