Remove .DS_Store

README.md

@@ -31,22 +31,26 @@ _Good idea to include screenshots or GIFs (see ttygif or Asciinema)_
 
 ### Conda _(prior!)_ ###
 Download and install **Conda**: [Latest Miniconda Installer](https://docs.conda.io/en/latest/miniconda.html#latest-miniconda-installer-links)  
-1. Donwload conda installer _(i.e. for Miniconda3 with Python 3.9 on Linux-64-bit)_:
+1. Donwload conda installer _(i.e. for Miniconda3 with Python 3.9 on MacOSX-64-bit)_:
 ```shel
-wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.10.3-Linux-x86_64.sh
+wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
 ```
+
 2. Install conda using installer bash script:
 _Follow the prompts on the installer screens_  
 ```shell
-bash Miniconda3-latest-Linux-x86_64.sh
+bash Miniconda3-latest-MacOSX-x86_64.sh
 ```
+
 3. Remove conda installer:
+```shell
+rm Miniconda3-latest-MacOSX-x86_64.sh
 ```
-rm Miniconda3-latest-Linux-x86_64.sh
-```
+
 4. Restart shell, close and reopen new terminal window
 
 ### Snakemake _(prior!)_ ###
+
 Install **Snakemake** using Conda package management system  
 _Follow the prompts on the installer screens_  
 ```shell
@@ -54,29 +58,41 @@ conda install -c bioconda -c conda-forge snakemake
 ```
 
 ### RQCP ###
-Download _or_ clone the **Reads Quality Control Pipeline** project  
+
+**Download** _OR_ clone the **Reads Quality Control Pipeline** project  
 
 #### Download ####
-1. Download source code archive (_zip_, **tar.gz**, _tar.bz2_, _tar_): [RQCP on GitLab](https://gitlab.com/ird_transvihmi/Reads_Quality_Control_Pipeline)  
 
+- Download source code archive (_zip_, **tar.gz**, _tar.bz2_, _tar_): [RQCP on GitLab](https://gitlab.com/ird_transvihmi/Reads_Quality_Control_Pipeline)  
+```shel
+wget  https://gitlab.com/ird_transvihmi/Reads_Quality_Control_Pipeline/-/archive/main/Reads_Quality_Control_Pipeline-main.tar.gz -O ~/Desktop/ 
+```
+
+_alternatively_:
 ![Image of download button](./visuals/download_button.png)  
 
-2. Extract and remove the the archive (i.e. tar.gz):
+- Extract and remove the the archive (i.e. tar.gz):
 ```shell
-tar -xzvf path/to/archive/Reads_Quality_Control_Pipeline.tar.gz
-rm path/to/archive/Reads_Quality_Control_Pipeline.tar.gz 
+tar -xzvf path/to/archive/Reads_Quality_Control_Pipeline-main.tar.gz
+rm path/to/archive/Reads_Quality_Control_Pipeline-main.tar.gz 
+mv ~/Desktop/Reads_Quality_Control_Pipeline-main ~/Desktop/Reads_Quality_Control_Pipeline
+cd ~/Desktop/Reads_Quality_Control_Pipeline
 ```
 
 #### Clone ####
-Clone with **SSH** when you want to authenticate only one time  
+
+- Clone with **SSH** when you want to authenticate only one time  
 Authenticate with GitLab by following the instructions in the [SSH documentation](https://docs.gitlab.com/ee/ssh/index.html)  
 ```shell
-git clone git@gitlab.com:ird_transvihmi/Reads_Quality_Control_Pipeline.git path/to/workdir/
+git clone git@gitlab.com:ird_transvihmi/Reads_Quality_Control_Pipeline.git
+
+cd Reads_Quality_Control_Pipeline
 ```
 
 Clone with **HTTPS** when you want to authenticate each time you perform an operation between your computer and GitLab  
 ```shell
-git clone https://gitlab.com/ird_transvihmi/Reads_Quality_Control_Pipeline.git path/to/workdir/
+git clone https://gitlab.com/ird_transvihmi/Reads_Quality_Control_Pipeline.git
+cd Reads_Quality_Control_Pipeline
 ```
 
 #### Difference between download and clone ####
@@ -191,8 +207,8 @@ You can also ask for new databases, for genomes references not yet included, to
 5. Call me to `+33.(0)4.67.41.55.xx` (No don't please _O\_o_!)
 
 ## Roadmap ##
-Finish documentation about "terminal" and "results"
 Add a wiki !  
+Finish documentation about "terminal" and "results"
 Add new features  
 
 ## Contributing ##

config/config.yaml

@@ -34,11 +34,11 @@ datasets:
     #- 'sickle-trim_single-end'
     #- 'fastq-join_single-end'
     #- 'fastq-join_paired-end'
-    #- 'all_merged'
+    #- 'all_merged_single-end'
 
 ## CUTADAPT ------------------------------------------------------------------------------------------
 cutadapt:
-  length: '75' # Discard reads shorter than length, after trim
+  length: '35' # Discard reads shorter than length, after trim
   kits:        # Sequence of an adapter ligated to the 3' end of the first read
     truseq:      'AGATCGGAAGAGC'                     # Illumina TruSeq / ScriptSeq based kits libraries
     nextera:     'CTGTCTCTTATACACATC'                # Illumina Nextera / TruSight based kits libraries
@@ -59,17 +59,17 @@ sickle-trim:
     #- 'illumina' # if illumina (CASAVA 1.3 to 1.7)
     #- 'solexa'   # if solexa   (CASAVA < 1.3)
   quality: '30'   # phred score limit
-  length: '75'    # read length limit, after trim
+  length: '35'    # read length limit, after trim
 
 ## FASTQ-JOIN ----------------------------------------------------------------------------------------
 fastq-join:
-  percent: '5'  # N-percent maximum difference (default: 8)
-  overlap: '25' # N-minimum overlap (default: 6)
+  percent: '8'  # N-percent maximum difference (default: 8)
+  overlap: '6' # N-minimum overlap (default: 6)
 
 ## FASTQSCREEN ---------------------------------------------------------------------------------------
 fastq-screen:
   config: 'config/fastq-screen.conf' # path to the fastq-screen configuration file
-  subset: '1000' # Don't use the whole sequence file, but create a temporary dataset of this specified number of read (default: '100000', set '0' for all dataset)
+  subset: '10000' # Don't use the whole sequence file, but create a temporary dataset of this specified number of read (default: '100000', set '0' for all dataset)
   aligner:
     - 'bwa'     # Burrows-Wheeler Aligner, for mapping low-divergent sequences against a large reference genome
     #- 'bowtie'  # Bowtie, an ultrafast, memory-efficient short read aligner

config/fastq-screen.conf

@@ -48,15 +48,15 @@ THREADS 1
 ##
 ##----------
 ## Human h38
-DATABASE	Human	 resources/databases/bwa/Human/Homo_sapiens_h38
+#DATABASE	Human	 resources/databases/bwa/Human/Homo_sapiens_h38
 #DATABASE	Human	 resources/databases/bowtie2/Human/Homo_sapiens_h38
 ##
 ## Mouse m39
-DATABASE	Mouse	 resources/databases/bwa/Mouse/Mus_musculus_m39
+#DATABASE	Mouse	 resources/databases/bwa/Mouse/Mus_musculus_m39
 #DATABASE	Mouse	 resources/databases/bowtie2/Mouse/Mus_musculus_m39
 ##
 ## Arabidopsis thaliana - sequence from NCBI: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.3_TAIR10/GCF_000001735.3_TAIR10_genomic.fna.gz
-DATABASE	Arabidopsis	 resources/databases/bwa/Arabidopsis/Arabidopsis_thaliana_t10
+#DATABASE	Arabidopsis	 resources/databases/bwa/Arabidopsis/Arabidopsis_thaliana_t10
 #DATABASE	Arabidopsis	 resources/databases/bowtie2/Arabidopsis/Arabidopsis_thaliana_t10
 ##
 ## Ecoli - sequence available from EMBL accession U00096.2
@@ -78,15 +78,15 @@ DATABASE	Vectors		 resources/databases/bwa/Vectors/UniVec_wo_phi-X174
 ##
 ##-----------
 ## Gorilla g4	
-DATABASE	Gorilla	 resources/databases/bwa/Gorilla/Gorilla_gorilla_g4
+#DATABASE	Gorilla	 resources/databases/bwa/Gorilla/Gorilla_gorilla_g4
 #DATABASE	Gorilla	 resources/databases/bowtie2/Gorilla/Gorilla_gorilla_g4
 ##
 ## Chimpanzee
-DATABASE	Chimpanzee	 resources/databases/bwa/Chimpanzee/Pan_troglodytes_t3
+#DATABASE	Chimpanzee	 resources/databases/bwa/Chimpanzee/Pan_troglodytes_t3
 #DATABASE	Chimpanzee	 resources/databases/bowtie2/Chimpanzee/Pan_troglodytes_t3
 ##
 ## Bat 10
-DATABASE	Bat	 resources/databases/bwa/Bat/Pteropus_vampyrus_v1
+#DATABASE	Bat	 resources/databases/bwa/Bat/Pteropus_vampyrus_v1
 #DATABASE	Bat	 resources/databases/bowtie2/Bat/Pteropus_vampyrus_v1
 ##
 ## HIV - HXB2