Merge pull request #141 from baigal628/master

Release of MAESTRO v1.5.0

.github/workflows/maestro-package-conda.yml

@@ -7,8 +7,8 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 5
-    defaults: 
-      run: 
+    defaults:
+      run:
         shell: bash
     steps:
     - uses: actions/checkout@v2
@@ -20,11 +20,11 @@ jobs:
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory
         echo $CONDA/bin >> $GITHUB_PATH
-    #- name: Cache conda pkgs 
-    #  uses: actions/cache@v2 
-    #  with: 
+    #- name: Cache conda pkgs
+    #  uses: actions/cache@v2
+    #  with:
     #    path: |
-    #      /usr/share/miniconda/pkgs 
+    #      /usr/share/miniconda/pkgs
     #      /home/runner/.conda/pkgs
     - name: Install dependencies
       run: |
@@ -47,33 +47,33 @@ jobs:
         conda build -q conda/MAESTRO --python=3.8 --output-folder bld-dir
     - name: Test installing package
       run: |
-        # Now add this folder as a highest priority channel 
-        conda config --add channels "file://`pwd`/bld-dir" 
-        # install MAESTRO from local repo 
+        # Now add this folder as a highest priority channel
+        conda config --add channels "file://`pwd`/bld-dir"
+        # install MAESTRO from local repo
         mamba create -q -n MAESTRO maestro
-        # Activate this environment 
-        source /usr/share/miniconda/etc/profile.d/conda.sh 
+        # Activate this environment
+        source /usr/share/miniconda/etc/profile.d/conda.sh
         conda activate MAESTRO
-        # list conda env packages for reference 
+        # list conda env packages for reference
         conda list
-    - name: Test installed MAESTRO package (cmdline) 
+    - name: Test installed MAESTRO package (cmdline)
       run: |
-        source /usr/share/miniconda/etc/profile.d/conda.sh 
-        conda activate MAESTRO        
-        giggle search 
+        source /usr/share/miniconda/etc/profile.d/conda.sh
+        conda activate MAESTRO
+        giggle search
         sinto -h
         lisa
         MAESTRO -v
-        MAESTRO multi-scatac-init -h
+        MAESTRO scatac-init -h
+        MAESTRO scrna-init -h
         MAESTRO samples-init -h
         R -e "library(MAESTRO);library(Seurat)"
         R -e "library(org.Hs.eg.db);library(org.Mm.eg.db)"
-    - name: Test installed MAESTRO package (other) 
+    - name: Test installed MAESTRO package (other)
       run: |
         # test python utility scripts
-        source /usr/share/miniconda/etc/profile.d/conda.sh 
-        conda activate MAESTRO        
+        source /usr/share/miniconda/etc/profile.d/conda.sh
+        conda activate MAESTRO
         cd test
         bash test.sh
         cd ..
-

.github/workflows/upload-package-anaconda.yml

@@ -8,8 +8,8 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 5
-    defaults: 
-      run: 
+    defaults:
+      run:
         shell: bash
     steps:
     - uses: actions/checkout@v2
@@ -21,11 +21,11 @@ jobs:
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory
         echo $CONDA/bin >> $GITHUB_PATH
-    #- name: Cache conda pkgs 
-    #  uses: actions/cache@v2 
-    #  with: 
+    #- name: Cache conda pkgs
+    #  uses: actions/cache@v2
+    #  with:
     #    path: |
-    #      /usr/share/miniconda/pkgs 
+    #      /usr/share/miniconda/pkgs
     #      /home/runner/.conda/pkgs
     - name: Install dependencies
       run: |
@@ -48,31 +48,32 @@ jobs:
         conda build -q conda/MAESTRO --python=3.8 --output-folder bld-dir
     - name: Test installing package
       run: |
-        # Now add this folder as a highest priority channel 
-        conda config --add channels "file://`pwd`/bld-dir" 
-        # install MAESTRO from local repo 
+        # Now add this folder as a highest priority channel
+        conda config --add channels "file://`pwd`/bld-dir"
+        # install MAESTRO from local repo
         mamba create -q -n MAESTRO maestro
-        # Activate this environment 
+        # Activate this environment
         source /usr/share/miniconda/etc/profile.d/conda.sh
         conda activate MAESTRO
-        # list conda env packages for reference 
+        # list conda env packages for reference
         conda list
-    - name: Test installed MAESTRO package (cmdline) 
+    - name: Test installed MAESTRO package (cmdline)
       run: |
-        source /usr/share/miniconda/etc/profile.d/conda.sh 
-        conda activate MAESTRO        
-        giggle search 
+        source /usr/share/miniconda/etc/profile.d/conda.sh
+        conda activate MAESTRO
+        giggle search
         sinto -h
         lisa
         MAESTRO -v
-        MAESTRO multi-scatac-init -h
+        MAESTRO scrna-init -h
+        MAESTRO scatac-init -h
         MAESTRO samples-init -h
         R -e "library(MAESTRO);library(Seurat)"
         R -e "library(org.Hs.eg.db);library(org.Mm.eg.db)"
-    - name: Test installed MAESTRO package (other) 
+    - name: Test installed MAESTRO package (other)
       run: |
-        source /usr/share/miniconda/etc/profile.d/conda.sh 
-        conda activate MAESTRO        
+        source /usr/share/miniconda/etc/profile.d/conda.sh
+        conda activate MAESTRO
         # test python utility scripts
         cd test
         bash test.sh
@@ -83,4 +84,3 @@ jobs:
       run: |
         mamba install anaconda-client
         anaconda upload bld-dir/**/maestro-*.tar.bz2
-

