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Some workflow test updates #2045

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Oct 3, 2020
Merged

Some workflow test updates #2045

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3ae7a9e
gromacs
cat-bro Oct 3, 2020
c5002c6
protein-quant-sil
cat-bro Oct 3, 2020
6614b58
md-simulations
cat-bro Oct 3, 2020
9bd4422
amplicon
cat-bro Oct 3, 2020
0d181e1
update doc
cat-bro Oct 3, 2020
c596a9f
fix urls in amplicon-job.yml
cat-bro Oct 3, 2020
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30 changes: 30 additions & 0 deletions ...omputational-chemistry/tutorials/analysis-md-simulations/workflows/main_workflow-test.yml
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@@ -0,0 +1,30 @@
---
- doc: Test Analysis of molecular dynamics simulations workflow
job:
protein_pdb:
class: File
location: https://zenodo.org/record/2537734/files/cbh1test.pdb
filetype: pdb
protein_mdsimulation_dcd:
class: File
location: https://zenodo.org/record/2537734/files/cbh1test.dcd
filetype: dcd
outputs:
rmsf_tabular_output:
asserts:
has_n_columns:
n: 2
has_line_matching:
expression: 1\s+0.29.*
pca_tabular_output:
asserts:
has_n_columns:
n: 4
has_line_matching:
expression: 1\s+0.047.*\s+0.0374.*\s+0.0436.*
rmsd_tabular_output:
asserts:
has_n_columns:
n: 2
has_line_matching:
expression: 2\s+0.21*
36 changes: 27 additions & 9 deletions topics/computational-chemistry/tutorials/analysis-md-simulations/workflows/main_workflow.ga
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Expand Up @@ -13,18 +13,18 @@
"inputs": [
{
"description": "",
"name": "dcd_trajectory_output_40.dcd_2.dcd"
"name": "protein_mdsimulation_dcd"
}
],
"label": "dcd_trajectory_output_40.dcd_2.dcd",
"label": "protein_mdsimulation_dcd",
"name": "Input dataset",
"outputs": [],
"position": {
"left": 200,
"top": 310
},
"tool_id": null,
"tool_state": "{\"name\": \"dcd_trajectory_output_40.dcd_2.dcd\"}",
"tool_state": "{\"name\": \"protein_mdsimulation_dcd\"}",
"tool_version": null,
"type": "data_input",
"uuid": "e26cd82e-19c8-4cf5-93c7-5a0a0e5201cc",
Expand All @@ -39,18 +39,18 @@
"inputs": [
{
"description": "",
"name": "minimizer_pdb_8.pdb_1.pdb"
"name": "protein_pdb"
}
],
"label": "minimizer_pdb_8.pdb_1.pdb",
"label": "protein_pdb",
"name": "Input dataset",
"outputs": [],
"position": {
"left": 200,
"top": 430
},
"tool_id": null,
"tool_state": "{\"name\": \"minimizer_pdb_8.pdb_1.pdb\"}",
"tool_state": "{\"name\": \"protein_pdb\"}",
"tool_version": null,
"type": "data_input",
"uuid": "cbe0e7c8-c572-4231-a55f-d04c72760cd4",
Expand Down Expand Up @@ -113,7 +113,13 @@
"tool_version": "2.3",
"type": "tool",
"uuid": "5b0988f7-6cb1-4dfc-95b5-d5493d77d579",
"workflow_outputs": []
"workflow_outputs": [
{
"label": "rmsd_tabular_output",
"output_name": "output",
"uuid": "6de2beaf-f80e-4788-8598-229a1c582757"
}
]
},
"3": {
"annotation": "",
Expand Down Expand Up @@ -168,7 +174,13 @@
"tool_version": "2.3",
"type": "tool",
"uuid": "aebc72d2-95bd-4b94-aa49-f8fbd55e7d54",
"workflow_outputs": []
"workflow_outputs": [
{
"label": "rmsf_tabular_output",
"output_name": "output",
"uuid": "1f2d715d-230a-4ec5-a509-e8ae501e7634"
}
]
},
"4": {
"annotation": "",
Expand Down Expand Up @@ -231,7 +243,13 @@
"tool_version": "2.3",
"type": "tool",
"uuid": "99415486-79b9-47d1-8111-02d0e6dcbed6",
"workflow_outputs": []
"workflow_outputs": [
{
"label": "pca_tabular_output",
"output_name": "output",
"uuid": "92b7a40f-9ffc-4f56-8cf3-deec52e7b8b5"
}
]
}
},
"tags": [
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2 changes: 1 addition & 1 deletion topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md
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Expand Up @@ -89,7 +89,7 @@ A prepared file is available via Zenodo. Alternatively, you can prepare the file
> ### {% icon comment %} Alternative upload
> As an alternative option, if you prefer to upload the cleaned file directly from Zenodo, you can do so with the following link:
> ```
> https://zenodo.org/record/2598415
> https://zenodo.org/record/2598415/files/1AKI_clean.pdb
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Thanks 👍

