diff --git a/.github/workflows/nextflow_CI.yml b/.github/workflows/nextflow_CI.yml index b54410e..d5ca39b 100644 --- a/.github/workflows/nextflow_CI.yml +++ b/.github/workflows/nextflow_CI.yml @@ -17,25 +17,9 @@ jobs: wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ - - name: Install Singularity - run: | - sudo apt-get update && sudo apt-get install -y \ - build-essential \ - libssl-dev \ - uuid-dev \ - libgpgme11-dev \ - squashfs-tools \ - libseccomp-dev \ - wget \ - pkg-config \ - git \ - cryptsetup - wget https://github.com/sylabs/singularity/releases/download/v3.10.0/singularity-ce_3.10.0-focal_amd64.deb - sudo dpkg -i singularity-ce_3.10.0-focal_amd64.deb - - name: Run pipeline test (user) run: | - nextflow run main.nf -profile singularity --prefix "covidmvp-user-$(date +%Y-%m-%d)" -params-file covidmvp_user.yaml + nextflow run main.nf -profile docker --prefix "covidmvp-user-$(date +%Y-%m-%d)" -params-file covidmvp_user.yaml test_sarscov2_reference: name: Run pipeline test (reference) @@ -48,22 +32,6 @@ jobs: wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ - - name: Install Singularity - run: | - sudo apt-get update && sudo apt-get install -y \ - build-essential \ - libssl-dev \ - uuid-dev \ - libgpgme11-dev \ - squashfs-tools \ - libseccomp-dev \ - wget \ - pkg-config \ - git \ - cryptsetup - wget https://github.com/sylabs/singularity/releases/download/v3.10.0/singularity-ce_3.10.0-focal_amd64.deb - sudo dpkg -i singularity-ce_3.10.0-focal_amd64.deb - - name: Run pipeline test (reference) run: | - nextflow run main.nf -profile singularity --prefix "covidmvp-$(date +%Y-%m-%d)" -params-file covidmvp_clinical_params.yaml + nextflow run main.nf -profile docker --prefix "covidmvp-$(date +%Y-%m-%d)" --end_date $(date +%Y-%m-%d) -params-file covidmvp_clinical_params.yaml diff --git a/conf/profiles.config b/conf/profiles.config index e0d4cb1..f6eaed4 100644 --- a/conf/profiles.config +++ b/conf/profiles.config @@ -65,7 +65,7 @@ profiles { } wave { wave.enabled = true - wave.strategy = ['singularity', 'container'] + wave.strategy = ['singularity'] } eagle { includeConfig 'eagle.config' } } \ No newline at end of file diff --git a/covidmvp_clinical_params.yaml b/covidmvp_clinical_params.yaml index 6c44072..ec60be6 100644 --- a/covidmvp_clinical_params.yaml +++ b/covidmvp_clinical_params.yaml @@ -8,7 +8,6 @@ skip_postprocessing: false skip_posting: true skip_harmonize: true start_date: "2020-01-01" -end_date: "(date +%Y-%m-%d)" metadata_source: "ViralAi_EpiCoV" metadata_config: "metadata_conf/metadata.yaml" outdir: "results/covidmvp" diff --git a/modules/local/convertgff2json.nf b/modules/local/convertgff2json.nf index 9f318f7..4dfa2a3 100644 --- a/modules/local/convertgff2json.nf +++ b/modules/local/convertgff2json.nf @@ -8,7 +8,7 @@ process CONVERTGFFTOJSON { conda "conda-forge::pandas=1.4.3" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.4.3' - : 'community.wave.seqera.io/library/pip_pandas:f80b46869e03f6ef'}" + : 'amancevice/pandas:1.4.3'}" input: tuple val(meta), path(gff) diff --git a/modules/local/extractMetadata.nf b/modules/local/extractMetadata.nf index 005c9de..f892978 100644 --- a/modules/local/extractMetadata.nf +++ b/modules/local/extractMetadata.nf @@ -3,7 +3,7 @@ process EXTRACTMETADATA { conda "conda-forge::pandas=1.4.3" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.4.3' - : 'community.wave.seqera.io/library/pip_pandas:f80b46869e03f6ef'}" + : 'amancevice/pandas:1.4.3'}" input: tuple val(meta), path(metadata) diff --git a/modules/local/extractVariants.nf b/modules/local/extractVariants.nf index b861c55..238c302 100644 --- a/modules/local/extractVariants.nf +++ b/modules/local/extractVariants.nf @@ -3,7 +3,7 @@ process EXTRACTVARIANTS { conda "conda-forge::pandas=1.4.3" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.4.3' - : 'community.wave.seqera.io/library/pip_pandas:f80b46869e03f6ef'}" + : 'amancevice/pandas:1.4.3'}" input: tuple val(meta), path(variants) diff --git a/modules/local/harmonize_metadata.nf b/modules/local/harmonize_metadata.nf index e5f4cbd..de40df2 100644 --- a/modules/local/harmonize_metadata.nf +++ b/modules/local/harmonize_metadata.nf @@ -4,7 +4,7 @@ process METADATA_HARMONIZER { conda "conda-forge::pandas=1.4.3" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.4.3' - : 'community.wave.seqera.io/library/pip_pandas:f80b46869e03f6ef'}" + : 'amancevice/pandas:1.4.3'}" input: tuple val(meta), path(metadata) diff --git a/modules/local/merge_classification_report.nf b/modules/local/merge_classification_report.nf index f9a6fb6..b40a270 100644 --- a/modules/local/merge_classification_report.nf +++ b/modules/local/merge_classification_report.nf @@ -3,7 +3,7 @@ process MERGE_CLASSIFFICATION_METADATA { conda "conda-forge::pandas=1.4.3" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.4.3' - : 'community.wave.seqera.io/library/pip_pandas:f80b46869e03f6ef'}" + : 'amancevice/pandas:1.4.3'}" input: tuple val(meta), path(metadata) diff --git a/modules/local/splitmutations_gvf.nf b/modules/local/splitmutations_gvf.nf index 5bcf46e..3d6c6c2 100644 --- a/modules/local/splitmutations_gvf.nf +++ b/modules/local/splitmutations_gvf.nf @@ -5,7 +5,7 @@ process NCOVSPLITMUTATIONSGVF { conda "conda-forge::pandas=1.4.3" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.4.3' - : 'community.wave.seqera.io/library/pip_pandas:f80b46869e03f6ef'}" + : 'amancevice/pandas:1.4.3'}" input: tuple val(meta), path(gvf) diff --git a/modules/local/splitmutations_pokay.nf b/modules/local/splitmutations_pokay.nf index 7396183..07f4cdd 100644 --- a/modules/local/splitmutations_pokay.nf +++ b/modules/local/splitmutations_pokay.nf @@ -5,7 +5,7 @@ process NCOVSPLITMUTATIONSPOKAY { conda "conda-forge::pandas=1.4.3" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.4.3' - : 'community.wave.seqera.io/library/pip_pandas:f80b46869e03f6ef'}" + : 'amancevice/pandas:1.4.3'}" input: tuple val(meta), path(annotations) diff --git a/modules/local/vcftogvf.nf b/modules/local/vcftogvf.nf index 9881995..4b8d25e 100644 --- a/modules/local/vcftogvf.nf +++ b/modules/local/vcftogvf.nf @@ -3,7 +3,7 @@ process VCFTOGVF { conda "conda-forge::pandas=1.4.3" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.4.3' - : 'community.wave.seqera.io/library/pip_pandas:f80b46869e03f6ef'}" + : 'amancevice/pandas:1.4.3'}" input: tuple val(meta), path(vcf)