From 5f9cf40f5a13ae127b3c232fe426f45dd6f91b9f Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Fri, 6 Mar 2020 12:23:23 +0100
Subject: [PATCH] Changing `publishDir` to take `params.outdir` and modifying
 `yml` for github actions

---
 .github/workflows/tcoffee.yml | 8 +++-----
 tools/tcoffee/main.nf         | 3 +--
 2 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/tcoffee.yml b/.github/workflows/tcoffee.yml
index d24596aa..f96c63d0 100644
--- a/.github/workflows/tcoffee.yml
+++ b/.github/workflows/tcoffee.yml
@@ -18,15 +18,13 @@ jobs:
           auth_header="$(git config --local --get http.https://github.com/.extraheader)"
           git submodule sync --recursive
           git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
-          ls -la test-datasets/tools/tcoffee/input/
-          echo "============"
-          rm ./test-datasets/tools/tcoffee/input/BBA0001.tfa
-          cp test-datasets/general/fasta/msa/BBA0001.tfa ./test-datasets/tools/tcoffee/input/
 
     - name: Install Nextflow
       run: |
         wget -qO- get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
 
+    ls -la test-datasets/tools/tcoffee/input/
+
     # Test the module
-    - run: nextflow run ./tools/tcoffee/test/ -ansi-log false
+    - run: cd tools/tcoffee/test/ | nextflow run . -ansi-log false
diff --git a/tools/tcoffee/main.nf b/tools/tcoffee/main.nf
index 55f7ab37..42945850 100644
--- a/tools/tcoffee/main.nf
+++ b/tools/tcoffee/main.nf
@@ -1,7 +1,6 @@
 process tcoffee {
     tag {fasta}
-    // publishDir "${params.outdir}/tcoffee" //not working
-    publishDir "${baseDir}/results/tcoffee", mode: 'copy'
+    publishDir "${params.outdir}/tcoffee"
     container 'quay.io/biocontainers/t_coffee:11.0.8--py27pl5.22.0_5'
 
     input: