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Add Group Assignment for Co-Assembly workflow #946

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d75b90b
Add Group Assignment for Co-Assembly workflow
Minamehr Sep 17, 2025
4dfc975
Fix: add release field to Group Assignment for Co-Assembly workflow
Minamehr Sep 17, 2025
fc9aa6a
Move and rename workflow: group-assignment-for-co-assembly → grouped-…
Minamehr Sep 18, 2025
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13 changes: 13 additions & 0 deletions workflows/data-fetching/grouped-fastq-merging/.dockstore.yml
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version: 1.2
workflows:
- name: main
subclass: Galaxy
publish: true
primaryDescriptorPath: /Grouped-FASTQ-merging.ga
testParameterFiles:
- /Grouped-FASTQ-merging-tests.yml
authors:
- name: Mina Hojat Ansari
orcid: 0000-0002-3602-7884
- name: Paul Zierep
orcid: 0000-0003-2982-388X
6 changes: 6 additions & 0 deletions workflows/data-fetching/grouped-fastq-merging/CHANGELOG.md
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# Changelog


## [0.1]- 2025-09-08

- First release of the Group Assignment for Co-Assembly.
246 changes: 246 additions & 0 deletions workflows/data-fetching/grouped-fastq-merging/Grouped-FASTQ-merging-tests.yml
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- doc: Test outline for Grouped FASTQ merging with fastq files
job:
metadata:
class: File
path: test-data/metadata.tabular
filetype: tabular
Trimmed paired reads:
class: Collection
collection_type: list:paired
elements:
- class: Collection
type: paired
identifier: IBSD09_test
elements:
- class: File
identifier: forward
location: https://zenodo.org/records/17151392/files/IBSD09_test_1.fastq
- class: File
identifier: reverse
location: https://zenodo.org/records/17151392/files/IBSD09_test_2.fastq
- class: Collection
type: paired
identifier: IBSD08_test
elements:
- class: File
identifier: forward
location: https://zenodo.org/records/17151392/files/IBSD08_test_1.fastq
- class: File
identifier: reverse
location: https://zenodo.org/records/17151392/files/IBSD08_test_2.fastq
- class: Collection
type: paired
identifier: IBSD02_test
elements:
- class: File
identifier: forward
location: https://zenodo.org/records/17151392/files/IBSD02_test_1.fastq
- class: File
identifier: reverse
location: https://zenodo.org/records/17151392/files/IBSD02_test_2.fastq
- class: Collection
type: paired
identifier: IBSD01_test
elements:
- class: File
identifier: forward
location: https://zenodo.org/records/17151392/files/IBSD01_test_1.fastq
- class: File
identifier: reverse
location: https://zenodo.org/records/17151392/files/IBSD01_test_2.fastq
- class: Collection
type: paired
identifier: IBSD03_test
elements:
- class: File
identifier: forward
location: https://zenodo.org/records/17151392/files/IBSD03_test_1.fastq
- class: File
identifier: reverse
location: https://zenodo.org/records/17151392/files/IBSD03_test_2.fastq
- class: Collection
type: paired
identifier: IBSD04_test
elements:
- class: File
identifier: forward
location: https://zenodo.org/records/17151392/files/IBSD04_test_1.fastq
- class: File
identifier: reverse
location: https://zenodo.org/records/17151392/files/IBSD04_test_2.fastq
- class: Collection
type: paired
identifier: IBSD05_test
elements:
- class: File
identifier: forward
location: https://zenodo.org/records/17151392/files/IBSD05_test_1.fastq
- class: File
identifier: reverse
location: https://zenodo.org/records/17151392/files/IBSD05_test_2.fastq
- class: Collection
type: paired
identifier: IBSD06_test
elements:
- class: File
identifier: forward
location: https://zenodo.org/records/17151392/files/IBSD06_test_1.fastq
- class: File
identifier: reverse
location: https://zenodo.org/records/17151392/files/IBSD06_test_2.fastq
outputs:
paired_output:
element_tests:
"group:2":
elements:
forward:
asserts:
- has_n_lines:
n: 8000
- has_size:
value: 710000
delta: 20000
- has_text_matching:
expression: "AA6AAAEEAEE6EE"
reverse:
asserts:
- has_n_lines:
n: 8000
- has_size:
value: 690000
delta: 20000
- has_text_matching:
expression: "AAAAAAAEEE"
"group:1":
elements:
forward:
asserts:
- has_n_lines:
n: 12000
- has_size:
value: 1100000
delta: 200000
- has_text_matching:
expression: "^@NB501724:38:HJFYHBGX2:"
reverse:
asserts:
- has_n_lines:
n: 12000
- has_size:
value: 1100000
delta: 200000
- has_text_matching:
expression: "AAAAAEEEEEEEEEEEE"
"group:3":
elements:
forward:
asserts:
- has_n_lines:
n: 4000
- has_size:
value: 354000
delta: 20000
- has_text_matching:
expression: "^@NB501724:38:HJFYHBGX2:"
reverse:
asserts:
- has_n_lines:
n: 4000
- has_size:
value: 347000
delta: 20000
- has_text_matching:
expression: "AAAAAEEEEEEEEEEEE"
"IBSD06_test":
elements:
forward:
asserts:
- has_n_lines:
n: 4000
- has_size:
value: 353500
delta: 20000
- has_text_matching:
expression: "AAAAA66AEAEEEEEEEEE6EEAEEEEE6A"
reverse:
asserts:
- has_n_lines:
n: 4000
- has_size:
value: 347000
delta: 20000
- has_text_matching:
expression: "AA6AA6E"
- doc: Test outline for Grouped FASTQ merging with providing filetype for .gz files
job:
metadata:
class: File
path: test-data/metadata2.tabular
filetype: tabular
Trimmed paired reads:
class: Collection
collection_type: list:paired
elements:
- class: Collection
type: paired
identifier: IBSC02_subset
elements:
- class: File
identifier: forward
location: https://zenodo.org/records/17151392/files/IBSC02_subset_1.fastq.gz
filetype: fastqsanger.gz
- class: File
identifier: reverse
location: https://zenodo.org/records/17151392/files/IBSC02_subset_2.fastq.gz
filetype: fastqsanger.gz
- class: Collection
type: paired
identifier: IBSM20_subset
elements:
- class: File
identifier: forward
location: https://zenodo.org/records/17151392/files/IBSM20_subset_1.fastq.gz
filetype: fastqsanger.gz
- class: File
identifier: reverse
location: https://zenodo.org/records/17151392/files/IBSM20_subset_2.fastq.gz
filetype: fastqsanger.gz
- class: Collection
type: paired
identifier: HC26_subset
elements:
- class: File
identifier: forward
location: https://zenodo.org/records/17151392/files/HC26_subset_1.fastq.gz
filetype: fastqsanger.gz
- class: File
identifier: reverse
location: https://zenodo.org/records/17151392/files/HC26_subset_2.fastq.gz
filetype: fastqsanger.gz
outputs:
paired_output:
element_tests:
"group:2":
elements:
forward:
asserts:
- has_size:
value: 103000
delta: 20000
reverse:
asserts:
- has_size:
value: 103000
delta: 20000
"group:1":
elements:
forward:
asserts:
- has_size:
value: 202000
delta: 20000
reverse:
asserts:
- has_size:
value: 201400
delta: 20000
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