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.gitlab-ci.yml
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# Include shared CI
include:
- project: "epi2melabs/ci-templates"
file: "wf-containers.yaml"
variables:
# We'll use the single-file case for these runs
NF_WORKFLOW_OPTS: "--fastq test_data/reads.fastq.gz"
TEST_CMD: "bash test/run_ingress_test.sh"
S3_TEST_DATA: "s3://ont-exd-int-s3-euwst1-epi2me-labs/wf-template/cw-1019/test_data"
CI_FLAVOUR: "new"
PYTEST_CONTAINER_NAME: "wf-common"
PYTEST_CONTAINER_CONFIG_KEY: "common_sha="
# Remove this block in downstream templates
singularity-run:
tags: [] # no need for big ram
# end
docker-run:
# Remove this directive in downstream templates
tags: [] # no need for big ram
# Define a 1D job matrix to inject a variable named MATRIX_NAME into
# the CI environment, we can use the value of MATRIX_NAME to determine
# which options to apply as part of the rules block below
# NOTE There is a slightly cleaner way to define this matrix to include
# the variables, but it is broken when using long strings! See CW-756
parallel:
matrix:
# TODO: do we really need to run all from s3?
- MATRIX_NAME: [
"single-file", "single-file-s3",
"case01", "case01-s3",
"case02", "case02-s3", "case02-no-fastcat_stats", "case02-no-fastcat_stats-s3",
"case03", "case03-s3",
"case04", "case04-s3",
"case05", "case05-s3",
"case06", "case06-s3",
"case07", "case07-s3",
"case08", "case08-s3", case08-unclassified, case08-unclassified-s3,
"case09", "case09-s3",
"case10", "case10-s3",
"case11", "case11-s3",
"case12", "case12-s3", "case12-unclassified", "case12-unclassified-s3",
"case13", "case13-s3",
"case14",
"case15",
"case16",
"case16-nonexisting-client-fields",
"case17",
"mutateParams",
"xam-single-file",
"xam-case01",
"xam-case02",
"xam-case02-no-bamstats",
"xam-case02-return_fastq",
"xam-case03",
"xam-case03-sample_sheet",
"xam-case03-keep_unaligned-sample_sheet",
"xam-case03-keep_unaligned-sample_sheet-return_fastq",
"xam-case03-barcode02", # test_data/xam_ingress/case03/barcode02 contains only uBAM
"xam-case03-barcode02-keep_unaligned",
"xam-case04",
"xam-case05",
"xam-case06",
"xam-case07",
"xam-case08",
"xam-case08-skip",
"xam-case09",
"xam-case10",
]
rules:
# NOTE As we're overriding the rules block for the included docker-run
# we must redefine this CI_COMMIT_BRANCH rule to prevent docker-run
# being incorrectly scheduled for "detached merge request pipelines" etc.
- if: ($CI_COMMIT_BRANCH == null || $CI_COMMIT_BRANCH == "dev-template")
when: never
- if: $MATRIX_NAME == "single-file"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/reads.fastq.gz"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/reads.fastq.gz fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "single-file-s3"
variables:
NF_WORKFLOW_OPTS: "--fastq $S3_TEST_DATA/reads.fastq.gz"
AFTER_NEXTFLOW_CMD: $TEST_CMD $S3_TEST_DATA/reads.fastq.gz fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case01"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case01"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/fastq_ingress/case01 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case01-s3"
variables:
NF_WORKFLOW_OPTS: "--fastq $S3_TEST_DATA/fastq_ingress/case01"
AFTER_NEXTFLOW_CMD: $TEST_CMD $S3_TEST_DATA/fastq_ingress/case01 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case02"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case02"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/fastq_ingress/case02 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case02-s3"
variables:
NF_WORKFLOW_OPTS: "--fastq $S3_TEST_DATA/fastq_ingress/case02"
AFTER_NEXTFLOW_CMD: $TEST_CMD $S3_TEST_DATA/fastq_ingress/case02 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case02-no-fastcat_stats"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case02 --wf.fastcat_stats false"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/fastq_ingress/case02 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case02-no-fastcat_stats-s3"
variables:
NF_WORKFLOW_OPTS: "--fastq $S3_TEST_DATA/fastq_ingress/case02 --wf.fastcat_stats false"
AFTER_NEXTFLOW_CMD: $TEST_CMD $S3_TEST_DATA/fastq_ingress/case02 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case03"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case03"
ASSERT_NEXTFLOW_FAILURE: "1"
ASSERT_NEXTFLOW_FAILURE_REXP: "Input directory '.*' cannot contain target files (ending in '.fastq' / '.fastq.gz' / '.fq' / '.fq.gz') and also sub-directories with such files."
