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 index 0000000000000000000000000000000000000000..46699450ed3e0b38c1d24d316ba08393b0773b13 GIT binary patch literal 4408 zcmeHLS5Om(77ZPwMMx9`3`kgDLlX@ygeFC#_a;TEw9q182~7+w6lqdI0s_Jc2uNFs zlm(U&LPtQPNs|(SbVA?V_w#1n`+qY#&pT)C$N9VWo-=pmK;oF`0e{y8BS1}^7QjP8 zA$?>CmjP%F&x%)tCjm7ofzU`oM52Q;sMGF$d-P#s8r_aBR+s|^6hD&u{?1pol~kHu^OD5RV0003LZhp?}`kO8s1vZZN% zlfaoMLFR~mEUI*`KTTM0{W0)g(*JScACmqjI{Al(|NXxH?>y|qLdnvvT9jkM95#Wm zteaKs3}*JLv@Kzgs}({BqRURzN_Hhu7nwr!0_;J;PFHsU+dCQio2FAf6#nZta|wtL*JRd;bpctE2Xl#aJTsO@%OjZ&qo9YD;-bt zVPn_Oo)j1NC^x1PCHsl9#)IY1=JiGL{_I@E)w#`+>(d`+CrAaegF{N*nDj}$nO*G? 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