From ef1aeafef6158fd79382754af26b4c92c958c822 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 8 Mar 2019 16:41:47 +0100
Subject: [PATCH 1/3] Remove incorrect comment in code example

---
 README.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/README.md b/README.md
index 969a7ec..4a637d5 100644
--- a/README.md
+++ b/README.md
@@ -46,7 +46,6 @@ Alternatively, instead of using the configuration profiles from this repository,
 pipeline directly calling the single institutional config file that you need with the `-c` parameter.
 
 ```bash
-## Example command for nf-core/rnaseq
 nextflow run /path/to/pipeline/ -c /path/to/my/configs/configs-master/conf/my_config.config
 ```
 

From a79564f0afc4e2d33351f6f2be48d7b2315bfd14 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Tue, 12 Mar 2019 17:02:24 +0100
Subject: [PATCH 2/3] Remove requirement for dev branch PRs

---
 .travis.yml | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index b200b4a..276304c 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -9,10 +9,6 @@ cache: pip
 matrix:
   fast_finish: true
 
-before_install:
-  # PRs to master are only ok if coming from dev branch
-  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])'
-
 install:
   # Install Nextflow
   - mkdir /tmp/nextflow && cd /tmp/nextflow
@@ -26,4 +22,7 @@ env:
 
 script:
   # Run the pipeline with the test profile and test remote config
-  - grep "{.*includeConfig.*[a-z]*\.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | tr -s ' ' | cut -d " " -f 2 | xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf -profile {}
+  - grep "{.*includeConfig.*[a-z]*\.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | \
+    tr -s ' ' | \
+    cut -d " " -f 2 | \
+    xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf -profile {}

From eaa1c8360fc3fd6b76e3b1b5f5f8dc9ce4c625b4 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Tue, 12 Mar 2019 17:25:16 +0100
Subject: [PATCH 3/3] Travis multiline yaml

---
 .travis.yml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 276304c..918a846 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -22,7 +22,8 @@ env:
 
 script:
   # Run the pipeline with the test profile and test remote config
-  - grep "{.*includeConfig.*[a-z]*\.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | \
-    tr -s ' ' | \
-    cut -d " " -f 2 | \
-    xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf -profile {}
+  - |
+      grep "{.*includeConfig.*[a-z]*\.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | \
+      tr -s ' ' | \
+      cut -d " " -f 2 | \
+      xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf -profile {}