Merge pull request #2 from macs3-project/feat/markdown

Feat/markdown: baigali's unpublished commit and fixes of version number

Author: taoliu

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MAESTRO
 Type: Package
 Title: Model-based Analyses of Single-cell Transcriptome and Regulome (MACS3 fork)
-Version: 1.5.2
+Version: 1.5.3
 Date: 2021-03-05
 Author: Chenfei Wang, Dongqing Sun, Tao Liu, Changxin Wan, Ming (Tommy) Tang, Gali Bai, Jiaojiao Zhou
 Maintainer: Dongqing Sun<dongqingsun96@gmail.com>, Gali Bai<gali.bai@hotmail.com>, Tao Liu <vladimir.liu@gmail.com>

MAESTRO/MAESTRO

@@ -1,11 +1,16 @@
+#!/usr/bin/env python
 # -*- coding: utf-8 -*-
+# Time-stamp: <2022-01-26 12:27:01 Tao Liu>
+
+# BEGIN of old header
 # @Author: Dongqing Sun
 # @E-mail: Dongqingsun96@gmail.com
 # @Date:   2021-06-07 11:11:58
 # @Last Modified by:   Gali Bai, Dongqing Sun
 # @Last Modified time: 2021-06-07 11:11:58
+# END of old header
 
-version = "1.5.1"
+version = "1.5.3"
 
 import logging
 import sys, os

MAESTRO/MAESTRO_ParameterValidate.py

@@ -29,12 +29,12 @@ def scatac_validator(args):
                 logging.error("--whitelist is required for 10x-genomics data!")
                 exit(1)
         if args.format == "bam":
-            if args.bam == "":
-                logging.error("--bam is required. Please provide the bam file with CB tag!")
+            if args.input_path == "":
+                logging.error("--input_path is required. Please specify the directory where bam files are stored!")
                 exit(1)
         if args.format == "fragments":
-            if args.frag == "":
-                logging.error("--frag is required. Please provide the fragment file generated by CellRanger ATAC!")
+            if args.input_path == "":
+                logging.error("--input_path is required. Please specify the directory where fragments files are stored!")
                 exit(1)
     if args.mapping == "chromap":
         if args.format == "fastq":

MAESTRO/Snakemake/scATAC/rules/sc_atac_link_fragment.smk

@@ -3,7 +3,7 @@ if config["gzip"]:
 		input:
 			frag = lambda wildcards: FILES[wildcards.sample]
 		output:
-			frag_sort = temp("Result/Mapping/{sample}/fragments_sorted_corrected_dedup_count.tsv")
+			frag_sort = temp("Result/Mapping/{sample}/fragments_sorted_corrected_dedup_count.tsv"),
 			frag_dedup = "Result/Mapping/{sample}/fragments_corrected_dedup_count.tsv",
 			fraggz = "Result/Mapping/{sample}/fragments_corrected_dedup_count.tsv.gz"
 		shell:
@@ -17,7 +17,7 @@ else:
 		input:
 			frag = lambda wildcards: FILES[wildcards.sample]
 		output:
-			frag_sort = temp("Result/Mapping/{sample}/fragments_sorted_corrected_dedup_count.tsv")
+			frag_sort = temp("Result/Mapping/{sample}/fragments_sorted_corrected_dedup_count.tsv"),
 			frag_dedup = "Result/Mapping/{sample}/fragments_corrected_dedup_count.tsv",
 			fraggz = "Result/Mapping/{sample}/fragments_corrected_dedup_count.tsv.gz"
 		shell:

README.md

@@ -28,17 +28,19 @@
   [sci-ATAC-seq](https://science.sciencemag.org/content/348/6237/910)
   for scATAC-seq protocols.
 
-This is the MACS3 project fork of MAESTRO. The long-term goal is to
-switch to all python implementation of scRNA+scATAC analysis and move
-from Seurat to Scanpy/Anndata.
+This is the MACS3 project fork of MAESTRO. We will maintain the
+MAESTRO pacakge here and send PR to the original repository at
+liulab-dfci/MAESTRO. The long-term goal in this fork is to switch to
+all python implementation of scRNA+scATAC analysis and move from
+Seurat to Scanpy/Anndata.
 
 <p align="center">
 <img src="./image/MAESTRO_workflow.png"/>
 </p>
 
 ## Documentation
 
-We are hosting MAESTRO documentation, instruction and tutorials at [MAESTRO Website](https://baigal628.github.io/MAESTRO_documentation/).
+We are hosting MAESTRO documentation, instruction and tutorials at [MAESTRO Website](https://macs3-project.github.io/MAESTRO/).
 
 ## Change Log
 
@@ -105,7 +107,7 @@ We are hosting MAESTRO documentation, instruction and tutorials at [MAESTRO Webs
 * Support single-nuclei RNA-seq pipeline.
 * Fix bug in sample initiation subcommand to read fastq with sample id greater than 9.
 * Update MAESTRO documentation to v1.5.1. Add snRNA-seq tutorials. Expand scRNA-seq tutorial with lisa2 TF prediction custom analysis. Add multi-scATAC-seq genome track plot for pseudobulk peaks. Explain multi-samples peak calling parameters.
-### v1.5.2 (MACS3 fork)
+### v1.5.2+ (MACS3 fork)
 * Temporary release. We will update some documentations and update some dependencies.
 * The mouse chromosome length file for GRCm38 has been fixed. 
 
@@ -137,7 +139,7 @@ $ conda config --add channels bioconda
 $ conda config --add channels conda-forge
 # To make the installation faster, we recommend using mamba
 $ conda install mamba -c conda-forge
-$ mamba create -n MAESTRO maestro=1.5.1 -c macs3-project
+$ mamba create -n MAESTRO -c macs3 maestro=1.5.3
 # Activate the environment
 $ conda activate MAESTRO
 ```

conda/MAESTRO/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: maestro
-  version: "1.5.2"
+  version: "1.5.3"
 source:
   path: ../../
 requirements:

setup.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Time-stamp: <2022-01-25 19:58:58 Tao Liu>
+# Time-stamp: <2022-01-26 13:49:23 Tao Liu>
 
 import sys,os
 # from distutils.core import setup
@@ -13,7 +13,7 @@
 def main():
     setup(
         name = "MAESTRO",
-        version = "1.5.2",
+        version = "1.5.3",
         package_dir = {'MAESTRO':'MAESTRO'},
         packages = ['MAESTRO'],
         package_data={'MAESTRO':['Snakemake/scRNA/*', 'Snakemake/integrate/*', 'Snakemake/scATAC/*', 'Snakemake/scATAC/rules/*', 'Snakemake/scRNA/rules/*', 'R/*', 'utils/*','annotations/*', 'html/*', '']},