From 8f73f5e29173cd9f99ba4fce02f61012aeacdb04 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 18 Nov 2024 10:22:33 +0000 Subject: [PATCH 1/2] Make cd less specific --- docs/hello_nextflow/03_hello_containers.md | 6 +----- docs/hello_nextflow/04_hello_genomics.md | 3 +-- 2 files changed, 2 insertions(+), 7 deletions(-) diff --git a/docs/hello_nextflow/03_hello_containers.md b/docs/hello_nextflow/03_hello_containers.md index 9cda3c24..82778edb 100644 --- a/docs/hello_nextflow/03_hello_containers.md +++ b/docs/hello_nextflow/03_hello_containers.md @@ -112,11 +112,7 @@ When you run a container, it is isolated from the host system by default. This means that the container can't access any files on the host system unless you explicitly tell it to. One way to do this is to **mount** a **volume** from the host system into the container. -Prior to working on the next task, confirm that you are in the `hello-nextflow` directory. - -```bash -cd /workspace/gitpod/hello-nextflow -``` +Prior to working on the next task, confirm that you are in the `hello-nextflow` directory. Thelast part of the path shown when you type `pwd` should be `hello-nextflow`. Then run: diff --git a/docs/hello_nextflow/04_hello_genomics.md b/docs/hello_nextflow/04_hello_genomics.md index 8ed15302..9dad70a1 100644 --- a/docs/hello_nextflow/04_hello_genomics.md +++ b/docs/hello_nextflow/04_hello_genomics.md @@ -54,8 +54,7 @@ The tools we need (Samtools and GATK) are not installed in the Gitpod environmen !!! note - Make sure you're in the correct working directory: - `cd /workspace/gitpod/hello-nextflow` + Make sure you're in the `hello-nextflow` directory so that the last part of the path shown when you type `pwd` is `hello-nextflow`. ### 0.1. Index a BAM input file with Samtools From 5183bc417a3ba92bf174d96f68b094bd2fa901ff Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 18 Nov 2024 10:31:06 +0000 Subject: [PATCH 2/2] Update docs/hello_nextflow/03_hello_containers.md Co-authored-by: Friederike Hanssen --- docs/hello_nextflow/03_hello_containers.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/hello_nextflow/03_hello_containers.md b/docs/hello_nextflow/03_hello_containers.md index 82778edb..ecb66184 100644 --- a/docs/hello_nextflow/03_hello_containers.md +++ b/docs/hello_nextflow/03_hello_containers.md @@ -112,7 +112,7 @@ When you run a container, it is isolated from the host system by default. This means that the container can't access any files on the host system unless you explicitly tell it to. One way to do this is to **mount** a **volume** from the host system into the container. -Prior to working on the next task, confirm that you are in the `hello-nextflow` directory. Thelast part of the path shown when you type `pwd` should be `hello-nextflow`. +Prior to working on the next task, confirm that you are in the `hello-nextflow` directory. The last part of the path shown when you type `pwd` should be `hello-nextflow`. Then run: