From f42c01e556c50fc18b1b375da28c1056aa200882 Mon Sep 17 00:00:00 2001 From: Steven Sutcliffe Date: Thu, 24 Oct 2024 08:40:09 -0400 Subject: [PATCH 1/7] Reverted changes to docker container settings for Azure test --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 883dc1c..7066d48 100644 --- a/nextflow.config +++ b/nextflow.config @@ -90,6 +90,7 @@ profiles { } docker { docker.enabled = true + docker.userEmulation = true conda.enabled = false singularity.enabled = false podman.enabled = false @@ -166,7 +167,6 @@ singularity.registry = 'quay.io' // Override the default Docker registry when required process.ext.override_configured_container_registry = true -process.containerOptions = '-u $(id -u):$(id -g)' // Nextflow plugins plugins { From b3d1671b83cd271784c2534d69eb15434c72286b Mon Sep 17 00:00:00 2001 From: Steven Sutcliffe Date: Thu, 24 Oct 2024 08:59:34 -0400 Subject: [PATCH 2/7] Modified the docker.emulation with new runOption --- nextflow.config | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 7066d48..6d910ad 100644 --- a/nextflow.config +++ b/nextflow.config @@ -90,7 +90,7 @@ profiles { } docker { docker.enabled = true - docker.userEmulation = true + docker.runOptions = '-u $(id -u):$(id -g)' conda.enabled = false singularity.enabled = false podman.enabled = false @@ -168,6 +168,7 @@ singularity.registry = 'quay.io' // Override the default Docker registry when required process.ext.override_configured_container_registry = true + // Nextflow plugins plugins { id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet From 1f4c750a203d8c8a44c769a1f9ed3f833cf7f1c3 Mon Sep 17 00:00:00 2001 From: Steven Sutcliffe Date: Fri, 25 Oct 2024 16:11:26 -0400 Subject: [PATCH 3/7] Updated documentation --- CHANGELOG.md | 4 ++++ docs/usage.md | 29 +++++++++++++++-------------- 2 files changed, 19 insertions(+), 14 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 07154b4..f39bb2e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## Development + +- Fixed the replacement of `docker.userEmulation` with `docker.runOptions = '-u $(id -u):$(id -g)'` that was causing a bug in Azure + ## [0.3.0] - 2024-10-21 - Added the ability to include a `sample_name` column in the input samplesheet.csv. Allows for compatibility with IRIDA-Next input configuration. diff --git a/docs/usage.md b/docs/usage.md index 8129c03..d36659c 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -39,24 +39,25 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p ### IRIDA-Next Optional Samplesheet Configuration -`arboratornf` accepts the [IRIDA-Next](https://github.com/phac-nml/irida-next) format for samplesheets which contain the following columns: `sample`, `sample_name`, `fastq_1`, `fastq_2`, `reference_assembly`, and `metadata_1` - `metadata_8`. The sample IDs within a samplesheet should be unique. - -A final samplesheet file consisting of both single- and paired-end data may look something like the one below. +`arboratornf` accepts the [IRIDA-Next](https://github.com/phac-nml/irida-next) format for samplesheets which contain the following columns: `sample`, `sample_name`, `mlst_alleles`, `metadata_partition`, and `metadata_1` through `metadata_8`. The IDs (sample column) within a samplesheet should be unique and contain no spaces. Any other additionally specified trailing columns will be ignored. ```console -sample,sample_name,fastq_1,fastq_2,reference_assembly,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8 -SAMPLE1,A1,/path/to/sample1_fastq1.fq,/path/to/sample1_fastq2.fq,/path/to/sample1_assembly.fa,,,,,,,, -SAMPLE2,B2,/path/to/sample2_fastq1.fq,,,,,,,,,, +sample,sample_name,mlst_alleles,metadata_partition,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8 +S1,sample1,S1.mlst.json,1,"Escherichia coli","EHEC/STEC","Canada","O157:H7",21,"2024/05/30","beef",true +S2,sample2,S2.mlst.json,1,"Escherichia coli","EHEC/STEC","The United States","O157:H7",55,"2024/05/21","milk",false +S3,sampleQ,S3.mlst.json,2,"Escherichia coli","EPEC","France","O125",14,"2024/04/30","cheese",true +S4,sampleQ,S4.mlst.json,2,"Escherichia coli","EPEC","France","O125",35,"2024/04/22","cheese",true +S5,sample#5,S5.mlst.json,3,"Escherichia coli","EAEC","Canada","O126:H27",61,"2012/09/01","milk",false +S6,,S6.mlst.json,unassociated,"Escherichia