From d9982be91647c5fa274f4b24c7b418788f4ca371 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 22 Nov 2024 13:40:43 +0000 Subject: [PATCH 1/5] Update assets tip to use NXF_HOME --- docs/hello_nextflow/09_hello_nf-core.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/hello_nextflow/09_hello_nf-core.md b/docs/hello_nextflow/09_hello_nf-core.md index 0f1d2402..62ade494 100644 --- a/docs/hello_nextflow/09_hello_nf-core.md +++ b/docs/hello_nextflow/09_hello_nf-core.md @@ -66,7 +66,7 @@ However nf-core is the largest open curated collection of Nextflow pipelines. One detail that sometimes trips people up is that the pipelines you pull this way are stored in a hidden assets folder: ```bash - tree $HOME/.nextflow/assets/ -L 2 + tree $NXF_HOME/assets/ -L 2 ``` ```console title="Output" From 38512471cab3bdd8b05443671827ffef49845abe Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 22 Nov 2024 13:51:32 +0000 Subject: [PATCH 2/5] set nxf_home in gitpod too --- .gitpod.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitpod.yml b/.gitpod.yml index 1067a404..d176ad17 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -29,6 +29,8 @@ tasks: command: docker pull -q nextflow/rnaseq-nf - name: Start Nextflow Tutorial + env: + NXF_HOME: "/home/gitpod/.nextflow" command: | cd hello-nextflow source $HOME/.bashrc From b15051afcb9b3a105bb99192a7af4b1af49603ce Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 22 Nov 2024 14:53:45 +0000 Subject: [PATCH 3/5] clarify default --- docs/hello_nextflow/09_hello_nf-core.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/hello_nextflow/09_hello_nf-core.md b/docs/hello_nextflow/09_hello_nf-core.md index 62ade494..c81e80af 100644 --- a/docs/hello_nextflow/09_hello_nf-core.md +++ b/docs/hello_nextflow/09_hello_nf-core.md @@ -63,7 +63,7 @@ However nf-core is the largest open curated collection of Nextflow pipelines. !!!tip - One detail that sometimes trips people up is that the pipelines you pull this way are stored in a hidden assets folder: + One detail that sometimes trips people up is that the pipelines you pull this way are stored in a hidden assets folder. By default this is at `$HOME/.nextflow/assets`, but in this training environment you can check `$NXF_HOME/assets`: ```bash tree $NXF_HOME/assets/ -L 2 From d833b9580198f7e7eaec845e5a00e1d8e5ecd416 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 22 Nov 2024 15:18:51 +0000 Subject: [PATCH 4/5] Update docs/hello_nextflow/09_hello_nf-core.md Co-authored-by: Christopher Hakkaart --- docs/hello_nextflow/09_hello_nf-core.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/hello_nextflow/09_hello_nf-core.md b/docs/hello_nextflow/09_hello_nf-core.md index c81e80af..3f88b55b 100644 --- a/docs/hello_nextflow/09_hello_nf-core.md +++ b/docs/hello_nextflow/09_hello_nf-core.md @@ -63,7 +63,7 @@ However nf-core is the largest open curated collection of Nextflow pipelines. !!!tip - One detail that sometimes trips people up is that the pipelines you pull this way are stored in a hidden assets folder. By default this is at `$HOME/.nextflow/assets`, but in this training environment you can check `$NXF_HOME/assets`: + Pulled pipelines are stored in a hidden assets folder. By default, this folder is `$HOME/.nextflow/assets`, but in this training environment the folder has been set to `$NXF_HOME/assets`: ```bash tree $NXF_HOME/assets/ -L 2 From 7a0bef323f2b47c7e0969cf2a70c4ac1ed45747c Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 22 Nov 2024 15:25:20 +0000 Subject: [PATCH 5/5] correct gitpod dir --- .gitpod.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitpod.yml b/.gitpod.yml index d176ad17..3cdc01b6 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -30,7 +30,7 @@ tasks: - name: Start Nextflow Tutorial env: - NXF_HOME: "/home/gitpod/.nextflow" + NXF_HOME: "/workspace/gitpod/.nextflow" command: | cd hello-nextflow source $HOME/.bashrc