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Changing publishDir to take params.outdir and modifying yml for github actions

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This commit is contained in:
JoseEspinosa 2020-03-06 12:23:23 +01:00
parent 5de4c86bac
commit 5f9cf40f5a
2 changed files with 4 additions and 7 deletions
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8
.github/workflows/tcoffee.yml vendored
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@ -18,15 +18,13 @@ jobs:
auth_header="$(git config --local --get http.https://github.com/.extraheader)" auth_header="$(git config --local --get http.https://github.com/.extraheader)"
git submodule sync --recursive git submodule sync --recursive
git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1 git -c "http.extraheader=$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 - name: Install Nextflow
run: | run: |
wget -qO- get.nextflow.io | bash wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/ sudo mv nextflow /usr/local/bin/
ls -la test-datasets/tools/tcoffee/input/
# Test the module # Test the module
- run: nextflow run ./tools/tcoffee/test/ -ansi-log false - run: cd tools/tcoffee/test/ | nextflow run . -ansi-log false

3
tools/tcoffee/main.nf
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@ -1,7 +1,6 @@
process tcoffee { process tcoffee {
tag {fasta} tag {fasta}
// publishDir "${params.outdir}/tcoffee" //not working publishDir "${params.outdir}/tcoffee"
publishDir "${baseDir}/results/tcoffee", mode: 'copy'
container 'quay.io/biocontainers/t_coffee:11.0.8--py27pl5.22.0_5' container 'quay.io/biocontainers/t_coffee:11.0.8--py27pl5.22.0_5'
input: input: