From 1192f09bc702876a646d5286b5abcf7c8b68eaac Mon Sep 17 00:00:00 2001 From: Rory Munro Date: Tue, 26 May 2026 16:43:05 +0000 Subject: [PATCH] Remove bigwig CI test --- .gitlab-ci.yml | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 261d126..a3c38bc 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -69,7 +69,7 @@ docker-run: - MATRIX_NAME: [ "int_discover_dna", "int_fixed_rna", "int_de_control_vs_control", "smoke_discover", "smoke_fixed", "smoke_direct_rna", "smoke_de", - "mouse_de_0countquant", "mods_bigwig_igv" + "mouse_de_0countquant" ] rules: # NOTE As we're overriding the rules block for the included docker-run @@ -181,14 +181,6 @@ docker-run: --de_analysis --ref_genome ${CI_PROJECT_NAME}/data/mouse_subset_test/mouse_subset.fa \ --ref_annotation ${CI_PROJECT_NAME}/data/mouse_subset_test/mouse_subset.gtf.gz \ --direct_rna --sample_sheet ${CI_PROJECT_NAME}/data/mouse_subset_test/sample_sheet.csv" - # MM/ML tag test - - if: $MATRIX_NAME == "mods_bigwig_igv" - variables: - NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -nv https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/mods_rna_subset.tar.gz -O ${CI_PROJECT_NAME}/data/mods_rna_subset.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/mods_rna_subset.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -nv https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_49/gencode.v49.annotation.gtf.gz -O ${CI_PROJECT_NAME}/data/gencode.v49.annotation.gtf.gz && wget -nv https://ont-open-data.s3.amazonaws.com/references/human/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz -O ${CI_PROJECT_NAME}/data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz" - NF_WORKFLOW_OPTS: "--bam ${CI_PROJECT_NAME}/data/mods_rna_subset/barcode01/merged.sorted.bam \ - --ref_genome ${CI_PROJECT_NAME}/data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \ - --ref_annotation ${CI_PROJECT_NAME}/data/gencode.v49.annotation.gtf.gz \ - --igv" singularity-run: