From 80637b1f22c0d4fb16e7777bcf250462bad42419 Mon Sep 17 00:00:00 2001
From: John Lafin <john.lafin@utsouthwestern.edu>
Date: Thu, 10 Oct 2024 11:22:58 -0500
Subject: [PATCH] Use nf-core container
---
CHANGES.md | 4 ++++
README.md | 3 +++
astrocyte_pkg.yml | 10 +++++++++-
docs/index.md | 4 ++++
workflow/configs/biohpc.config | 8 ++++++++
workflow/main.nf | 1 -
6 files changed, 28 insertions(+), 2 deletions(-)
diff --git a/CHANGES.md b/CHANGES.md
index 6f7fb16..72a2602 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,3 +1,7 @@
+2024-10-10
+
+Enabled containerization with nf-core cellranger image.
+
2024-06-20
Added support for barnyard reference.
diff --git a/README.md b/README.md
index cfa34ae..b7a9e1d 100755
--- a/README.md
+++ b/README.md
@@ -13,6 +13,9 @@ Output are standard cellranger outputs, including a cell-by-gene matrix in
both MTX and h5 formats, a summary of the run in an HTML output, and a BAM
file of aligned reads. These outputs can then be used for downstream analysis.
+Note: this workflow runs cellranger-count in a container, and is neither
+provided nor supported by 10x Genomics.
+
## Parameters
- Fastq: The fastq files for the sample. Regardless of the files that are
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index 4416824..04abe5b 100755
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -66,9 +66,17 @@ documentation_files:
# A list of cluster environment modules that this workflow requires to run.
# Specify versioned module names to ensure reproducibility.
workflow_modules:
- - 'cellranger/7.1.0'
- 'singularity/3.9.9'
+ # A list of container images requires to run this workflow.
+# Specify full path and version names to ensure reproducibility.
+# This keyword is required when 'container' is specified in Astrocyte 0.4.1 and above.
+# Singularity supports different registries, please specify the protocol to use.
+# Such as, "docker://", "shub://", "library://", etc. We encourage you to use the GitLab
+# container registry of BioHPC to save and manage your container images.
+workflow_containers:
+ - docker://quay.io/nf-core/cellranger:7.1.0
+
# A list of parameters used by the workflow, defining how to present them,
# options etc in the web interface. For each parameter:
#
diff --git a/docs/index.md b/docs/index.md
index 86081a4..fa3d5b5 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -5,6 +5,10 @@ Chromium single cell gene expression workflows. It accepts fastq.gz files as
input, which can be generated with the "BICF CellRanger mkfastq" Astrocyte
workflow.
+Note: this workflow runs cellranger-count in a container, and is neither
+provided nor supported by 10x Genomics.
+
+
## Parameters
To run this workflow, you must supply the following parameters:
diff --git a/workflow/configs/biohpc.config b/workflow/configs/biohpc.config
index a668f1d..9c84979 100755
--- a/workflow/configs/biohpc.config
+++ b/workflow/configs/biohpc.config
@@ -3,8 +3,16 @@ process {
clusterOptions = '--no-kill'
queue = '512GB,256GB,256GBv1,128GB'
time = '8h'
+ container = 'docker://quay.io/nf-core/cellranger:7.1.0'
}
+singularity {
+ enabled = true
+ runOptions = '--nv'
+ cacheDir = "${projectDir}/images/singularity"
+}
+
+
// Overwrite execution report files
// Required for nextflow version >22.10.0
diff --git a/workflow/main.nf b/workflow/main.nf
index edf3b02..9271c58 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -20,7 +20,6 @@ params.astrocyte = false
// Run cellranger count
process cr_count {
publishDir "${params.outDir}", mode: 'copy'
- module 'cellranger/7.1.0'
module 'singularity/3.9.9'
errorStrategy 'ignore'
--
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