From 73760950f07bd16f57a23770ce2c5bd831a11236 Mon Sep 17 00:00:00 2001
From: edsu7 <22638361+edsu7@users.noreply.github.com>
Date: Thu, 7 Mar 2024 13:15:12 -0500
Subject: [PATCH 1/5] [wfpm v0.8.0] started a new version
argo-data-submission-wf@1.2.0 from argo-data-submission-wf@1.1.0 which was
released
---
argo-data-submission-wf/main.nf | 2 +-
argo-data-submission-wf/pkg.json | 2 +-
argo-data-submission-wf/tests/checker.nf | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/argo-data-submission-wf/main.nf b/argo-data-submission-wf/main.nf
index 9f40ce9..d312845 100755
--- a/argo-data-submission-wf/main.nf
+++ b/argo-data-submission-wf/main.nf
@@ -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 = ""
diff --git a/argo-data-submission-wf/pkg.json b/argo-data-submission-wf/pkg.json
index 12e51bc..ce45cb7 100644
--- a/argo-data-submission-wf/pkg.json
+++ b/argo-data-submission-wf/pkg.json
@@ -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,
diff --git a/argo-data-submission-wf/tests/checker.nf b/argo-data-submission-wf/tests/checker.nf
index fff7399..5265702 100755
--- a/argo-data-submission-wf/tests/checker.nf
+++ b/argo-data-submission-wf/tests/checker.nf
@@ -26,7 +26,7 @@
*/
nextflow.enable.dsl = 2
-version = '1.1.0'
+version = '1.2.0'
// universal params
params.publish_dir = ""
From f27aa3124f8a759f300c3390c0c44a873ca03222 Mon Sep 17 00:00:00 2001
From: edsu7 <22638361+edsu7@users.noreply.github.com>
Date: Thu, 7 Mar 2024 15:51:15 -0500
Subject: [PATCH 2/5] fix post json tsv handling
---
argo-data-submission-wf/main.nf | 10 +++++-----
nextflow.config | 4 ++--
test_data/tiny-grch38-chr11-530001-537000.fa.gz | Bin 0 -> 4408 bytes
3 files changed, 7 insertions(+), 7 deletions(-)
create mode 100644 test_data/tiny-grch38-chr11-530001-537000.fa.gz
diff --git a/argo-data-submission-wf/main.nf b/argo-data-submission-wf/main.nf
index d312845..0e7171d 100755
--- a/argo-data-submission-wf/main.nf
+++ b/argo-data-submission-wf/main.nf
@@ -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
+ file_info_tsv=payloadJsonToTsvs.out.file_tsv
} else {
sanityCheck(
payloadJsonToTsvs.out.experiment_tsv,
@@ -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){
diff --git a/nextflow.config b/nextflow.config
index 9f15b9f..460efd0 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -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'
}
}
diff --git a/test_data/tiny-grch38-chr11-530001-537000.fa.gz b/test_data/tiny-grch38-chr11-530001-537000.fa.gz
new file mode 100644
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HcmV?d00001
From 861cfa295da7037a01324cd6248c9d76dc18c84f Mon Sep 17 00:00:00 2001
From: edsu7 <22638361+edsu7@users.noreply.github.com>
Date: Mon, 11 Mar 2024 11:07:05 -0400
Subject: [PATCH 3/5] bump version
---
ega-download-wf/main.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/ega-download-wf/main.nf b/ega-download-wf/main.nf
index a58d36d..c0c305a 100755
--- a/ega-download-wf/main.nf
+++ b/ega-download-wf/main.nf
@@ -22,7 +22,7 @@
*/
nextflow.enable.dsl = 2
-version = '0.1.6'
+version = '1.2.0'
// universal params go here, change default value as needed
params.container = ""
From db6ec345ee5cba229acd9bb4347175ed4291ce96 Mon Sep 17 00:00:00 2001
From: edsu7 <22638361+edsu7@users.noreply.github.com>
Date: Mon, 11 Mar 2024 11:21:02 -0400
Subject: [PATCH 4/5] wrong version bump
---
ega-download-wf/main.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/ega-download-wf/main.nf b/ega-download-wf/main.nf
index c0c305a..a58d36d 100755
--- a/ega-download-wf/main.nf
+++ b/ega-download-wf/main.nf
@@ -22,7 +22,7 @@
*/
nextflow.enable.dsl = 2
-version = '1.2.0'
+version = '0.1.6'
// universal params go here, change default value as needed
params.container = ""
From 312deb6a2b0cfb36c17692b31812b1493c658e4c Mon Sep 17 00:00:00 2001
From: edsu7 <22638361+edsu7@users.noreply.github.com>
Date: Mon, 11 Mar 2024 12:23:35 -0400
Subject: [PATCH 5/5] add index files
---
.../tiny-grch38-chr11-530001-537000.fa.gz.fai | 1 +
.../tiny-grch38-chr11-530001-537000.fa.gz.gzi | Bin 0 -> 136 bytes
2 files changed, 1 insertion(+)
create mode 100644 test_data/tiny-grch38-chr11-530001-537000.fa.gz.fai
create mode 100644 test_data/tiny-grch38-chr11-530001-537000.fa.gz.gzi
diff --git a/test_data/tiny-grch38-chr11-530001-537000.fa.gz.fai b/test_data/tiny-grch38-chr11-530001-537000.fa.gz.fai
new file mode 100644
index 0000000..88de907
--- /dev/null
+++ b/test_data/tiny-grch38-chr11-530001-537000.fa.gz.fai
@@ -0,0 +1 @@
+chr11 537000 40 50 51
diff --git a/test_data/tiny-grch38-chr11-530001-537000.fa.gz.gzi b/test_data/tiny-grch38-chr11-530001-537000.fa.gz.gzi
new file mode 100644
index 0000000000000000000000000000000000000000..8421b47db56643b8724e831ff65623f0c53848d2
GIT binary patch
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literal 0
HcmV?d00001