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run_scModule.sh
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#!/usr/bin/bash
# Copyright (C) 2020 Fulong Yu
#
# CUT&RUNTools 2.0 is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 2 of the License.
#
# CUT&RUNTools 2.0 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
#
# A copy of the GNU General Public License has been distributed along with CUT&RUNTools and is found in LICENSE.md.
configrue_file=$1 # $scriptdir/sc-config.json
SCRIPT=`readlink -f $0`
SCRIPTPATH=`dirname $SCRIPT`
scriptdir=$SCRIPTPATH/src
# convert configuration JSON files to bash variables
eval "$(jq -r '.software_config | to_entries | .[] | .key + "=\"" + .value + "\""' < $configrue_file)"
eval "$(jq -r '.input_output | to_entries | .[] | .key + "=\"" + .value + "\""' < $configrue_file)"
eval "$(jq -r '.run_pipeline | to_entries | .[] | .key + "=\"" + .value + "\""' < $configrue_file)"
workdir=$workdir/$experiment_name
if [ "$entire_pipeline" == "TRUE" ]
then
logdir=$workdir/sc_logs
qcdir=$workdir/sc_qc
sc_countMatrix_dir=$workdir/sc_countMatrix
bamdir=$workdir/sc_aligned.aug10/dup.marked.clean
sc_pseudoBulk_dir=$workdir/sc_pseudoBulk
matrix_type=$matrix_type
bin_size=$bin_size
featureFile=$featureFile
sc_cluster_dir=$workdir/sc_cluster
echo "==================================== The entire pipeline will run! ======================================================================"
>&2 echo -e "## Experiment name: $experiment_name"
sleep 0.1
>&2 echo -e "## Input FASTQ folder: $fastq_directory"
sleep 0.1
>&2 echo -e "## Workdir folder: $workdir"
sleep 0.1
>&2 echo -e "## Log files floder: $logdir"
sleep 0.1
>&2 echo -e "## QC reports and figures folder: $qcdir"
sleep 0.1
>&2 echo -e "## Experiment type: $experiment_type"
sleep 0.1
>&2 echo -e "## Reference genome: $genome"
sleep 0.1
>&2 echo -e "## Processors used: $cores"
sleep 0.1
>&2 echo -e "## BAM folder of cells: $bamdir"
sleep 0.1
>&2 echo -e "## Peak_caller: $peak_caller"
sleep 0.1
>&2 echo -e "## Cell filter [read in peak %]: $percentage_rip"
sleep 0.1
>&2 echo -e "## Cell filter [qulified reads]: $num_reads_threshold"
sleep 0.1
>&2 echo -e "## Count matrix folder: $sc_countMatrix_dir"
sleep 0.1
>&2 echo -e "## Count matrix type: $matrix_type"
sleep 0.1
>&2 echo -e "## Cell clustering folder: $sc_cluster_dir"
sleep 0.1
>&2 echo -e "## Cell clustering [resolution]: $cluster_resolution"
sleep 0.1
>&2 echo -e "## Cell clustering [PCs]: $cluster_pc"
sleep 0.1
>&2 echo -e "## Pseudo-bulk data folder: $sc_pseudoBulk_dir"
echo -e "========================================================================================================================================="
# step1 fastq -> peak
. $scriptdir/fastq2peak.sh
# step2 cells -> count_matrix
. $scriptdir/cells2count_matrix.sh
# step3 count_matrix -> clustering
. $scriptdir/count_matrix2clustering.sh
# step4 cells -> psuedoBulk
. $scriptdir/cells2psuedoBulk.sh
fi
if [ "$entire_pipeline" != "TRUE" ]
then
echo "==================================== Individual step will run! =========================================================="
# run step1
if [ "$individual_step" == "fastq2peak" ]
then
echo "==================================== step 1 (raw data processing) will be performed! ===================================="
>&2 echo -e "## Experiment name: $experiment_name"
sleep 0.1
>&2 echo -e "## Input FASTQ folder: $fastq_directory"
sleep 0.1
>&2 echo -e "## Workdir folder: $workdir"
sleep 0.1
>&2 echo -e "## Log files floder: $logdir"
sleep 0.1
>&2 echo -e "## QC reports and figures folder: $qcdir"
sleep 0.1
>&2 echo -e "## Experiment type: $experiment_type"
sleep 0.1
>&2 echo -e "## Reference genome: $genome"
sleep 0.1
>&2 echo -e "## Processors used: $cores"
sleep 0.1
>&2 echo -e "## BAM folder of cells: $bamdir"
sleep 0.1
>&2 echo -e "## Peak_caller: $peak_caller"
sleep 0.1
>&2 echo -e "## Cell filter [read in peak]: $percentage_rip"
sleep 0.1
>&2 echo -e "## Cell filter [qulified reads]: $num_reads_threshold"
echo "========================================================================================================================="
. $scriptdir/fastq2peak.sh
# run step2
elif [ "$individual_step" == "cells2count_matrix" ]
then
echo "==================================== step 2 (count matrix generation) will be performed! ================================"
>&2 echo -e "## Input individual BAM folder: $step2_bamfile_dir"
sleep 0.1
>&2 echo -e "## Output count matrix folder: $step2_output_dir"
sleep 0.1
>&2 echo -e "## Cells passed QC file: $step2_qc_pass_file"
sleep 0.1
>&2 echo -e "## Count matrix type: $matrix_type"
sleep 0.1
echo "========================================================================================================================="
. $scriptdir/cells2count_matrix.sh
# run step3
elif [ "$individual_step" == "count_matrix2clustering" ]
then
echo "==================================== step 3 (clustering analysis) will be performed! ===================================="
>&2 echo -e "## Input count matrix file: $step3_count_matrix"
sleep 0.1
>&2 echo -e "## Output clustering folder: $step3_output_dir"
sleep 0.1
>&2 echo -e "## Cell clustering [resolution]: $cluster_resolution"
sleep 0.1
>&2 echo -e "## Cell clustering [PCs]: $cluster_pc"
echo "========================================================================================================================="
. $scriptdir/count_matrix2clustering.sh
# run step4
elif [ "$individual_step" == "cells2psuedoBulk" ]
then
echo "==================================== step 4 (cell-type-specific aggregation) will be performed! ========================="
>&2 echo -e "## Input individual BAM folder: $step4_bamfile_dir"
sleep 0.1
>&2 echo -e "## Cell label file: $step4_cell_anno_file"
sleep 0.1
>&2 echo -e "## Output cell type-specific pseudo-bulk folder: $step4_output_dir"
echo "========================================================================================================================="
. $scriptdir/cells2psuedoBulk.sh
# error
else
echo "[ERROR] Please specify the individual_step as one of fastq2peak; cells2count_matrix; count_matrix2clustering; cells2psuedoBulk"
exit 1
fi
fi