fix the output names for trimming pe

README.md

@@ -66,7 +66,14 @@ Once successfull, you need to activate the newly created environment, obsered th
 
 ### Install the ChIP-seq template
 
-In the destination folder of your choice, run the following commands:
+In the destination folder of your choice, otherwise create the folder such as:
+
+```bash
+mkdir snakemake-chip-seq
+cd snakemake-chip-seq
+``` 
+
+and run the following commands:
 
 ```bash
 VERSION="v0.0.9"
@@ -76,8 +83,8 @@ wget -qO- https://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-chip-seq/-/archiv
 this command will download, extract (without the root folder) the following files:
 
 ```
-CHANGELOG.md
 config/
+CHANGELOG.md
 Dockerfile
 LICENSE
 README.md
@@ -88,6 +95,14 @@ workflow/
 you may want to delete the `LICENSE`, `Dockerfile`, `CHANGELOG.md` and `README.md` if you wish, 
 they are not used by `snakemake` for runtime.
 
+### Fetch test datasets
+
+Using the [nextflow datasets](https://github.com/nf-core/test-datasets), clone it using `git`:
+
+```bash
+git clone -b chipseq --depth 1 https://github.com/nf-core/test-datasets.git
+```
+
 
 #### (Optional) Useful aliases
 
@@ -115,8 +130,6 @@ Once `(base)` *conda* activated, you can update your `snakemake` version with:
 
 `mamba upgrade -n snakemake snakemake`
 
-
-
 ## Usage
 
 The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=snakemake-workflows/chipseq).
@@ -162,14 +175,6 @@ salloc: Nodes iris-139 are ready for job
 (snakemake) aginolhac@iris-139(14:17:23)-> 29:49)(2424900 1N/T/1CN): ~ $
 ```
 
-### Fetch test datasets
-
-Using the [nextflow datasets](https://github.com/nf-core/test-datasets), clone it using `git`:
-
-```bash
-git clone -b --depth 1 chipseq https://github.com/nf-core/test-datasets.git
-```
-
 
 ### Dry-run
 

workflow/rules/trim.smk

-rule trimming_se:
-    input:
-        get_fastqs
-    output:
-        fastq="results/trimmed_se/{sample}-{unit}.fastq.gz",
-        discarded="trimmed_se/{sample}-{unit}.discarded.fastq.gz",
-        settings="trimmed_se/{sample}-{unit}.settings"  
-    params:
-        adapters = config["trimming"]["se"],
-        others = config["trimming"]["others"]
-    threads: config["trimming"]["threads"]
-    log:
-        "logs/trimming/{sample}-{unit}.se.log"
-    wrapper:
-        "0.76.0/bio/adapterremoval"
-
-rule trimming_pe:
-    input:
-        get_fastqs
-    output:
-        fq1="trimmed_pe/{sample}-{unit}_R1.fastq.gz",                           # trimmed mate1 reads
-        fq2="trimmed_pe/{sample}-{unit}_R2.fastq.gz",                           # trimmed mate2 reads
-        collapsed="trimmed_pe/{sample}-{unit}.collapsed.fastq.gz",              # overlapping mate-pairs which have been merged into a single read
-        collapsed_trunc="trimmed_pe/{sample}-{unit}.collapsed_trunc.fastq.gz",  # collapsed reads that were quality trimmed
-        singleton="trimmed_pe/{sample}-{unit}.singleton.fastq.gz",              # mate-pairs for which the mate has been discarded
-        discarded="trimmed_pe/{sample}-{unit}.discarded.fastq.gz",              # reads that did not pass filters
-        settings="trimmed_pe/{sample}-{unit}.settings" 
-    params:
-        adapters = config["trimming"]["pe"],
-        others = config["trimming"]["others"]
-    threads: config["trimming"]["threads"]
-    log:
-        "logs/trimming/{sample}-{unit}.pe.log"
-    wrapper:
-        "0.76.0/bio/adapterremoval"
-