From 905e842f362116b736ce05fd5b5db43b0f27dd89 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Sat, 11 Jul 2020 14:36:12 +0200 Subject: [PATCH] Update more paths --- .github/workflows/cutadapt.yml | 6 +++--- .github/workflows/docker.yml | 6 +++--- .github/workflows/fastqc.yml | 4 ++-- .github/workflows/samtools_index.yml | 4 ++-- .github/workflows/samtools_sort.yml | 4 ++-- .github/workflows/tcoffee.yml | 4 ++-- .github/workflows/trim_galore.yml | 4 ++-- 7 files changed, 16 insertions(+), 16 deletions(-) diff --git a/.github/workflows/cutadapt.yml b/.github/workflows/cutadapt.yml index ba92681d..dfb15238 100644 --- a/.github/workflows/cutadapt.yml +++ b/.github/workflows/cutadapt.yml @@ -2,7 +2,7 @@ name: cutadapt on: push: {} pull_request: - paths: tools/cutadapt/* + paths: software/cutadapt/* jobs: run_ci_test: @@ -25,10 +25,10 @@ jobs: - name: Test module with paired-end data run: | - cd tools/cutadapt/test_paired/ + cd software/cutadapt/test_paired/ nextflow run . -ansi-log false - name: Test module with single-end data run: | - cd tools/cutadapt/test_single/ + cd software/cutadapt/test_single/ nextflow run . -ansi-log false diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml index c4a39fe1..d63a83a3 100644 --- a/.github/workflows/docker.yml +++ b/.github/workflows/docker.yml @@ -5,8 +5,8 @@ on: branches: master # Only if a conda environment file or a docker build file has been updated paths: - - tools/*/environment.yml - - tools/*/Dockerfile + - software/*/environment.yml + - software/*/Dockerfile jobs: build_docker: @@ -36,7 +36,7 @@ jobs: echo $TOOL done; echo '-----' - for d in tools/*; do + for d in software/*; do for TOOL in $TOOLS; do echo "$d -- $TOOL" if echo $d/ | grep -q "$TOOL"; then diff --git a/.github/workflows/fastqc.yml b/.github/workflows/fastqc.yml index 9cfcfa55..4ddcbefe 100644 --- a/.github/workflows/fastqc.yml +++ b/.github/workflows/fastqc.yml @@ -2,7 +2,7 @@ name: FastQC on: push: {} pull_request: - paths: tools/fastqc/* + paths: software/fastqc/* jobs: run_ci_test: @@ -20,4 +20,4 @@ jobs: sudo mv nextflow /usr/local/bin/ # Test the module - - run: nextflow run ./tools/fastqc/test/ -ansi-log false + - run: nextflow run ./software/fastqc/test/ -ansi-log false diff --git a/.github/workflows/samtools_index.yml b/.github/workflows/samtools_index.yml index 302e0b6d..260c868d 100644 --- a/.github/workflows/samtools_index.yml +++ b/.github/workflows/samtools_index.yml @@ -2,7 +2,7 @@ name: samtools index on: push: {} pull_request: - paths: tools/samtools/index* + paths: software/samtools/index* jobs: run_ci_test: @@ -20,4 +20,4 @@ jobs: sudo mv nextflow /usr/local/bin/ # Test the module - - run: nextflow run ./tools/samtools/index/test/ -ansi-log false + - run: nextflow run ./software/samtools/index/test/ -ansi-log false diff --git a/.github/workflows/samtools_sort.yml b/.github/workflows/samtools_sort.yml index cc9ce4f8..b020dfbd 100644 --- a/.github/workflows/samtools_sort.yml +++ b/.github/workflows/samtools_sort.yml @@ -2,7 +2,7 @@ name: samtools sort on: push: {} pull_request: - paths: tools/samtools/sort* + paths: software/samtools/sort* jobs: run_ci_test: @@ -20,4 +20,4 @@ jobs: sudo mv nextflow /usr/local/bin/ # Test the module - - run: nextflow run ./tools/samtools/sort/test/ -ansi-log false + - run: nextflow run ./software/samtools/sort/test/ -ansi-log false diff --git a/.github/workflows/tcoffee.yml b/.github/workflows/tcoffee.yml index ab235e1b..7ec3431e 100644 --- a/.github/workflows/tcoffee.yml +++ b/.github/workflows/tcoffee.yml @@ -2,7 +2,7 @@ name: tcoffee on: push: {} pull_request: - paths: tools/tcoffee/* + paths: software/tcoffee/* jobs: run_ci_test: @@ -26,5 +26,5 @@ jobs: # Test the module - run: | - cd tools/tcoffee/test/ + cd software/tcoffee/test/ nextflow run . -ansi-log false diff --git a/.github/workflows/trim_galore.yml b/.github/workflows/trim_galore.yml index d914313e..ae823971 100644 --- a/.github/workflows/trim_galore.yml +++ b/.github/workflows/trim_galore.yml @@ -2,7 +2,7 @@ name: Trim Galore! on: push: {} pull_request: - paths: tools/trim_galore/* + paths: software/trim_galore/* jobs: run_ci_test: @@ -20,4 +20,4 @@ jobs: sudo mv nextflow /usr/local/bin/ # Test the module - - run: nextflow run ./tools/trim_galore/test/ -ansi-log false + - run: nextflow run ./software/trim_galore/test/ -ansi-log false