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Argo data submission [email protected] #97

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merged 5 commits into from
Mar 12, 2024
Merged

Argo data submission [email protected] #97

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7376095
[wfpm v0.8.0] started a new version [email protected] fro…
edsu7 Mar 7, 2024
f27aa31
fix post json tsv handling
edsu7 Mar 7, 2024
861cfa2
bump version
edsu7 Mar 11, 2024
db6ec34
wrong version bump
edsu7 Mar 11, 2024
312deb6
add index files
edsu7 Mar 11, 2024
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12 changes: 6 additions & 6 deletions argo-data-submission-wf/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
*/

nextflow.enable.dsl = 2
version = '1.1.0'
version = '1.2.0'

// universal params go here, change default value as needed
params.container = ""
Expand Down Expand Up @@ -293,9 +293,9 @@ workflow ArgoDataSubmissionWf {
)

if (params.skip_sanity_check){
experiment_info_tsv=file(payloadJsonToTsvs.out.experiment_tsv)
read_group_info_tsv=file(og_read_group_info_tsv)
file_info_tsv=file(og_file_info_tsv)
experiment_info_tsv=payloadJsonToTsvs.out.experiment_tsv
read_group_info_tsv=payloadJsonToTsvs.out.read_group_tsv
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test

file_info_tsv=payloadJsonToTsvs.out.file_tsv
} else {
sanityCheck(
payloadJsonToTsvs.out.experiment_tsv,
Expand All @@ -306,8 +306,8 @@ workflow ArgoDataSubmissionWf {
)

experiment_info_tsv=sanityCheck.out.updated_experiment_info_tsv
read_group_info_tsv=file(og_read_group_info_tsv)
file_info_tsv=file(og_file_info_tsv)
read_group_info_tsv=payloadJsonToTsvs.out.read_group_tsv
file_info_tsv=payloadJsonToTsvs.out.file_tsv
}
} else {
if (params.skip_sanity_check){
Expand Down
2 changes: 1 addition & 1 deletion argo-data-submission-wf/pkg.json
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"name": "argo-data-submission-wf",
"version": "1.1.0",
"version": "1.2.0",
"description": "ARGO data submission workflow",
"main": "main.nf",
"deprecated": false,
Expand Down
2 changes: 1 addition & 1 deletion argo-data-submission-wf/tests/checker.nf
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Expand Up @@ -26,7 +26,7 @@
*/

nextflow.enable.dsl = 2
version = '1.1.0'
version = '1.2.0'

// universal params
params.publish_dir = ""
Expand Down
4 changes: 2 additions & 2 deletions nextflow.config
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Expand Up @@ -76,13 +76,13 @@ profiles {
rdpc_qa {
params.song_url = 'https://submission-song.rdpc-qa.cumulus.genomeinformatics.org'
params.score_url = 'https://submission-score.rdpc-qa.cumulus.genomeinformatics.org'
params.clinical_url = 'https://clinical.qa.argo.cancercollaboratory.org'
params.clinical_url = 'https://clinical.argo-qa.cumulus.genomeinformatics.org'
params.schema_url = 'https://submission-song.rdpc-qa.cumulus.genomeinformatics.org/schemas/sequencing_experiment'
}
rdpc_dev {
params.song_url = 'https://submission-song.rdpc-dev.cumulus.genomeinformatics.org'
params.score_url = 'https://submission-score.rdpc-dev.cumulus.genomeinformatics.org'
params.clinical_url = 'https://clinical.dev.argo.cancercollaboratory.org'
params.clinical_url = 'https://clinical.argo-dev.cumulus.genomeinformatics.org'
params.schema_url = 'https://submission-song.rdpc-dev.cumulus.genomeinformatics.org/schemas/sequencing_experiment'
}
}
Binary file added test_data/tiny-grch38-chr11-530001-537000.fa.gz
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1 change: 1 addition & 0 deletions test_data/tiny-grch38-chr11-530001-537000.fa.gz.fai
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@@ -0,0 +1 @@
chr11 537000 40 50 51
Binary file added test_data/tiny-grch38-chr11-530001-537000.fa.gz.gzi
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