Update README.md

README.md

@@ -1,8 +1,13 @@
-# The Data Preprocessing workflow
+# The Data Preprocessing Workflow
 
 ## Summary
 
-This workflow is a replicate of the [QA protocol](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/data-preprocessing/) implemented at JGI for Illumina reads and use the program “rqcfilter2” from BBTools(38:96) which implements them as a pipeline. 
+This workflow is a replicate of the [QA protocol](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/data-preprocessing/) implemented at JGI for Illumina reads.
+
+This workflow utilizes the program `rqcfilter2` from BBTools to perform quality control on raw Illumina reads for **shortreads**. The workflow performs quality trimming, artifact removal, linker trimming, adapter trimming, and spike-in removal (using `BBDuk`), and performs human/cat/dog/mouse/microbe removal (using `BMap`).
+
+This workflow performs quality control on long reads from PacBio. The workflow performs duplicate removal (using `pbmarkdup`), inverted repeat filtering (using BBTools 
+`icecreamfinder.sh`), adapter trimming, and final filtering of reads with residual adapter sequences (using `bbduk`). The workflow is designed to handle input files in various formats, including .bam, .fq, or .fq.gz.
 
 ## Required Database
 
@@ -17,33 +22,27 @@ This workflow is a replicate of the [QA protocol](https://jgi.doe.gov/data-and-t
 	rm RQCFilterData.tgz
 ```
 
-## Running Workflow in Cromwell
-
-Description of the files:
- - `.wdl` file: the WDL file for workflow definition
- - `.json` file: the example input for the workflow
- - `.conf` file: the conf file for running Cromwell.
- - `.sh` file: the shell script for running the example workflow
-
 ## The Docker image and Dockerfile can be found here
 
-[microbiomedata/bbtools:38.92](https://hub.docker.com/r/microbiomedata/bbtools)
+[microbiomedata/bbtools:38.96](https://hub.docker.com/r/microbiomedata/bbtools)
 
 ## Input files
 
-1. database path, 
-2. fastq (illumina paired-end interleaved fastq), 
-3. project name 
-4. resource where run the workflow
-5. informed_by 
+1. the path to the interleaved fastq file (longreads and shortreads) 
+2. forwards reads fastq file (when input_interleaved is false)
+3. reverse reads fastq file (when input_interleaved is false)  
+4. project id
+5. if the input is interleaved (boolean) 
+6. if the input is shortreads (boolean)
 
 ```
 {
-    "nmdc_rqcfilter.database": "/global/cfs/projectdirs/m3408/aim2/database", 
-    "nmdc_rqcfilter.input_files": "/global/cfs/cdirs/m3408/ficus/8434.3.102077.AGTTCC.fastq.gz", 
-    "nmdc_rqcfilter.proj":"nmdc:xxxxxxx",
-    "nmdc_rqcfilter.resouce":"NERSC -- perlmutter",
-    "nmdc_rqcfilter.informed_by": "nmdc:xxxxxxxx"
+	"rqcfilter.input_files": ["https://portal.nersc.gov/project/m3408//test_data/smalltest.int.fastq.gz"],
+    	"rqcfilter.input_fq1": [],
+    	"rqcfilter.input_fq2": [],
+    	"rqcfilter.proj": "nmdc:xxxxxxx",
+   	"rqcfilter.interleaved": true,
+    	"rqcfilter.shortRead": true
 }
 ```
 
@@ -54,13 +53,22 @@ The output will have one directory named by prefix of the fastq input file and a
 The main QC fastq output is named by prefix.anqdpht.fast.gz. 
 
 ```
-|-- 8434.1.102069.ACAGTG.anqdpht.fastq.gz
-|-- filterStats.txt
-|-- filterStats.json
-|-- filterStats2.txt
-|-- adaptersDetected.fa
-|-- reproduce.sh
-|-- spikein.fq.gz
-|-- status.log
-|-- ...
+* Short Reads
+    output/
+    ├── nmdc_xxxxxxx_filtered.fastq.gz
+    ├── nmdc_xxxxxxx_filterStats.txt
+    ├── nmdc_xxxxxxx_filterStats2.txt
+    ├── nmdc_xxxxxxx_readsQC.info
+    └── nmdc_xxxxxxx_qa_stats.json
+# Long Reads
+    output/
+    ├── nmdc_xxxxxxx_pbmarkdupStats.txt
+    ├── nmdc_xxxxxxx_readsQC.info
+    ├── nmdc_xxxxxxx_bbdukEndsStats.json
+    ├── nmdc_xxxxxxx_icecreamStats.json
+    ├── nmdc_xxxxxxx_filtered.fastq.gz
+    └── nmdc_xxxxxxx_stats.json
 ```
+
+## Link to Doc Site
+Please refer [here](https://nmdc-workflow-documentation.readthedocs.io/en/latest/chapters/1_RQC_index.html) for more information.