From 7cfdfa5ac57f4c5ffac387dabadb5e085969299b Mon Sep 17 00:00:00 2001
From: "Dr. Ernie Prabhakar" <19791+drernie@users.noreply.github.com>
Date: Tue, 24 Dec 2024 12:24:17 -0800
Subject: [PATCH] make sarek, fetchngs

---
 Makefile      | 2 +-
 README-DEV.md | 7 +++++++
 README.md     | 2 +-
 3 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index 85400ad7..b77008bd 100644
--- a/Makefile
+++ b/Makefile
@@ -121,7 +121,7 @@ $(PIPELINE): nf-git-ver
 	NXF_PLUGINS_TEST_REPOSITORY=$(NXF_PLUGINS_TEST_REPOSITORY) NXF_VER=$(NXF_VER) $(NF_GIT) run nf-core/$(PIPELINE) -r master -profile test,docker -plugins $(PROJECT)@$(VERSION) --outdir "$(PIPE_OUT)"
 
 fetchngs: nf-git-ver
-	NXF_VER=$(NXF_VER) $(NF_GIT) run nf-core/fetchngs -profile docker -r dev -latest --pub "$(TEST_URI)"
+	NXF_PLUGINS_TEST_REPOSITORY=$(NXF_PLUGINS_TEST_REPOSITORY) NXF_VER=$(NXF_VER) $(NF_GIT) run nf-core/fetchngs -r master -profile test,docker -plugins $(PROJECT)@$(VERSION) --input ../nf-quilt/wf/ids.csv --outdir s3://$(WRITE_BUCKET)/nf-quilt/fetchngs
 
 #
 # Show dependencies
diff --git a/README-DEV.md b/README-DEV.md
index d8b1515f..2c5183d9 100644
--- a/README-DEV.md
+++ b/README-DEV.md
@@ -85,6 +85,13 @@ For example:
 ./launch.sh run ./main.nf -profile standard -plugins $(PROJECT) --outdir "quilt+s3://bucket#package=test/hurdat"
 ```
 
+There are standard Makefile targets for both `sarek` and `fetchngs` pipelines, which will test against the latest published versions of nf-quilt:
+
+```bash
+make sarek
+make fetchngs
+```
+
 ### Unit Testing
 
 You can cleanly compile and run all unit tests with:
diff --git a/README.md b/README.md
index 35905f60..378a1838 100644
--- a/README.md
+++ b/README.md
@@ -91,7 +91,7 @@ the `<> CODE | URI` section at the top of the package page.
 ### Output URIs
 
 You can specify a Quilt+ URI as the `--outdir` parameter in your Nextflow
-pipeline if you want to specify the package name and metadata for the output,
+pipeline, if you want to specify the package name and metadata for the output,
 but don't care about the precise location in S3. For example:
 
 ```shell