From 25906ed2e5f677275c0229ef54c9be091c0a3b06 Mon Sep 17 00:00:00 2001 From: Matt Parker Date: Thu, 15 Jun 2023 11:14:59 +0000 Subject: [PATCH] Move test data --- .gitlab-ci.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 1e13983..2d828b9 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -39,7 +39,7 @@ docker-run: - if: $MATRIX_NAME == "amr" variables: NF_WORKFLOW_OPTS: "-executor.$$local.memory 16GB \ - --fastq test_data/isolates_fastq --sample_sheet test_data/isolates_sample_sheet.csv --threads 3 --chunk_size 100000 --isolates" + --fastq s3://ont-exd-int-s3-euwst1-epi2me-labs/wf-bacterial-genomes/test_data/isolates_fastq --sample_sheet test_data/isolates_sample_sheet.csv --threads 3 --chunk_size 100000 --isolates" NF_IGNORE_PROCESSES: "runProkka,medakaVariant,medakaVariantConsensus,makePerSampleReports" - if: $MATRIX_NAME == "sample-sheet" variables: @@ -49,19 +49,19 @@ docker-run: - if: $MATRIX_NAME == "mlst" variables: NF_WORKFLOW_OPTS: "-executor.$$local.memory 16GB \ - --fastq test_data/isolates_fastq/barcode08 --threads 3 --chunk_size 100000 --isolates" + --fastq s3://ont-exd-int-s3-euwst1-epi2me-labs/wf-bacterial-genomes/test_data/isolates_fastq/barcode08 --threads 3 --chunk_size 100000 --isolates" NF_IGNORE_PROCESSES: "runProkka,medakaVariant,medakaVariantConsensus" - if: $MATRIX_NAME == "barcode04" # isolates barcode04 only has 4 reads and flye will fail due to low coverage variables: - NF_WORKFLOW_OPTS: "--fastq test_data/isolates_fastq/barcode04 \ + NF_WORKFLOW_OPTS: "--fastq s3://ont-exd-int-s3-euwst1-epi2me-labs/wf-bacterial-genomes/test_data/isolates_fastq/barcode04 \ --threads 3 --chunk_size 100000" NF_IGNORE_PROCESSES: "alignReads,readStats,coverStats,splitRegions,\ medakaConsensus,medakaNetwork,medakaVariant,medakaVariantConsensus,makeReport,runProkka,makePerSampleReports" - if: $MATRIX_NAME == "mixed-species" variables: NF_WORKFLOW_OPTS: "-executor.$$local.memory 16GB \ - --fastq test_data/isolates_fastq/ --sample_sheet test_data/isolates_mixed_sample_sheet.csv --threads 3 --chunk_size 100000 --isolates" + --fastq s3://ont-exd-int-s3-euwst1-epi2me-labs/wf-bacterial-genomes/test_data/isolates_fastq/ --sample_sheet test_data/isolates_mixed_sample_sheet.csv --threads 3 --chunk_size 100000 --isolates" NF_IGNORE_PROCESSES: "runProkka,medakaVariant,medakaVariantConsensus" - if: $MATRIX_NAME == "reference-iso" variables: