kfukuta/wf-transcriptomes-v202
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Merge branch 'remove-bigwig' into 'dev'

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Remove bigwig CI test

See merge request epi2melabs/workflows/wf-transcriptomes!302
This commit is contained in:
Rory Munro 2026-05-26 16:43:06 +00:00
commit a4b08414cb
1 changed files with 1 additions and 9 deletions
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.gitlab-ci.yml
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@ -69,7 +69,7 @@ docker-run:
- MATRIX_NAME: [ - MATRIX_NAME: [
"int_discover_dna", "int_fixed_rna", "int_de_control_vs_control", "int_discover_dna", "int_fixed_rna", "int_de_control_vs_control",
"smoke_discover", "smoke_fixed", "smoke_direct_rna", "smoke_de", "smoke_discover", "smoke_fixed", "smoke_direct_rna", "smoke_de",
"mouse_de_0countquant", "mods_bigwig_igv" "mouse_de_0countquant"
] ]
rules: rules:
# NOTE As we're overriding the rules block for the included docker-run # 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 \ --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 \ --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" --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: singularity-run: