Verified Commit 4d521fcb authored by Aurélien Ginolhac's avatar Aurélien Ginolhac 🚴
Browse files

fix the output names for trimming pe

parent b686c25d
......@@ -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
......
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"
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