From 34f47abd07b75849ed18468ea1cf57fdaefc622a Mon Sep 17 00:00:00 2001 From: nelnk861 Date: Wed, 21 Feb 2024 14:07:10 +0100 Subject: [PATCH 1/6] DATAOPS-626: Updated multiqc container --- config/nextflow_config/singularity.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/config/nextflow_config/singularity.config b/config/nextflow_config/singularity.config index 6eb0c60..a4ffd25 100644 --- a/config/nextflow_config/singularity.config +++ b/config/nextflow_config/singularity.config @@ -20,10 +20,10 @@ process { container = 'https://depot.galaxyproject.org/singularity/illumina-interop:1.2.4--hdbdd923_2' } withName: 'MULTIQC_PER_FLOWCELL' { - container = 'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' + container = 'https://depot.galaxyproject.org/singularity/multiqc:1.9--pyh9f0ad1d_0' } withName: 'MULTIQC_PER_PROJECT' { - container = 'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' + container = 'https://depot.galaxyproject.org/singularity/multiqc:1.9--pyh9f0ad1d_0' } } From c0d80255b25b80e490ca90524f36a0b971e1042a Mon Sep 17 00:00:00 2001 From: nelnk861 Date: Thu, 22 Feb 2024 10:43:54 +0100 Subject: [PATCH 2/6] Update README setup instructions --- README.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/README.md b/README.md index 14b810b..2102caa 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,16 @@ This is a Nextflow pipeline for generating sequencing reports for the SNP&Se ## Pre-requisites You need to: - install Nextflow (e.g. using conda `conda create -n nextflow-env nextflow` or downloading from [nextflow.io](https://www.nextflow.io/)). + - Make Nextflow binary executable: + ```bash + chmod +x /usr/local/bin/nextflow + ``` - install [Singularity (version > 2.6)](https://singularity.lbl.gov/install-linux#adding-the-mirror-and-installing). + - Install test requirements: + ```bash + pip install -r requirements-dev.txt + ``` + - ins Optional: - (currently mandatory: see known issues) Download the fastq-screen database by downloading fastq-screen from [here](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_v0.13.0.tar.gz), extract the archive and then run `fastq_screen --get_genomes`. From 190475e2e0da6ec49018a6021b4512cc3e727521 Mon Sep 17 00:00:00 2001 From: nelnk861 Date: Fri, 23 Feb 2024 09:10:06 +0100 Subject: [PATCH 3/6] updating new version of multiqc --- config/nextflow_config/singularity.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/config/nextflow_config/singularity.config b/config/nextflow_config/singularity.config index a4ffd25..4618df8 100644 --- a/config/nextflow_config/singularity.config +++ b/config/nextflow_config/singularity.config @@ -20,10 +20,10 @@ process { container = 'https://depot.galaxyproject.org/singularity/illumina-interop:1.2.4--hdbdd923_2' } withName: 'MULTIQC_PER_FLOWCELL' { - container = 'https://depot.galaxyproject.org/singularity/multiqc:1.9--pyh9f0ad1d_0' + container = 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_1' } withName: 'MULTIQC_PER_PROJECT' { - container = 'https://depot.galaxyproject.org/singularity/multiqc:1.9--pyh9f0ad1d_0' + container = 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_1' } } From b23d21c215dc76ae3efaf26ba0aff7e674f5365a Mon Sep 17 00:00:00 2001 From: nelnk861 Date: Tue, 27 Feb 2024 15:27:46 +0100 Subject: [PATCH 4/6] reverted changes in README file --- README.md | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 2102caa..d9f9675 100644 --- a/README.md +++ b/README.md @@ -4,16 +4,9 @@ This is a Nextflow pipeline for generating sequencing reports for the SNP&Se ## Pre-requisites You need to: - install Nextflow (e.g. using conda `conda create -n nextflow-env nextflow` or downloading from [nextflow.io](https://www.nextflow.io/)). - - Make Nextflow binary executable: - ```bash - chmod +x /usr/local/bin/nextflow - ``` + - install [Singularity (version > 2.6)](https://singularity.lbl.gov/install-linux#adding-the-mirror-and-installing). - - Install test requirements: - ```bash - pip install -r requirements-dev.txt - ``` - - ins + Optional: - (currently mandatory: see known issues) Download the fastq-screen database by downloading fastq-screen from [here](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_v0.13.0.tar.gz), extract the archive and then run `fastq_screen --get_genomes`. From 956642266c4dad6925fe3cee9725bd722cd8e86e Mon Sep 17 00:00:00 2001 From: nelnk861 Date: Tue, 27 Feb 2024 15:28:35 +0100 Subject: [PATCH 5/6] reverted changes in README file --- README.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/README.md b/README.md index d9f9675..14b810b 100644 --- a/README.md +++ b/README.md @@ -4,10 +4,8 @@ This is a Nextflow pipeline for generating sequencing reports for the SNP&Se ## Pre-requisites You need to: - install Nextflow (e.g. using conda `conda create -n nextflow-env nextflow` or downloading from [nextflow.io](https://www.nextflow.io/)). - - install [Singularity (version > 2.6)](https://singularity.lbl.gov/install-linux#adding-the-mirror-and-installing). - Optional: - (currently mandatory: see known issues) Download the fastq-screen database by downloading fastq-screen from [here](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_v0.13.0.tar.gz), extract the archive and then run `fastq_screen --get_genomes`. From 3f87ec8b0270f5cbdd87f601c2412bcd30b5885e Mon Sep 17 00:00:00 2001 From: nelnk861 Date: Mon, 4 Mar 2024 15:38:28 +0100 Subject: [PATCH 6/6] Updated multiqc singularity container version --- config/nextflow_config/singularity.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/config/nextflow_config/singularity.config b/config/nextflow_config/singularity.config index 4618df8..3e37f21 100644 --- a/config/nextflow_config/singularity.config +++ b/config/nextflow_config/singularity.config @@ -20,10 +20,10 @@ process { container = 'https://depot.galaxyproject.org/singularity/illumina-interop:1.2.4--hdbdd923_2' } withName: 'MULTIQC_PER_FLOWCELL' { - container = 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_1' + container = 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' } withName: 'MULTIQC_PER_PROJECT' { - container = 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_1' + container = 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' } }