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Commit 8619ed5e authored by John Lafin's avatar John Lafin
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fix sample and id for barnyard

parent aed9ea90
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1 merge request!2Ci
Pipeline #13579 passed with stages
in 27 minutes and 37 seconds
...@@ -25,7 +25,11 @@ test-count-human: # Run cellranger count on the human data ...@@ -25,7 +25,11 @@ test-count-human: # Run cellranger count on the human data
before_script: before_script:
- export PATH="/opt/nextflow:/opt/cellranger-7.1.0:$PATH" - export PATH="/opt/nextflow:/opt/cellranger-7.1.0:$PATH"
script: script:
- nextflow run workflow/main.nf --reference=/data/ref_data/refdata-gex-GRCh38-2020-A --fastq=/data/test_data/Brain_Tumor_3p_LT_fastqs --noBam=true - >
nextflow run workflow/main.nf
--reference=/data/ref_data/refdata-gex-GRCh38-2020-A
--fastq=/data/test_data/Brain_Tumor_3p_LT_fastqs
--noBam=true
- nextflow clean -f -keep-logs - nextflow clean -f -keep-logs
test-count-barnyard: # Run cellranger count on the barnyard data test-count-barnyard: # Run cellranger count on the barnyard data
...@@ -36,5 +40,11 @@ test-count-barnyard: # Run cellranger count on the barnyard data ...@@ -36,5 +40,11 @@ test-count-barnyard: # Run cellranger count on the barnyard data
before_script: before_script:
- export PATH="/opt/nextflow:/opt/cellranger-7.1.0:$PATH" - export PATH="/opt/nextflow:/opt/cellranger-7.1.0:$PATH"
script: script:
- nextflow run workflow/main.nf --fastq=/data/test_data/hgmm_100_fastqs --reference=/data/ref_data/refdata-gex-GRCh38-and-mm10-2020-A --noBam=true - >
nextflow run workflow/main.nf
--id=hgmm_100
--sample=hgmm_100
--fastq=/data/test_data/hgmm_100_fastqs
--reference=/data/ref_data/refdata-gex-GRCh38-and-mm10-2020-A
--noBam=true
- nextflow clean -f -keep-logs - nextflow clean -f -keep-logs
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