diff --git a/argo-data-submission-wf/main.nf b/argo-data-submission-wf/main.nf index 9f40ce9..0e7171d 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 = "" @@ -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/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 = "" 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 0000000..4669945 Binary files /dev/null and b/test_data/tiny-grch38-chr11-530001-537000.fa.gz differ 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 0000000..8421b47 Binary files /dev/null and b/test_data/tiny-grch38-chr11-530001-537000.fa.gz.gzi differ