> ```
> {% include snippets/import_via_link.md %}
{: .comment}
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14 changes: 14 additions & 0 deletions .../computational-chemistry/tutorials/md-simulation-gromacs/workflows/main_workflow-test.yml
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---
- doc: Test GROMACS Training workflow
job: {}
outputs:
gro_output:
asserts:
has_text:
text: "LYSOZYME in water"
xtc_output:
asserts:
has_size:
value: 2337500
delta: 30000

13 changes: 11 additions & 2 deletions topics/computational-chemistry/tutorials/md-simulation-gromacs/workflows/main_workflow.ga
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Expand Up @@ -636,8 +636,17 @@
"name":"report"
}
],
"workflow_outputs":[

"workflow_outputs": [
{
"label": "xtc_output",
"output_name": "output4",
"uuid": "027305f5-213b-40af-8e2b-c376d5d2e294"
},
{
"label": "gro_output",
"output_name": "output1",
"uuid": "e745fd4c-f607-4215-84e4-c62587c8c07a"
}
],
"input_connections":{
"top_input":{
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20 changes: 10 additions & 10 deletions topics/metagenomics/tutorials/general-tutorial/workflows/amplicon-job.yml
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@@ -1,19 +1,19 @@
---
silva:
'SILVA Reference':
class: File
location: https://zenodo.org/record/815875/files/silva.v4.fasta
location: https://zenodo.org/api/files/0e062e89-e6ce-463b-a8cb-0151e5aabc69/silva.v4.fasta
filetype: fasta
anguil_soil_sample:
'Anguil Soil Sample':
class: File
location: https://zenodo.org/record/815875/files/SRR651839_anguil.fasta
location: https://zenodo.org/api/files/0e062e89-e6ce-463b-a8cb-0151e5aabc69/SRR651839_anguil.fasta
filetype: fasta
pampa_soil_sample:
'Pampa Soil Sample':
class: File
location: https://zenodo.org/record/815875/files/SRR531818_pampa.fasta
trainset_alignment:
location: https://zenodo.org/api/files/0e062e89-e6ce-463b-a8cb-0151e5aabc69/SRR531818_pampa.fasta
'Trainset PDS alignment':
class: File
location: https://zenodo.org/record/815875/files/trainset16_022016.pds.fasta
trainset_taxonomy:
location: https://zenodo.org/api/files/0e062e89-e6ce-463b-a8cb-0151e5aabc69/trainset16_022016.pds.fasta
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@cat-bro do you know which URL type is the recommended one? You changed it here to be a UID like. But below you are using https://zenodo.org/record/1051552/files/HEK_SILAC-K6R6_ST905_part.mzml the record ones again.

I'm wondering if one more stable than the other?

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@bgruening I don't know which URL is recommended. The files urls are used in the data libraries. There was probably no need to update the links in this case.

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Do you want to redo the changes to this file then? Otherwise 👍 from me! Thanks.

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done :--)

'Trainset PDS taxonomy':
class: File
location: https://zenodo.org/record/815875/files/trainset16_022016.pds.tax
location: https://zenodo.org/api/files/0e062e89-e6ce-463b-a8cb-0151e5aabc69/trainset16_022016.pds.tax
filetype: mothur.seq.taxonomy
2 changes: 1 addition & 1 deletion topics/metagenomics/tutorials/general-tutorial/workflows/amplicon-test.yml
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Expand Up @@ -5,4 +5,4 @@
mothur_make_shared_shared:
asserts:
has_text:
text: "0.03 anguil 4015 250 145 167 181 122"
text: "0.03 anguil"
17 changes: 17 additions & 0 deletions topics/proteomics/tutorials/protein-quant-sil/workflows/workflow-test.yml
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---
- doc: Test ID Plus Quant SIL Training workflow
job:
'mzML file':
class: File
location: https://zenodo.org/record/1051552/files/HEK_SILAC-K6R6_ST905_part.mzml
filetype: mzml
'fasta file':
class: File
location: https://zenodo.org/record/892005/files/Human_database_including_decoys_%28cRAP_added%29.fasta
filetype: fasta
outputs:
protein_quant:
asserts:
has_text_matching:
expression: '"sp|P61604|CH10_HUMAN"\s+1\s+0.99'

2 changes: 1 addition & 1 deletion topics/proteomics/tutorials/protein-quant-sil/workflows/workflow.ga
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Expand Up @@ -861,7 +861,7 @@
{
"output_name": "param_out",
"uuid": "c5ec6e2a-8a27-447a-a3ad-28a79954143b",
"label": null
"label": "protein_quant"
}
],
"input_connections": {
Expand Down