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@@ -57,7 +57,7 @@
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"ftp_username": "igf",
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"ftp_project_path": "/www/html/report/project",
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"all_cell_marker_list": "/project/tgu/resources/pipeline_resource/cell_markers/PangaloDB/PanglaoDB_markers_27_Mar_2020.tsv",
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- "cellranger_exe": "/project/tgu/resources/cellranger-5.0.0/bin/cellranger",
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+ "cellranger_exe": "/project/tgu/resources/cellranger-6.1.1/bin/cellranger",
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"base_result_dir": "/project/tgu/data2/results",
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"cellranger_job_timeout": 259200,
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"cutadapt_singularity_image": "/project/tgu/resources/pipeline_resource/singularity_images/cutadapt/cutadapt_v3.1.sif",
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@@ -70,6 +70,15 @@
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"nextflow_exe": "/project/tgu/software/nextflow/nextflow",
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"nextflow_singularity_cache_dir": "/project/tgu/resources/pipeline_resource/nextflow_singularity_cachedir",
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"seqrun_demult_notebook_template": "/project/tgu/software/interop-notebook-image/templates/demult_report_v0.0.1.ipynb",
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+ "gtf_ref_path": "/project/tgu/resources/pipeline_resource/gene/gtf",
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+ "star_exe": "/project/tgu/software/STAR/bin/STAR",
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+ "star_ref_path": "/project/tgu/resources/pipeline_resource/transcriptome/STAR",
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+ "rsem_exe_dir": "/project/tgu/software/RSEM",
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+ "rsem_ref_path": "/project/tgu/resources/pipeline_resource/transcriptome/rsem",
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+ "ucsc_exe_dir": "/project/tgu/software/ucsc",
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+ "refflat_ref_path": "/project/tgu/resources/pipeline_resource/gene/refFlat",
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+ "ribosomal_interval_ref_path": "/project/tgu/resources/pipeline_resource/intervals/ribosomal",
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+ "cellranger_ref_path": "/project/tgu/resources/pipeline_resource/transcriptome/cellranger",
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"hpc_queue_list": {
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"hpc_1G": {
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"pbs_resource": "-lselect=1:ncpus=1:mem=1gb -lwalltime=06:00:00",
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Avik Datta