From 97e220947038a0ac96cd6874c5c248baacd5bd27 Mon Sep 17 00:00:00 2001 From: fellen31 <52530259+fellen31@users.noreply.github.com> Date: Thu, 22 Jun 2023 10:57:14 +0200 Subject: [PATCH 1/4] Update README.md --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 5d5791c109..cf937f6b33 100644 --- a/README.md +++ b/README.md @@ -383,7 +383,9 @@ The Singularity image download finds containers using two methods: 1. It runs `nextflow config` on the downloaded workflow to look for a `process.container` statement for the whole pipeline. This is the typical method used for DSL1 pipelines. 2. It scrapes any files it finds with a `.nf` file extension in the workflow `modules` directory for lines - that look like `container = "xxx"`. This is the typical method for DSL2 pipelines, which have one container per process. + that look like `container "xxx"`. This is the typical method for DSL2 pipelines, which have one container per process. + +> ⚠️ Containers specified with single quotes (container 'xxx') will not be picked up by `nf-core download`. Some DSL2 modules have container addresses for docker (eg. `biocontainers/fastqc:0.11.9--0`) and also URLs for direct downloads of a Singularity continaer (eg. `https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0`). Where both are found, the download URL is preferred. From ffc8bf0679bd8fd35dfba9cf57f73d4072e43411 Mon Sep 17 00:00:00 2001 From: Felix Lenner Date: Thu, 22 Jun 2023 10:57:56 +0200 Subject: [PATCH 2/4] change a comment --- nf_core/download.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/download.py b/nf_core/download.py index 347268ea04..8700dd8509 100644 --- a/nf_core/download.py +++ b/nf_core/download.py @@ -699,7 +699,7 @@ def find_container_images(self, workflow_directory): if file.endswith(".nf"): file_path = os.path.join(subdir, file) with open(file_path, "r") as fh: - # Look for any lines with `container = "xxx"` + # Look for any lines with `container "xxx"` this_container = None contents = fh.read() matches = re.findall(r"container\s*\"([^\"]*)\"", contents, re.S) From 091ee2a47fffa108cec2448d7247f5f1577d7ea4 Mon Sep 17 00:00:00 2001 From: fellen31 <52530259+fellen31@users.noreply.github.com> Date: Thu, 22 Jun 2023 11:43:10 +0200 Subject: [PATCH 3/4] clarify --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index cf937f6b33..0c69b9e822 100644 --- a/README.md +++ b/README.md @@ -385,9 +385,9 @@ The Singularity image download finds containers using two methods: 2. It scrapes any files it finds with a `.nf` file extension in the workflow `modules` directory for lines that look like `container "xxx"`. This is the typical method for DSL2 pipelines, which have one container per process. -> ⚠️ Containers specified with single quotes (container 'xxx') will not be picked up by `nf-core download`. +> ⚠️ Containers specified within lines that look like `container 'xxx'` will not be picked up by `nf-core download`. -Some DSL2 modules have container addresses for docker (eg. `biocontainers/fastqc:0.11.9--0`) and also URLs for direct downloads of a Singularity continaer (eg. `https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0`). +Some DSL2 modules have container addresses for docker (eg. `biocontainers/fastqc:0.11.9--0`) and also URLs for direct downloads of a Singularity container (eg. `https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0`). Where both are found, the download URL is preferred. Once a full list of containers is found, they are processed in the following order: From aea7354b3c81f90fafacb4dc3e06c605e385a3cf Mon Sep 17 00:00:00 2001 From: Felix Lenner Date: Thu, 22 Jun 2023 11:45:43 +0200 Subject: [PATCH 4/4] prettier --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 0c69b9e822..6e4ed5c3ff 100644 --- a/README.md +++ b/README.md @@ -385,7 +385,7 @@ The Singularity image download finds containers using two methods: 2. It scrapes any files it finds with a `.nf` file extension in the workflow `modules` directory for lines that look like `container "xxx"`. This is the typical method for DSL2 pipelines, which have one container per process. -> ⚠️ Containers specified within lines that look like `container 'xxx'` will not be picked up by `nf-core download`. +> ⚠️ Containers specified within lines that look like `container 'xxx'` will not be picked up by `nf-core download`. Some DSL2 modules have container addresses for docker (eg. `biocontainers/fastqc:0.11.9--0`) and also URLs for direct downloads of a Singularity container (eg. `https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0`). Where both are found, the download URL is preferred.