Change remaining nfstem to nf-stem

CHANGELOG.md

@@ -1,4 +1,4 @@
-# adamrtalbot/nfstem: Changelog
+# adamrtalbot/nf-stem: Changelog
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

README.md

@@ -5,7 +5,7 @@
 - It is generated using the template and should be compatible with `nf-core sync` for the foreseeable future
 - It uses the `nf-validate` plugin to reduce boilerplate code
 - It removes some additional files such as `docs/`
-- It uses Nextflow code to replace the Java classes in `lib/` (see [the initialise subworkflow](./subworkflows/local/initialise/main.nf))
+- It uses Nextflow code to replace the Java classes in `lib/` (see [the initialise subworkflow](./subworkflows/local/initialise.nf))
 - It uses `results` as a default value for `--outdir` to remove one additional parameter user need to supply
 - It removes email and slack integration for simplicity
 - It removes Github features so developers can add their own
@@ -69,7 +69,7 @@ CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
 Now, you can run the pipeline using:
 
 ```bash
-nextflow run adamrtalbot/nfstem \
+nextflow run adamrtalbot/nf-stem \
    -profile <docker/singularity/.../institute> \
    --input samplesheet.csv
 ```
@@ -81,7 +81,7 @@ nextflow run adamrtalbot/nfstem \
 
 ## Credits
 
-adamrtalbot/nfstem was originally written by Adam Talbot.
+adamrtalbot/nf-stem was originally written by Adam Talbot.
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 

modules.json

@@ -1,6 +1,6 @@
 {
-    "name": "adamrtalbot/nfstem",
-    "homePage": "https://github.com/adamrtalbot/nfstem",
+    "name": "adamrtalbot/nf-stem",
+    "homePage": "https://github.com/adamrtalbot/nf-stem",
     "repos": {
         "https://github.com/nf-core/modules.git": {
             "modules": {

nextflow_schema.json

@@ -1,7 +1,7 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/adamrtalbot/nfstem/master/nextflow_schema.json",
-    "title": "adamrtalbot/nfstem pipeline parameters",
+    "$id": "https://raw.githubusercontent.com/adamrtalbot/nf-stem/master/nextflow_schema.json",
+    "title": "adamrtalbot/nf-stem pipeline parameters",
     "description": "Minimal nf-core pipeline compatible with template",
     "type": "object",
     "definitions": {