DESCRIPTION

@@ -1,14 +1,14 @@
 Package: MAESTRO
 Type: Package
 Title: Model-based Analyses of Single-cell Transcriptome and Regulome
-Version: 1.4.0
+Version: 1.5.0
 Date: 2021-03-05
 Author: Chenfei Wang, Dongqing Sun, Tao Liu, Changxin Wan, Ming (Tommy) Tang, Gali Bai
 Maintainer: Dongqing Sun<dongqingsun96@gmail.com>, Gali Bai<gali.bai@hotmail.com>
 Description: MAESTRO is an intergrative analysis pipeline to support downstream analysis of single-cell RNA-seq and single-cell ATAC-seq dataset. MAESTRO provides funtion for quality control, normalization, clustering, differential gene and peak analysis, marker gene based annotation, transcription factor identification using Cistome toolkit, and intergrative analysis for scRNA-seq and scATACseq.
 URL: https://github.com/LiuLab-dfci/MAESTRO
-Depends: R (>= 3.6.1)
-Imports: Seurat (>= 3.1.2), Signac (>= 1.1.1), ggplot2 (>= 3.0.0), ggrepel, cowplot, Matrix (>=
+Depends: R (>= 4.0.2)
+Imports: Seurat (>= 4.0.0), Signac (>= 1.1.1), ggplot2 (>= 3.0.0), ggrepel, cowplot, Matrix (>=
          1.2.14), dplyr, png, RColorBrewer, scales, pheatmap, MAGeCKFlute, DESeq2, Gmisc,
          grid, karyoploteR, presto, AnnotationDbi, org.Hs.eg.db, org.Mm.eg.db, GenomeInfoDb
 Suggests: knitr, pagoda2, RCA, MAST, scABC, devtools, uwot, cisTopic, chromVAR, motifmatchr,

MAESTRO/MAESTRO

@@ -1,11 +1,11 @@
 # -*- coding: utf-8 -*-
 # @Author: Dongqing Sun
 # @E-mail: Dongqingsun96@gmail.com
-# @Date:   2020-02-13 16:11:58
-# @Last Modified by:   Dongqing Sun
-# @Last Modified time: 2020-02-28 13:58:10
+# @Date:   2021-06-07 11:11:58
+# @Last Modified by:   Gali Bai, Dongqing Sun
+# @Last Modified time: 2021-06-07 11:11:58
 
-version = "1.3.1"
+version = "1.5.0"
 
 import logging
 import sys, os
@@ -34,8 +34,6 @@ def main():
     scatac_parser(subparsers)
     scrna_parser(subparsers)
     integrate_parser(subparsers)
-    multi_scatac_parser(subparsers)
-    #multi_scrna_parser(subparsers)
 
     sample_parser(subparsers)
     mtxtoh5_parser(subparsers)
@@ -61,6 +59,7 @@ def main():
         exit(0)
     elif args.subcommand == "samples-init":
         sample_json(args)
+
     elif args.subcommand == "scatac-init":
         scatac_validator(args)
         scatac_config(args)
@@ -72,9 +71,6 @@ def main():
     elif args.subcommand == "integrate-init":
         integrate_config(args)
 
