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sc rnaseq tests
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mapo9 committed May 16, 2024
1 parent c6f95bf commit c72146c
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Showing 4 changed files with 34 additions and 1 deletion.
1 change: 1 addition & 0 deletions .github/workflows/ci.yml
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Expand Up @@ -63,6 +63,7 @@ jobs:
"test_clontech_umi",
"test_nebnext_umi",
"test_rnaseq_bulk",
"test_rnaseq_sc",
]
fail-fast: false
steps:
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2 changes: 1 addition & 1 deletion conf/test_rnaseq_bulk.config
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Expand Up @@ -4,7 +4,7 @@
* -------------------------------------------------
* Defines bundled input files and everything required
* to run a fast and simple test. Use as follows:
* nextflow run nf-core/airrflow -profile test_10x_sc,<docker/singularity>
* nextflow run nf-core/airrflow -profile test_rnaseq_bulk,<docker/singularity>
*/

params {
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31 changes: 31 additions & 0 deletions conf/test_rnaseq_sc.config
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@@ -0,0 +1,31 @@
/*
* -------------------------------------------------
* Nextflow config file for running tests
* -------------------------------------------------
* Defines bundled input files and everything required
* to run a fast and simple test. Use as follows:
* nextflow run nf-core/airrflow -profile test_rnaseq_sc,<docker/singularity>
*/

params {
config_profile_name = 'Test single-cell RNA-seq based workflow using TRUST4'
config_profile_description = 'Minimal test dataset to check pipeline function with raw single-cell RNA-seq data'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = 6.GB
max_time = 48.h

// params
mode = 'fastq'
library_generation_method = 'trust4'
clonal_threshold = 0
barcode_read = R1
umi_position = R1
read_format = "bc:0:15,um:16:27"
skip_lineage = True

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-rnaseq/sc_rnaseq_metadata.tsv'
coord_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-rnaseq/IMGT+C.fa'
}
1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -307,6 +307,7 @@ profiles {
test_clontech_umi { includeConfig 'conf/test_clontech_umi.config' }
test_nebnext_umi { includeConfig 'conf/test_nebnext_umi.config' }
test_rnaseq_bulk { includeConfig 'conf/test_rnaseq_bulk.config' }
test_rnaseq_sc { includeConfig 'conf/test_rnaseq_sc.config' }
nebnext_umi_tcr { includeConfig 'conf/nebnext_umi_tcr.config' }
nebnext_umi_bcr { includeConfig 'conf/nebnext_umi_bcr.config' }
clontech_umi_bcr { includeConfig 'conf/clontech_umi_bcr.config' }
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