- if: $MATRIX_NAME == "case03-s3"
variables:
NF_WORKFLOW_OPTS: "--fastq $S3_TEST_DATA/fastq_ingress/case03"
ASSERT_NEXTFLOW_FAILURE: "1"
ASSERT_NEXTFLOW_FAILURE_REXP: "Input directory '.*' cannot contain target files (ending in '.fastq' / '.fastq.gz' / '.fq' / '.fq.gz') and also sub-directories with such files."
- if: $MATRIX_NAME == "case04"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case04"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/fastq_ingress/case04 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case04-s3"
variables:
NF_WORKFLOW_OPTS: "--fastq $S3_TEST_DATA/fastq_ingress/case04"
AFTER_NEXTFLOW_CMD: $TEST_CMD $S3_TEST_DATA/fastq_ingress/case04 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case05"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case05 --sample_sheet test_data/fastq_ingress/case05/sample_sheet.csv"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/fastq_ingress/case05 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case05-s3"
variables:
NF_WORKFLOW_OPTS: "--fastq $S3_TEST_DATA/fastq_ingress/case05 --sample_sheet $S3_TEST_DATA/fastq_ingress/case05/sample_sheet.csv"
AFTER_NEXTFLOW_CMD: $TEST_CMD $S3_TEST_DATA/fastq_ingress/case05 fastq $$PWD/$$CI_PROJECT_NAME $S3_TEST_DATA/fastq_ingress/case05/sample_sheet.csv
- if: $MATRIX_NAME == "case06"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case06 --sample_sheet test_data/fastq_ingress/case06/sample_sheet.csv"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/fastq_ingress/case06 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case06-s3"
variables:
NF_WORKFLOW_OPTS: "--fastq $S3_TEST_DATA/fastq_ingress/case06 --sample_sheet $S3_TEST_DATA/fastq_ingress/case06/sample_sheet.csv"
AFTER_NEXTFLOW_CMD: $TEST_CMD $S3_TEST_DATA/fastq_ingress/case06 fastq $$PWD/$$CI_PROJECT_NAME $S3_TEST_DATA/fastq_ingress/case06/sample_sheet.csv
- if: $MATRIX_NAME == "case07"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case07 --sample_sheet test_data/fastq_ingress/case07/sample_sheet.csv"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/fastq_ingress/case07 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case07-s3"
variables:
NF_WORKFLOW_OPTS: "--fastq $S3_TEST_DATA/fastq_ingress/case07 --sample_sheet $S3_TEST_DATA/fastq_ingress/case07/sample_sheet.csv"
AFTER_NEXTFLOW_CMD: $TEST_CMD $S3_TEST_DATA/fastq_ingress/case07 fastq $$PWD/$$CI_PROJECT_NAME $S3_TEST_DATA/fastq_ingress/case07/sample_sheet.csv
- if: $MATRIX_NAME == "case08"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case08"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/fastq_ingress/case08 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case08-s3"
variables:
NF_WORKFLOW_OPTS: "--fastq $S3_TEST_DATA/fastq_ingress/case08"
AFTER_NEXTFLOW_CMD: $TEST_CMD $S3_TEST_DATA/fastq_ingress/case08 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case08-unclassified"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case08 --analyse_unclassified"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/fastq_ingress/case08 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case08-unclassified-s3"
variables:
NF_WORKFLOW_OPTS: "--fastq $S3_TEST_DATA/fastq_ingress/case08 --analyse_unclassified"
AFTER_NEXTFLOW_CMD: $TEST_CMD $S3_TEST_DATA/fastq_ingress/case08 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case09"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case09"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/fastq_ingress/case09 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case09-s3"
variables:
NF_WORKFLOW_OPTS: "--fastq $S3_TEST_DATA/fastq_ingress/case09"
AFTER_NEXTFLOW_CMD: $TEST_CMD $S3_TEST_DATA/fastq_ingress/case09 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case10"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case10"
ASSERT_NEXTFLOW_FAILURE: "1"
ASSERT_NEXTFLOW_FAILURE_REXP: "Input directory '.*' cannot contain more than one level of sub-directories with target files (ending in '.fastq' / '.fastq.gz' / '.fq' / '.fq.gz')."
