From d7a448f467d445bca9de65ac373f70d6bbe20879 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Wed, 20 Sep 2023 10:13:10 +0100 Subject: [PATCH] Updates for sanger testing --- .github/workflows/ci.yml | 4 +-- .github/workflows/sanger_test.yml | 29 ----------------- .../github_testing/TreeValTinyTest-Local.yaml | 31 ------------------- conf/github_test.config | 25 --------------- conf/local_github_test.config | 25 --------------- nextflow.config | 2 -- 6 files changed, 2 insertions(+), 114 deletions(-) delete mode 100644 .github/workflows/sanger_test.yml delete mode 100755 assets/github_testing/TreeValTinyTest-Local.yaml delete mode 100755 conf/github_test.config delete mode 100755 conf/local_github_test.config diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9d7b7c9b..c082bc5d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -43,9 +43,9 @@ jobs: - name: Run RAPID pipeline with test data # Remember that you can parallelise this by using strategy.matrix run: | - nextflow run ${GITHUB_WORKSPACE} -entry RAPID -profile github_test,docker --outdir ./results-rapid + nextflow run ${GITHUB_WORKSPACE} -entry RAPID -profile test,docker --outdir ./results-rapid - name: Run FULL pipeline with test data # Remember that you can parallelise this by using strategy.matrix run: | - nextflow run ${GITHUB_WORKSPACE} -profile github_test,docker --outdir ./results-full + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results-full diff --git a/.github/workflows/sanger_test.yml b/.github/workflows/sanger_test.yml deleted file mode 100644 index e69af1ef..00000000 --- a/.github/workflows/sanger_test.yml +++ /dev/null @@ -1,29 +0,0 @@ -name: sanger-tol LSF tests - -on: - workflow_dispatch: -jobs: - run-tower: - name: Run LSF tests - runs-on: ubuntu-latest - steps: - - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - revision: ${{ github.sha }} - workdir: ${{ secrets.TOWER_WORKDIR_PARENT }}/work/${{ github.repository }}/work-${{ github.sha }} - parameters: | - { - "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ github.sha }}", - } - profiles: test,sanger,singularity,cleanup - - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json diff --git a/assets/github_testing/TreeValTinyTest-Local.yaml b/assets/github_testing/TreeValTinyTest-Local.yaml deleted file mode 100755 index 532d0fd6..00000000 --- a/assets/github_testing/TreeValTinyTest-Local.yaml +++ /dev/null @@ -1,31 +0,0 @@ -assembly: - level: scaffold - sample_id: grTriPseu1 - latin_name: to_provide_taxonomic_rank - classT: fungi - asmVersion: 1 - dbVersion: "1" - gevalType: DTOL -reference_file: /nfs/treeoflife-01/teams/tola/users/dp24/treeval/TreeValTinyData/assembly/draft/grTriPseu1.fa -assem_reads: - pacbio: /nfs/treeoflife-01/teams/tola/users/dp24/treeval/TreeValTinyData/genomic_data/pacbio/ - hic: /nfs/treeoflife-01/teams/tola/users/dp24/treeval/TreeValTinyData/genomic_data/hic-arima/ - supplementary: path -alignment: - data_dir: /nfs/treeoflife-01/teams/tola/users/dp24/treeval/TreeValTinyData/gene_alignment_data/ - common_name: "" # For future implementation (adding bee, wasp, ant etc) - geneset: "LaetiporusSulphureus.gfLaeSulp1" - #Path should end up looking like "{data_dir}{classT}/{common_name}/csv_data/{geneset}-data.csv" -self_comp: - motif_len: 0 - mummer_chunk: 10 -synteny: - synteny_genome_path: /nfs/treeoflife-01/teams/tola/users/dp24/treeval/TreeValTinyData/synteny/ -outdir: "NEEDS TESTING" -intron: - size: "50k" -telomere: - teloseq: TTAGGG -busco: - lineages_path: /nfs/treeoflife-01/teams/tola/users/dp24/treeval/TreeValTinyData/busco/subset/ - lineage: fungi_odb10 diff --git a/conf/github_test.config b/conf/github_test.config deleted file mode 100755 index a5acbb0d..00000000 --- a/conf/github_test.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 FULL test' - config_profile_description = 'FULL 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 = "${projectDir}/assets/github_testing/TreeValTinyTest.yaml" - outdir = "TinyTest" -} diff --git a/conf/local_github_test.config b/conf/local_github_test.config deleted file mode 100755 index 8544b962..00000000 --- a/conf/local_github_test.config +++ /dev/null @@ -1,25 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running minimal tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a fast and simple pipeline test. - - Use as follows: - nextflow run sanger-tol/treeval -profile s3_test, --outdir - ----------------------------------------------------------------------------------------- -*/ - -params { - config_profile_name = 'GitHub FULL test' - config_profile_description = 'FULL Test Data for GitHub Actions test' - - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - - // Input data - input = "${projectDir}/assets/github_testing/TreeValTinyTest-Local.yaml" - outdir = "TinyTest" -} diff --git a/nextflow.config b/nextflow.config index 90516ac0..b13595f6 100755 --- a/nextflow.config +++ b/nextflow.config @@ -154,8 +154,6 @@ profiles { test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/farm_test.config' } - github_test { includeConfig 'conf/github_test.config' } - local_github_test { includeConfig 'conf/local_github_test.config' } }