Skip to content

Commit 9e82dc8

Browse files
mvdbeekmvdbeek
authored
Merge pull request #1100 from SantaMcCloud/update_func_protein_annot_wf
Update Functional_annotation_of_protein_sequences WF
2 parents c3d6828 + 06d0c1d commit 9e82dc8

File tree

9 files changed

+1425
-245
lines changed

9 files changed

+1425
-245
lines changed

workflows/genome_annotation/functional-annotation/functional-annotation-protein-sequences/.dockstore.yml renamed to workflows/genome_annotation/functional-annotation/functional-annotation-of-sequences/.dockstore.yml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -3,9 +3,9 @@ workflows:
33
- name: main
44
subclass: Galaxy
55
publish: true
6-
primaryDescriptorPath: /Functional_annotation_of_protein_sequences.ga
6+
primaryDescriptorPath: /Functional_annotation_of_sequences.ga
77
testParameterFiles:
8-
- /Functional_annotation_of_protein_sequences-tests.yml
8+
- /Functional_annotation_of_sequences-tests.yml
99
authors:
1010
- name: Romane Libouban
1111
email: romane.libouban@irisa.fr

‎workflows/genome_annotation/functional-annotation/functional-annotation-of-sequences/CHANGELOG.md‎

Lines changed: 14 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,14 @@
1+
# Changelog
2+
3+
## [0.2] - 2026-02-07
4+
5+
- Change the input to a collection such that multiple sequences can be run in parallel
6+
- Add a subworkflow that allows to run eggNOG with different types of sequences (protein, CDS, genome and metagenome).
7+
- Add the option that eggNOG and/or InterProScan can be skipped
8+
- Add the option to swap the input type for InterProScan
9+
- Add toolshed.g2.bx.psu.edu/repos/iuc/kegg_pathways_completeness/kegg_pathways_completeness/1.3.0+galaxy0 to calculate the pathway completeness with KOs coming from eggNOG
10+
- Change name of the workflow since now it is not specific for proteins anymore
11+
12+
## [0.1] - 2024-12-04
13+
14+
Initial version of the Functional annotation of protein sequence Workflow.

‎workflows/genome_annotation/functional-annotation/functional-annotation-of-sequences/Functional_annotation_of_sequences-tests.yml‎

Lines changed: 88 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,88 @@
1+
- doc: Test outline for Functional_annotation_of_sequences.ga for protein
2+
job:
3+
Sequence collection:
4+
class: Collection
5+
collection_type: list
6+
elements:
7+
- class: File
8+
identifier: test-sequence
9+
location: https://zenodo.org/record/8414802/files/protein_sequences.fasta
10+
filetype: fasta
11+
hashes:
12+
- hash_function: SHA-1
13+
hash_value: 0e1026d6917ac03bcd174a85b18e69c2a6470f98
14+
Run eggNOG + completeness calculation: true
15+
Run InterProScan: true
16+
eggNOG mode select: proteins
17+
InterProScan mode select: Protein
18+
outputs:
19+
interproscan xml:
20+
element_tests:
21+
test-sequence:
22+
location: https://zenodo.org/records/13951790/files/interProScan.xml?download=1&preview=1
23+
compare: sim_size
24+
delta: 7000000
25+
interproscan tabular:
26+
element_tests:
27+
test-sequence:
28+
location: https://zenodo.org/records/13951790/files/interProScan.tabular?download=1&preview=1
29+
compare: sim_size
30+
delta: 2000000
31+
kegg pathways table:
32+
asserts:
33+
- that: "has_text"
34+
text: "module_accession completeness pathway_name pathway_class matching_ko missing_ko"
35+
- doc: Test outline for Functional_annotation_of_protein_sequences.ga for metagenome
36+
job:
37+
Sequence collection:
38+
class: Collection
39+
collection_type: list
40+
elements:
41+
- class: File
42+
identifier: 50contig_reads_binette_bin1.fasta
43+
location: https://zenodo.org/records/18635101/files/50contig_reads_binette_bin2.fasta
44+
- class: File
45+
identifier: 50contig_reads_binette_bin2.fasta
46+
location: https://zenodo.org/records/18635101/files/50contig_reads_binette_bin3.fasta
47+
Run eggNOG + completeness calculation: true
48+
Run InterProScan: false
49+
eggNOG mode select: metagenome
50+
InterProScan mode select: DNA/RNA
51+
outputs:
52+
kegg pathways table:
53+
asserts:
54+
- that: "has_text"
55+
text: "module_accession completeness pathway_name pathway_class matching_ko missing_ko"
56+
- that: "has_n_lines"
57+
n: 3
58+
delta: 1
59+
- doc: Test outline for Functional_annotation_of_sequences.ga for InterProScan
60+
job:
61+
Sequence collection:
62+
class: Collection
63+
collection_type: list
64+
elements:
65+
- class: File
66+
identifier: test-sequence
67+
location: https://zenodo.org/record/8414802/files/protein_sequences.fasta
68+
filetype: fasta
69+
hashes:
70+
- hash_function: SHA-1
71+
hash_value: 0e1026d6917ac03bcd174a85b18e69c2a6470f98
72+
Run eggNOG + completeness calculation: false
73+
Run InterProScan: true
74+
eggNOG mode select: proteins
75+
InterProScan mode select: Protein
76+
outputs:
77+
interproscan xml:
78+
element_tests:
79+
test-sequence:
80+
location: https://zenodo.org/records/13951790/files/interProScan.xml?download=1&preview=1
81+
compare: sim_size
82+
delta: 7000000
83+
interproscan tabular:
84+
element_tests:
85+
test-sequence:
86+
location: https://zenodo.org/records/13951790/files/interProScan.tabular?download=1&preview=1
87+
compare: sim_size
88+
delta: 2000000

0 commit comments

Comments
 (0)