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Test for mods output [CW-7416]

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This commit is contained in:
Neil Horner 2026-07-14 10:05:38 +00:00
parent 66b0e377a9
commit 205ba78998
1 changed files with 7 additions and 0 deletions
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7
.gitlab-ci.yml
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@ -191,6 +191,13 @@ docker-run:
--ref_annotation ${CI_PROJECT_NAME}/data/gencode.v22.annotation.chr20.gtf \ --ref_annotation ${CI_PROJECT_NAME}/data/gencode.v22.annotation.chr20.gtf \
--sample_sheet ${CI_PROJECT_NAME}/data/mods_rna_subset/sample_sheet.csv \ --sample_sheet ${CI_PROJECT_NAME}/data/mods_rna_subset/sample_sheet.csv \
--igv" --igv"
AFTER_NEXTFLOW_CMD: >
for sample in sample01 sample02; do
for suffix in mods.bedmethyl.gz mods.inosine.bw mods.m5C.bw mods.m6A.bw mods.pseU.bw mods.summary.tsv; do
test -f ${CI_PROJECT_NAME}/samples/$${sample}/mods/$${sample}.$${suffix};
done;
done;
- if: $MATRIX_NAME == "mouse_splice_error" - if: $MATRIX_NAME == "mouse_splice_error"
variables: variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/mouse_splice_fail.tar.gz -O ${CI_PROJECT_NAME}/data/mouse_splice_fail.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/mouse_splice_fail.tar.gz -C ${CI_PROJECT_NAME}/data/" NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/mouse_splice_fail.tar.gz -O ${CI_PROJECT_NAME}/data/mouse_splice_fail.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/mouse_splice_fail.tar.gz -C ${CI_PROJECT_NAME}/data/"