From ef87050dd73f8248b9ed8e94edfb74c896f0f698 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 22 Nov 2023 14:59:34 +0100 Subject: [PATCH] revert changes for the three workflows failing --- .../.dockstore.yml | 8 ++------ .../CHANGELOG.md | 4 ---- ...r-analysis-tests.yml => pe-wgs-ivar-analysis-test.yml} | 0 .../pe-wgs-ivar-analysis.ga | 2 +- .../.dockstore.yml | 8 ++------ .../CHANGELOG.md | 5 ----- ...ic-variation-tests.yml => pe-artic-variation-test.yml} | 6 ++++-- .../pe-artic-variation.ga | 2 +- .../.dockstore.yml | 8 ++------ .../CHANGELOG.md | 4 ---- ...-wgs-variation-tests.yml => se-wgs-variation-test.yml} | 0 .../se-wgs-variation.ga | 2 +- 12 files changed, 13 insertions(+), 36 deletions(-) rename workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/{pe-wgs-ivar-analysis-tests.yml => pe-wgs-ivar-analysis-test.yml} (100%) rename workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/{pe-artic-variation-tests.yml => pe-artic-variation-test.yml} (78%) rename workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/{se-wgs-variation-tests.yml => se-wgs-variation-test.yml} (100%) diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/.dockstore.yml b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/.dockstore.yml index 185307ed9..6986ad2a0 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/.dockstore.yml +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/.dockstore.yml @@ -1,11 +1,7 @@ version: 1.2 workflows: - name: 'SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE' - subclass: Galaxy - publish: true primaryDescriptorPath: /pe-wgs-ivar-analysis.ga + subclass: Galaxy testParameterFiles: - - /pe-wgs-ivar-analysis-tests.yml - authors: - - name: Peter van Heusden - orcid: 0000-0001-6553-5274 + - /pe-wgs-ivar-analysis-test.yml diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/CHANGELOG.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/CHANGELOG.md index 7ca69c8ef..5e1eab082 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/CHANGELOG.md +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/CHANGELOG.md @@ -1,9 +1,5 @@ # Changelog -## [0.2.4] 2023-11-20 - -- Fix author in dockstore - ## [0.2.3] 2022-05-25 ### Changed diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/pe-wgs-ivar-analysis-tests.yml b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/pe-wgs-ivar-analysis-test.yml similarity index 100% rename from workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/pe-wgs-ivar-analysis-tests.yml rename to workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/pe-wgs-ivar-analysis-test.yml diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/pe-wgs-ivar-analysis.ga b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/pe-wgs-ivar-analysis.ga index 28d5e46ba..eaad1c6a8 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/pe-wgs-ivar-analysis.ga +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/pe-wgs-ivar-analysis.ga @@ -8,7 +8,7 @@ "name": "Peter van Heusden" } ], - "release": "0.2.4", + "release": "0.2.3", "format-version": "0.1", "license": "MIT", "name": "SARS-CoV-2 Illumina Amplicon pipeline - iVar based", diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/.dockstore.yml b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/.dockstore.yml index 6ba503958..d83eddc48 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/.dockstore.yml +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/.dockstore.yml @@ -1,11 +1,7 @@ version: 1.2 workflows: - name: 'COVID-19-PE-ARTIC-ILLUMINA' - subclass: Galaxy - publish: true primaryDescriptorPath: /pe-artic-variation.ga + subclass: Galaxy testParameterFiles: - - /pe-artic-variation-tests.yml - authors: - - name: Wolfgang Maier - orcid: 0000-0002-9464-6640 + - /pe-artic-variation-test.yml diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/CHANGELOG.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/CHANGELOG.md index a7de29f91..b2711c923 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/CHANGELOG.md +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/CHANGELOG.md @@ -1,10 +1,5 @@ # Changelog -## [0.5.1] 2023-11-20 - -- Fix author in dockstore -- Use zenodo link instead of googleapis for fastq - ## [0.5] - 2022-02-08 ### Fixed diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation-tests.yml b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation-test.yml similarity index 78% rename from workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation-tests.yml rename to workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation-test.yml index 3ed229833..132610cbf 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation-tests.yml +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation-test.yml @@ -22,10 +22,12 @@ elements: - identifier: forward class: File - location: "https://zenodo.org/records/10174466/files/SRR11578257_R1.fastq.gz?download=1" + location: "https://storage.googleapis.com/nih-sequence-read-archive/sra-src/SRR11578257/VIC818_R1.fq.gz" + filetype: fastqsanger.gz - identifier: reverse class: File - location: "https://zenodo.org/records/10174466/files/SRR11578257_R2.fastq.gz?download=1" + location: "https://storage.googleapis.com/nih-sequence-read-archive/sra-src/SRR11578257/VIC818_R2.fq.gz" + filetype: fastqsanger.gz outputs: annotated_softfiltered_variants: attributes: {} diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation.ga b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation.ga index 0cc0ab975..83e0c7df7 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation.ga +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation.ga @@ -11,7 +11,7 @@ "format-version": "0.1", "license": "MIT", "name": "COVID-19: variation analysis on ARTIC PE data", - "release": "0.5.1", + "release": "0.5", "steps": { "0": { "annotation": "Illumina reads from ARTIC assay with fastqsanger encoding", diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/.dockstore.yml b/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/.dockstore.yml index 1bbc1d902..08471be94 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/.dockstore.yml +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/.dockstore.yml @@ -1,11 +1,7 @@ version: 1.2 workflows: - name: 'COVID-19-SE-WGS-ILLUMINA' - subclass: Galaxy - publish: true primaryDescriptorPath: /se-wgs-variation.ga + subclass: Galaxy testParameterFiles: - - /se-wgs-variation-tests.yml - authors: - - name: Wolfgang Maier - orcid: 0000-0002-9464-6640 + - /se-wgs-variation-test.yml diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/CHANGELOG.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/CHANGELOG.md index e0d19d225..547051c78 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/CHANGELOG.md +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/CHANGELOG.md @@ -1,9 +1,5 @@ # Changelog -## [0.1.4] 2023-11-20 - -- Fix author in dockstore - ## [0.1.3] 2021-12-13 ### Added diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/se-wgs-variation-tests.yml b/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/se-wgs-variation-test.yml similarity index 100% rename from workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/se-wgs-variation-tests.yml rename to workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/se-wgs-variation-test.yml diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/se-wgs-variation.ga b/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/se-wgs-variation.ga index c00b641e3..a1b5b3e0d 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/se-wgs-variation.ga +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/se-wgs-variation.ga @@ -11,7 +11,7 @@ "format-version": "0.1", "license": "MIT", "name": "COVID-19: variation analysis on WGS SE data", - "release": "0.1.4", + "release": "0.1.3", "steps": { "0": { "annotation": "Illumina reads with fastqsanger encoding",