annotate 1.0.0/modules/custom/dump_software_versions/README.md @ 0:801b85b03a17 draft default tip

planemo upload
author galaxytrakr
date Thu, 28 May 2026 20:31:42 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
1 # NextFlow DSL2 Module
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
2
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
3 ```bash
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
4 DUMP_SOFTWARE_VERSIONS
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
5 ```
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
6
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
7 ## Description
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
8
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
9 Given an `YAML` format file, produce a final `.yml` file which has unique entries and a corresponding `.mqc.yml` file for use with `multiqc`.
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
10
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
11 \
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
12  
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
13
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
14 ### `input:`
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
15
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
16 ___
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
17
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
18 Type: `path`
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
19
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
20 Takes in a `path` (`versions`) type pointing to the file to be used to produce a final `.yml` file without any duplicate entries and a `.mqc.yml` file. Generally, this is passed by mixing `versions` from various run time channels and finally passed to this module to produce a final software versions list.
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
21
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
22 Ex:
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
23
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
24 ```groovy
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
25 [ '/hpc/scratch/test/work/9b/e7bf7e28806419c1c9a571dacd1f67/versions.yml' ]
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
26 ```
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
27
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
28 \
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
29  
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
30
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
31 ### `output:`
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
32
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
33 ___
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
34
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
35 #### `yml`
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
36
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
37 Type: `path`
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
38
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
39 NextFlow output type of `path` type pointing to an `YAML` file with software versions.
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
40
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
41 \
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
42  
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
43
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
44 #### `mqc_yml`
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
45
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
46 Type: `path`
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
47
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
48 NextFlow output type of `path` pointing to `.mqc.yml` file which can be used to produce a software versions' table with `multiqc`.
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
49
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
50 \
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
51  
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
52
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
53 #### `versions`
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
54
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
55 Type: `path`
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
56
801b85b03a17 planemo upload
galaxytrakr
parents:
diff changeset
57 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.