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Split‑pipe

split-pipe a bioinformatics pipeline developed by [Parse Biosciences] for processing single-cell RNA sequencing data generated using their Split-Seq technology. The pipeline takes raw FASTQ files and produces processed data in the form of a cell-by-gene count matrix, which can be used as input for popular open-source analysis tools such as Scanpy and Seurat. It enables streamlined and efficient processing of sequencing results from start to finish.

How to run in Rorqual

Pipeline.0.9.6

First load the module

module load StdEnv/2023
module load python/3.10
PYTHONENV0=/lustre09/project/6004655/COMMON/soft2/packages/splitpipe/ParseBiosciences-Pipeline.0.9.6p/venv
export PYTHONPATH=$PYTHONENV0/lib/python3.10/site-packages:$PYTHONPATH
export PATH="/lustre09/project/6004655/COMMON/soft2/packages/anaconda/miniconda3/bin:$PATH"
source $PYTHONENV0/bin/activate

Now you should have access to it 

split-pipe --help
usage: split-pipe [-h] [-m MODE] [-k KIT] [-p PARFILE] [-f FQ1] [--fq2 FQ2] [--genome_dir GENOME_DIR] [-o OUTPUT_DIR] [--sample SAMPLE_NAME [WELLS ...]] [--samp_list SAMP_LIST]
                  [--samp_sltab SAMP_SLTAB] [--no_allwell] [--genome_name [GENOME_NAME ...]] [--genes [GENES ...]] [--fasta [FASTA ...]] [--sublibraries [SUBLIBRARIES ...]]
                  [--sublib_list SUBLIB_LIST] [--tscp_use TSCP_USE] [--tscp_min TSCP_MIN] [--tscp_max TSCP_MAX] [--cell_use CELL_USE] [--cell_est CELL_EST] [--cell_xf CELL_XF]
                  [--cell_min CELL_MIN] [--cell_max CELL_MAX] [--save_anndata] [--save_figs] [--kit_list] [--bc_list] [--bc_round_set ROUND NAME] [--rseed RSEED] [--nthreads NTHREADS]
                  [--keep_going] [--reuse] [--keep_temps] [--one_step] [--clear_env_files] [--dryrun] [-e] [-V]

Pipeline.1.0.5

First load the module

module load StdEnv/2023
module load python/3.10
PYTHONENV0=/lustre09/project/6004655/COMMON/soft2/packages/splitpipe/ParseBiosciences-Pipeline.1.0.5p/venv
export PYTHONPATH=$PYTHONENV0/lib/python3.10/site-packages:$PYTHONPATH
export PATH="/lustre09/project/6004655/COMMON/soft2/packages/anaconda/miniconda3/bin:$PATH"
source $PYTHONENV0/bin/activate

Now you should have access to it 

split-pipe --help
usage: split-pipe [-h] [-m MODE] [-k KIT] [-p PARFILE] [-f FQ1] [--fq2 FQ2] [--genome_dir GENOME_DIR] [-o OUTPUT_DIR] [--sample SAMPLE_NAME [WELLS ...]] [--samp_list SAMP_LIST]
                  [--samp_sltab SAMP_SLTAB] [--no_allwell] [--genome_name [GENOME_NAME ...]] [--genes [GENES ...]] [--fasta [FASTA ...]] [--sublibraries [SUBLIBRARIES ...]]
                  [--sublib_list SUBLIB_LIST] [--tscp_use TSCP_USE] [--tscp_min TSCP_MIN] [--tscp_max TSCP_MAX] [--cell_use CELL_USE] [--cell_est CELL_EST] [--cell_xf CELL_XF]
                  [--cell_min CELL_MIN] [--cell_max CELL_MAX] [--save_anndata] [--save_figs] [--kit_list] [--bc_list] [--bc_round_set ROUND NAME] [--rseed RSEED] [--nthreads NTHREADS]
                  [--keep_going] [--reuse] [--keep_temps] [--one_step] [--clear_env_files] [--dryrun] [-e] [-V]

