From 1b34481e5997dfc9d03a866a2be179211785d0ee Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Wed, 13 Sep 2023 09:25:15 +0100 Subject: [PATCH] Updates to testing profiles --- .github/workflows/ci.yml | 8 +++--- conf/farm_rapid.config | 23 ----------------- conf/{farm_full.config => farm_test.config} | 1 + conf/github_rapid.config | 25 ------------------- ...{github_full.config => github_test.config} | 2 +- conf/local_github_rapid.config | 25 ------------------- ...b_full.config => local_github_test.config} | 2 +- 7 files changed, 7 insertions(+), 79 deletions(-) delete mode 100755 conf/farm_rapid.config rename conf/{farm_full.config => farm_test.config} (95%) delete mode 100755 conf/github_rapid.config rename conf/{github_full.config => github_test.config} (96%) delete mode 100755 conf/local_github_rapid.config rename conf/{local_github_full.config => local_github_test.config} (96%) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f4b23bf5..89b33330 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -40,12 +40,12 @@ jobs: run: | curl https://dp24.cog.sanger.ac.uk/TreeValTinyData.tar.gz | tar xzf - - - name: Run FULL pipeline with test data + - name: Run RAPID pipeline with test data # Remember that you can parallelise this by using strategy.matrix run: | - nextflow run ${GITHUB_WORKSPACE} -entry FULL -profile github_full,docker --outdir ./results + nextflow run ${GITHUB_WORKSPACE} -entry RAPID -profile github_test,docker --outdir ./results-rapid - - name: Run RAPID pipeline with test data + - name: Run FULL pipeline with test data # Remember that you can parallelise this by using strategy.matrix run: | - nextflow run ${GITHUB_WORKSPACE} -entry RAPID -profile github_rapid,docker --outdir ./results + nextflow run ${GITHUB_WORKSPACE} -entry FULL -profile github_test,docker --outdir ./results-full diff --git a/conf/farm_rapid.config b/conf/farm_rapid.config deleted file mode 100755 index 5beaa889..00000000 --- a/conf/farm_rapid.config +++ /dev/null @@ -1,23 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running full-size tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a full size pipeline test. - - Use as follows: - nextflow run sanger-tol/treeval -profile farm_rapid,singularity,sanger - - On LSF / tol farm: - bsub -Is -tty -e error -o out -n 2 -q oversubscribed -M4000 -R'select[mem>4000] rusage[mem=4000] span[hosts=1]' 'nextflow run main.nf -profile test_full,singularity,sanger' - ----------------------------------------------------------------------------------------- -*/ - -cleanup = true - -params { - config_profile_name = "RAPID local test profile" - config_profile_description = "RAPID test dataset to check pipeline function, using a current subset local dataset" - - input = "${projectDir}/assets/local_testing/nxOscDF5033.yaml" -} diff --git a/conf/farm_full.config b/conf/farm_test.config similarity index 95% rename from conf/farm_full.config rename to conf/farm_test.config index 6389f53c..68b15e3a 100755 --- a/conf/farm_full.config +++ b/conf/farm_test.config @@ -20,4 +20,5 @@ params { config_profile_description = "FULL test dataset to check pipeline function, using a current full local dataset" input = "${projectDir}/assets/local_testing/nxOscDF5033.yaml" + output = nxOscDF5033 } diff --git a/conf/github_rapid.config b/conf/github_rapid.config deleted file mode 100755 index 51c5decf..00000000 --- a/conf/github_rapid.config +++ /dev/null @@ -1,25 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running minimal tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a fast and simple pipeline test. - - Use as follows: - nextflow run sanger-tol/treeval -profile s3_test, --outdir - ----------------------------------------------------------------------------------------- -*/ - -params { - config_profile_name = 'GitHub RAPID test' - config_profile_description = 'Subset Test Data for GitHub Actions test' - - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - - // Input data - input = "${projectDir}/assets/github_testing/TreeValTinyTest.yaml" - outdir = "TinyTest-RAPID" -} diff --git a/conf/github_full.config b/conf/github_test.config similarity index 96% rename from conf/github_full.config rename to conf/github_test.config index 6842cc8a..a5acbb0d 100755 --- a/conf/github_full.config +++ b/conf/github_test.config @@ -21,5 +21,5 @@ params { // Input data input = "${projectDir}/assets/github_testing/TreeValTinyTest.yaml" - outdir = "TinyTest-FULL" + outdir = "TinyTest" } diff --git a/conf/local_github_rapid.config b/conf/local_github_rapid.config deleted file mode 100755 index a2d00484..00000000 --- a/conf/local_github_rapid.config +++ /dev/null @@ -1,25 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running minimal tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a fast and simple pipeline test. - - Use as follows: - nextflow run sanger-tol/treeval -profile s3_test, --outdir - ----------------------------------------------------------------------------------------- -*/ - -params { - config_profile_name = 'GitHub RAPID test' - config_profile_description = 'Subset Test Data for GitHub Actions test' - - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - - // Input data - input = "${projectDir}/assets/github_testing/TreeValTinyTest-Local.yaml" - outdir = "TinyTest-RAPID" -} diff --git a/conf/local_github_full.config b/conf/local_github_test.config similarity index 96% rename from conf/local_github_full.config rename to conf/local_github_test.config index af80fc82..8544b962 100755 --- a/conf/local_github_full.config +++ b/conf/local_github_test.config @@ -21,5 +21,5 @@ params { // Input data input = "${projectDir}/assets/github_testing/TreeValTinyTest-Local.yaml" - outdir = "TinyTest-FULL" + outdir = "TinyTest" }