add modifications from user feedbacks

README.md

@@ -67,10 +67,13 @@ In any case, if you use this workflow in a paper, don't forget to give credits t
 
 *  Step 2: Configure workflow
 
-Configure the workflow according to your needs via editing the `config.yaml`, `design.txt` and `multiqc_config.yaml` files in the `config/` directory.
+Configure the workflow according to your needs via editing the [config.yaml](https://gitlab.pasteur.fr/hub/chipflow/-/tree/master#how-to-fill-the-config-file), [design.txt](https://gitlab.pasteur.fr/hub/chipflow/-/tree/master#how-to-fill-the-design) and  [multiqc_config.yaml](https://gitlab.pasteur.fr/hub/chipflow/-/edit/master/README.md#how-to-fill-the-multiqc-config) files in the `config/` directory.
 
 You need to copy the singularity image in the cloned ChIPflow directory and rename it as "chipflow.img".
 
+`mv chipflow_latest.sif chipflow/chipflow.img`
+
+
 *  Step 3: Execute workflow
 
 Test your configuration by performing a dry-run via
@@ -106,12 +109,18 @@ All FASTQ files have to observe the following name nomenclature: `MARK_COND_REP_
 | Wildcard |                          Description                                |
 |----------|---------------------------------------------------------------------|
 |   MARK   | Histone mark or Transcription Factor (TF) name (i.e. H3K4me1, Klf4) |
-|   COND   | Biological condition name (i.e. Normal, Cancer)                     |
+|   COND   | Biological condition name (i.e. Normal, Cancer, Cells)                     |
 |   REP    | Replicate number (i.e. Rep1 or Rep2)                                |
 |   MATE   | Identification of mate pair sequencing (i.e. R1 or R2)              |
 
 All the FASTQ files must be stored in the same directory.
 
+Example of FASTQ file names:
+
+- `H3K27ac_shCtrl_Rep1_R1.fastq.gz` and its corresponding INPUT file: `INPUT_shCtrl_Rep1_R1.fastq.gz`
+- `TF4_HeLa_rep1_R1.fastq.gz` and its corresponding INPUT file: `Input_HeLa_rep1_R1.fastq.gz`
+- `CTCF_WT_REP1_R1.fastq.gz` and its corresponding INPUT file: `INPUT_WT_REP1_R1.fastq.gz`
+
 ### How to fill the design
 
 The experimental analysis design is summarise in a tabulated design file that the user have to fill before running the pipeline.
@@ -177,6 +186,26 @@ bowtie2_mapping:
     threads: 4
 ```
 
+### How to fill the multiqc config
+
+At the beginning of `config/multiqc_config.yaml` file, you have the possibility to customize header of MultiQC report according to your experiment as you can see below: 
+
+```
+# Title to use for the report.
+title: "ChIP-seq analysis"
+subtitle: "ChIP-seq analysis of CTCF factor in breast tumor cells"                  # Set your own text
+intro_text: "MultiQC reports summarise analysis results produced from ChIPflow"     
+
+# Add generic information to the top of reports
+report_header_info:
+    - Contact E-mail: 'rlegendre@pasteur.fr'                                        # Set your own text
+    - Application Type: 'ChIP-seq'                                                  # Set your own text
+    - Project Type: 'Differential peak expression'                                  # Set your own text
+    - Sequencing Platform: 'NextSeq2000'                                            # Set your own text
+    - Sequencing Setup: 'PE75'                                                      # Set your own text
+```
+<img src="images/multiqc_header.png" width="600">
+
 ## How to cite ChIPflow ?
 
 https://doi.org/10.1101/2021.02.02.429342