- if: $MATRIX_NAME == "case10-s3"
variables:
NF_WORKFLOW_OPTS: "--fastq $S3_TEST_DATA/fastq_ingress/case10"
ASSERT_NEXTFLOW_FAILURE: "1"
ASSERT_NEXTFLOW_FAILURE_REXP: "Input directory '.*' cannot contain more than one level of sub-directories with target files (ending in '.fastq' / '.fastq.gz' / '.fq' / '.fq.gz')."
- if: $MATRIX_NAME == "case11"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case11 --sample_sheet test_data/fastq_ingress/case11/sample_sheet.csv"
ASSERT_NEXTFLOW_FAILURE: "1"
ASSERT_NEXTFLOW_FAILURE_REXP: "Invalid sample sheet: values in 'alias' column not unique"
- if: $MATRIX_NAME == "case11-s3"
variables:
NF_WORKFLOW_OPTS: "--fastq $S3_TEST_DATA/fastq_ingress/case11 --sample_sheet $S3_TEST_DATA/fastq_ingress/case11/sample_sheet.csv"
ASSERT_NEXTFLOW_FAILURE: "1"
ASSERT_NEXTFLOW_FAILURE_REXP: "Invalid sample sheet: values in 'alias' column not unique"
- if: $MATRIX_NAME == "case12"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case12"
ASSERT_NEXTFLOW_FAILURE: "1"
ASSERT_NEXTFLOW_FAILURE_REXP: "Input directory '.*' must contain either target files (ending in '.fastq' / '.fastq.gz' / '.fq' / '.fq.gz') or sub-directories containing such files."
- if: $MATRIX_NAME == "case12-s3"
variables:
NF_WORKFLOW_OPTS: "--fastq $S3_TEST_DATA/fastq_ingress/case12"
ASSERT_NEXTFLOW_FAILURE: "1"
ASSERT_NEXTFLOW_FAILURE_REXP: "Input directory '.*' must contain either target files (ending in .*) or sub-directories containing such files (no more than one layer deep)."
- if: $MATRIX_NAME == "case12-unclassified"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case12 --analyse_unclassified"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/fastq_ingress/case12 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case12-unclassified-s3"
variables:
NF_WORKFLOW_OPTS: "--fastq $S3_TEST_DATA/fastq_ingress/case12 --analyse_unclassified"
AFTER_NEXTFLOW_CMD: $TEST_CMD $S3_TEST_DATA/fastq_ingress/case12 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case13"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case13"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/fastq_ingress/case13 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case13-s3"
variables:
NF_WORKFLOW_OPTS: "--fastq $S3_TEST_DATA/fastq_ingress/case13"
AFTER_NEXTFLOW_CMD: $TEST_CMD $S3_TEST_DATA/fastq_ingress/case13 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case14"
variables:
NF_WORKFLOW_OPTS: "--fastq 'test_data/fastq_ingress/case14/reads01 space.fastq'"
AFTER_NEXTFLOW_CMD: "$TEST_CMD 'test_data/fastq_ingress/case14/reads01 space.fastq' fastq $$PWD/$$CI_PROJECT_NAME"
- if: $MATRIX_NAME == "case15"
variables:
NF_WORKFLOW_OPTS: "--fastq 'test_data/fastq_ingress/case 15'"
AFTER_NEXTFLOW_CMD: "$TEST_CMD 'test_data/fastq_ingress/case 15' fastq $$PWD/$$CI_PROJECT_NAME"
- if: $MATRIX_NAME == "case16"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case16 --sample_sheet test_data/fastq_ingress/case16/sample_sheet.csv --client_fields test_data/fastq_ingress/case16/client_fields.json"
AFTER_NEXTFLOW_CMD: >
$TEST_CMD test_data/fastq_ingress/case16 fastq $$PWD/$$CI_PROJECT_NAME
&& grep "Dwight" $$PWD/$$CI_PROJECT_NAME/wf-template-report.html
- if: $MATRIX_NAME == "case16-nonexisting-client-fields"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case16 --sample_sheet test_data/fastq_ingress/case16/sample_sheet.csv --client_fields test_data/fastq_ingress/case16/client_fields_not_there.json"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/fastq_ingress/case16 fastq $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "case17"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq_ingress/case17 --sample_sheet test_data/fastq_ingress/case17/sample_sheet.csv --client_fields test_data/fastq_ingress/case17/client_fields.json"
AFTER_NEXTFLOW_CMD: >
$TEST_CMD test_data/fastq_ingress/case17 fastq $$PWD/$$CI_PROJECT_NAME
&& grep "ERROR: Client info is not correctly formatted" $$PWD/$$CI_PROJECT_NAME/wf-template-report.html
- if: $MATRIX_NAME == "mutateParams"
variables:
NF_WORKFLOW_OPTS: "--fastq no_reads.gz --mutate_fastq test_data/reads.fastq.gz"
# now the cases for xam_ingress
- if: $MATRIX_NAME == "xam-single-file"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/reads.bam"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/xam_ingress/reads.bam bam $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "xam-case01"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case01"
ASSERT_NEXTFLOW_FAILURE: "1"
ASSERT_NEXTFLOW_FAILURE_REXP: "Found mixed headers in (u)BAM files of sample 'case01'."