Pipeline.1.6.0

First load the module

module load StdEnv/2023
module load python/3.13.2
module load  rust/1.85.0
PYTHONENV0=/lustre09/project/6004655/COMMON/soft2/packages/splitpipe/ParseBiosciences-Pipeline.1.6.0/venv
export PYTHONPATH=$PYTHONENV0/lib/python3.13/site-packages:$PYTHONPATH
export PATH="/lustre09/project/6004655/COMMON/soft2/packages/anaconda/miniconda3/bin:$PATH"
source $PYTHONENV0/bin/activate

Now you should have access to it 

split-pipe --help
usage: split-pipe [-h] [-m MODE] [-c CHEMISTRY] [-k KIT] [-p PARFILE] [--run_name RUN_NAME] [-f [FQ1 ...]] [--fq2 [FQ2 ...]] [-o OUTPUT_DIR] [-g GENOME_DIR] [--parent_dir PARENT_DIR] [--targeted_list TARGETED_LIST] [--sample SAMPLE_NAME WELLS] [--samp_list SAMP_LIST] [--samp_sltab SAMP_SLTAB]
                  [--yes_allwell] [--no_allsample] [--genome_name [GENOME_NAME ...]] [--genes [GENES ...]] [--fasta [FASTA ...]] [--gfasta GENOME_NAME FASTA] [--mkref_validate] [--sublibraries [SUBLIBRARIES ...]] [--sublib_list SUBLIB_LIST] [--sublib_pref SUBLIB_PREF] [--sublib_suff SUBLIB_SUFF]
                  [--cell_list CELL_LIST] [--crispr] [--crsp_guides CRSP_GUIDES] [--crsp_read_thresh CRSP_READ_THRESH] [--crsp_tscp_thresh CRSP_TSCP_THRESH] [--crsp_use_star] [--immune_check] [--bcr_analysis] [--tcr_analysis] [--immune_genome IMMUNE_GENOME] [--use_imgt_db]
                  [--immune_read_thresh IMMUNE_READ_THRESH] [--save_anndata] [--kit_list [KIT_LIST]] [--chem_list] [--bc_list] [--sample_bc_rounds SAMPLE_BC_ROUNDS] [--rseed RSEED] [--nthreads NTHREADS] [--no_keep_going] [--no_fq_name_check] [--agg_sum_transpose] [--keep_temps] [--one_step]
                  [--until_step UNTIL_STEP] [--star_extra_args STAR_EXTRA_ARGS] [--clear_runproc] [--start_timeout START_TIMEOUT] [--chem_score_skip] [--kit_score_skip] [--dryrun] [-e] [-V]

SplitPipe data processing pipeline v1.6.0

How to make reference

The follwoing show make the reference for Pipeline.1.0.5: 

unset PYTHONPATH

module load StdEnv/2023
module load python/3.10
PYTHONENV0=/lustre09/project/6004655/COMMON/soft2/packages/splitpipe/ParseBiosciences-Pipeline.1.0.5p/venv
export PYTHONPATH=$PYTHONENV0/lib/python3.10/site-packages:$PYTHONPATH
source $PYTHONENV0/bin/activate

export PATH="/lustre09/project/6004655/COMMON/soft2/packages/anaconda/miniconda3/bin:$PATH"

export MUGQIC_INSTALL_HOME=/cvmfs/soft.mugqic/CentOS6
module use $MUGQIC_INSTALL_HOME/modulefiles
module load mugqic/star/2.7.2b
module load mugqic/samtools/1.9

split-pipe --mode mkref  --genome_name hg38 --fasta  /lustre09/project/6004655/COMMON/soft2/packages/splitpipe/samamiri/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz  --genes /lustre09/project/6004655/COMMON/soft2/packages/splitpipe/samamiri/Homo_sapiens.GRCh38.93.gtf.gz --output_dir /lustre09/project/6004655/COMMON/soft2/packages/splitpipe/samamiri/hg38_star

Reference