-    elif args.subcommand == "multi-scatac-init":
-        multi_scatac_config(args)
-
     elif args.subcommand == "mtx-to-h5":
         mtx_2_h5(directory = args.directory, outprefix = args.outprefix, matrix_file = args.matrix, feature_file = args.feature, barcode_file = args.barcode, gene_column = args.gene_column, genome = args.species, datatype = args.datatype)
 

MAESTRO/MAESTRO_ParameterValidate.py

@@ -19,11 +19,8 @@ def scatac_validator(args):
     """
     if args.platform == "10x-genomics":
         if args.format == "fastq":
-            if args.fastq_dir == "":
-                logging.error("--fastq-dir is required. Please specify the directory where fastq files are stored!")
-                exit(1)
-            if args.fastq_prefix == "":
-                logging.error("--fastq-prefix is required. Please provide the sample name of fastq files!")
+            if args.input_path == "":
+                logging.error("--input_path is required. Please specify the directory where fastq files are stored!")
                 exit(1)
             if args.fasta == "":
                 logging.error("--fasta is required if fastq files are provided!")
@@ -39,30 +36,29 @@ def scatac_validator(args):
             if args.frag == "":
                 logging.error("--frag is required. Please provide the fragment file generated by CellRanger ATAC!")
                 exit(1)
+    if args.mapping == "chromap":
+        if args.format == "fastq":
+            if args.index == "":
+                logging.error("--index is required if using chromap as alignment tool!")
 
     if args.platform == "sci-ATAC-seq":
         if args.format == "fastq":
-            if args.fastq_dir == "":
-                logging.error("--fastq-dir is required. Please specify the directory where fastq files are stored!")
-                exit(1)
-            if args.fastq_prefix == "":
-                logging.error("--fastq-prefix is required. Please provide the sample name of fastq files!")
+            if args.input_path == "":
+                logging.error("--input_path is required. Please specify the directory where fastq files are stored!")
                 exit(1)
             if args.fasta == "":
                 logging.error("--fasta is required if fastq files are provided!")
                 exit(1)
-        if args.format == "bam":
-            if args.bam == "":
-                logging.error("--bam is required. Please provide the bam file with CB tag!")
-                exit(1)
         if args.format == "fragments":
             logging.error("Format of 'fragments' is supported only when the platform is '10x-genomics'.")
             exit(1)
+        if args.mapping == "chromap" or args.mapping == "":
+            logging.error("sci-ATAC-seq only support mapping with minimap2")
 
     if args.platform == "microfluidic":
         if args.format == "fastq":
-            if args.fastq_dir == "":
-                logging.error("--fastq-dir is required. Please specify the directory where fastq files are stored!")
+            if args.input_path == "":
+                logging.error("--input_path is required. Please specify the directory where fastq files are stored!")
                 exit(1)
             if args.fasta == "":
                 logging.error("--fasta is required if fastq files are provided!")
@@ -88,19 +84,13 @@ def scrna_validator(args):
     """
 
     if args.platform == "10x-genomics":
-        if args.fastq_dir == "":
-            logging.error("--fastq-dir is required. Please specify the directory where fastq files are stored!")
-            exit(1)
-        if args.fastq_prefix == "":
-            logging.error("--fastq-prefix is required. Please provide the sample name of fastq files!")
-            exit(1)
         if args.whitelist == "":
             logging.error("--whitelist is required for 10x-genomics data!")
             exit(1)
 
     if args.platform == "Dropseq":
-        if args.fastq_dir == "":
-            logging.error("--fastq-dir is required for Dropsea data. Please specify the directory where fastq files are stored!")
+        if args.input_path == "":
+            logging.error("--input_path is required for Dropsea data. Please specify the directory where fastq files are stored!")
             exit(1)
         if args.fastq_barcode == "":
             logging.error("--fastq-barcode is required for Dropsea data. Please specify the barcode fastq file!")
@@ -113,8 +103,8 @@ def scrna_validator(args):
             exit(1)
 
     if args.platform == "Smartseq2":
-        if args.fastq_dir == "":
-            logging.error("--fastq-dir is required. Please specify the directory where fastq files are stored!")
+        if args.input_path == "":
+            logging.error("--input_path is required. Please specify the directory where fastq files are stored!")
             exit(1)
         if args.rsem == "":
             logging.error("--rsem is required. Please provide the prefix of transcript references for RSEM. See --rsem help for more details.")