coli","EAEC","Canada","O111:H21",43,"2011/12/25","fruit",false ``` -| Column | Description | -| ---------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `sample` | Custom sample name. Samples should be unique within a samplesheet. | -| `sample_name` | Sample name used in outputs (filenames and sample names) | -| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `fastq_2` | (Optional) Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `reference_assembly` | (Optional) Full path to a FASTA file representing a reference assembly derived from this sample. This field provides a method for selecting a reference genome for the whole pipeline. | -| `metadata_1` to `metadata_8` | (Optional) Permits up to 8 columns for user-defined contextual metadata associated with each `sample`. | +| Column | Description | +| ------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `sample` | Custom sample name. Samples should be unique within a samplesheet. | +| `sample_name` | Sample name used in outputs (filenames and sample names) | +| `mlst_alleles` | A URI path to a JSON-formatted genomic profile. An example of this file is provided in [tests/data/profiles/S1.mlst.json](../tests/data/profiles/S1.mlst.json). | +| `metadata_partition` | The specific metadata column used to partition the genomic profiles. For example, this column might refer to the outbreak number and the contain such entries as "1", "2", etc. | +| `metadata_1..metadata_8` | Metadata that will be associated with each genomic profile. These metadata will be summarized in the Arborator outputs. | An [example samplesheet](../tests/data/samplesheets/samplesheet-samplename.csv) has been provided with the pipeline. From 278a966b9e4bc634350701edaaf67024e510b58e Mon Sep 17 00:00:00 2001 From: Steven Sutcliffe Date: Fri, 25 Oct 2024 16:32:48 -0400 Subject: [PATCH 4/7] Updated prettier version for pre-commit --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0c31cdb..df0b550 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,5 +1,5 @@ repos: - repo: https://github.com/pre-commit/mirrors-prettier - rev: "v2.7.1" + rev: "v3.2.5" hooks: - id: prettier From 152a6bf329c586804c835e913566f7b1ffc0bd21 Mon Sep 17 00:00:00 2001 From: Steven Sutcliffe Date: Fri, 25 Oct 2024 16:38:09 -0400 Subject: [PATCH 5/7] Second attempt to update prettier version --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index df0b550..5a29607 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,5 +1,5 @@ repos: - repo: https://github.com/pre-commit/mirrors-prettier - rev: "v3.2.5" + rev: "v3.0.0" hooks: - id: prettier From 36739f163ab8ca8120c909d0c04f971f0766c08b Mon Sep 17 00:00:00 2001 From: Steven Sutcliffe Date: Thu, 31 Oct 2024 10:39:33 -0400 Subject: [PATCH 6/7] Update version number: patch --- CHANGELOG.md | 3 ++- nextflow.config | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f39bb2e..f10f3d0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## Development +## [0.3.1] - 2024-10-31 - Fixed the replacement of `docker.userEmulation` with `docker.runOptions = '-u $(id -u):$(id -g)'` that was causing a bug in Azure @@ -40,3 +40,4 @@ Initial release of the arboratornf pipeline to be used for running [Arborator](h [0.1.0]: https://github.com/phac-nml/arboratornf/releases/tag/0.1.0 [0.2.0]: https://github.com/phac-nml/arboratornf/releases/tag/0.2.0 [0.3.0]: https://github.com/phac-nml/arboratornf/releases/tag/0.3.0 +[0.3.1]: https://github.com/phac-nml/arboratornf/releases/tag/0.3.1 diff --git a/nextflow.config b/nextflow.config index 6d910ad..6c43005 100644 --- a/nextflow.config +++ b/nextflow.config @@ -214,7 +214,7 @@ manifest { description = """Arborator: Genomic Profile Clustering and Summary""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '0.3.0' + version = '0.3.1' doi = '' defaultBranch = 'main' } From ca5ca1fc11e24dda039c98b4963d6016aeb25762 Mon Sep 17 00:00:00 2001 From: Steven Sutcliffe Date: Tue, 5 Nov 2024 09:48:13 -0500 Subject: [PATCH 7/7] Change the release date --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f10f3d0..70266a9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [0.3.1] - 2024-10-31 +## [0.3.1] - 2024-11-05 - Fixed the replacement of `docker.userEmulation` with `docker.runOptions = '-u $(id -u):$(id -g)'` that was causing a bug in Azure