- if: $MATRIX_NAME == "xam-case02"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case02"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/xam_ingress/case02 bam $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "xam-case02-no-bamstats"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case02 --wf.bamstats false"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/xam_ingress/case02 bam $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "xam-case02-return_fastq"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case02 --wf.return_fastq"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/xam_ingress/case02 bam $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "xam-case03"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case03"
ASSERT_NEXTFLOW_FAILURE: "1"
ASSERT_NEXTFLOW_FAILURE_REXP: "Found mixed headers in (u)BAM files of sample 'barcode03'."
- if: $MATRIX_NAME == "xam-case03-keep_unaligned"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case03 --wf.keep_unaligned"
ASSERT_NEXTFLOW_FAILURE: "1"
ASSERT_NEXTFLOW_FAILURE_REXP: "Found mixed headers in (u)BAM files of sample 'barcode03'."
- if: $MATRIX_NAME == "xam-case03-sample_sheet"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case03 --sample_sheet test_data/xam_ingress/case03/sample_sheet.csv"
AFTER_NEXTFLOW_CMD: >
$TEST_CMD test_data/xam_ingress/case03 bam $$PWD/$$CI_PROJECT_NAME
&& grep "Input directory 'barcode03' was found, but sample sheet '.*' has no such entry." .nextflow.log
- if: $MATRIX_NAME == "xam-case03-keep_unaligned-sample_sheet"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case03 --sample_sheet test_data/xam_ingress/case03/sample_sheet.csv --wf.keep_unaligned"
AFTER_NEXTFLOW_CMD: >
$TEST_CMD test_data/xam_ingress/case03 bam $$PWD/$$CI_PROJECT_NAME
&& grep "Input directory 'barcode03' was found, but sample sheet '.*' has no such entry." .nextflow.log
- if: $MATRIX_NAME == "xam-case03-keep_unaligned-sample_sheet-return_fastq"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case03 --sample_sheet test_data/xam_ingress/case03/sample_sheet.csv --wf.keep_unaligned --wf.return_fastq"
AFTER_NEXTFLOW_CMD: >
$TEST_CMD test_data/xam_ingress/case03 bam $$PWD/$$CI_PROJECT_NAME
&& grep "Input directory 'barcode03' was found, but sample sheet '.*' has no such entry." .nextflow.log
- if: $MATRIX_NAME == "xam-case03-barcode02"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case03/barcode02"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/xam_ingress/case03/barcode02 bam $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "xam-case03-barcode02-keep_unaligned"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case03/barcode02 --wf.keep_unaligned"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/xam_ingress/case03/barcode02 bam $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "xam-case04"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case04"
ASSERT_NEXTFLOW_FAILURE: "1"
ASSERT_NEXTFLOW_FAILURE_REXP: "Found mixed headers in (u)BAM files of sample 'case04'."
- if: $MATRIX_NAME == "xam-case05"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case05/"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/xam_ingress/case05 bam $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "xam-case06"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case06/"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/xam_ingress/case06/ bam $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "xam-case07"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case07/"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/xam_ingress/case07/ bam $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "xam-case08"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case08/reads.ubam --wf.keep_unaligned"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/xam_ingress/case08/reads.ubam bam $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "xam-case08-skip"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case08/reads.ubam --wf.keep_unaligned false"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/xam_ingress/case08/reads.ubam bam $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "xam-case09"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case09/reads.bam"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/xam_ingress/case09/reads.bam bam $$PWD/$$CI_PROJECT_NAME
- if: $MATRIX_NAME == "xam-case10"
variables:
NF_WORKFLOW_OPTS: "--bam test_data/xam_ingress/case10/reads.bam"
AFTER_NEXTFLOW_CMD: $TEST_CMD test_data/xam_ingress/case10/reads.bam bam $$PWD/$$CI_PROJECT_NAME