Commit a85dcfe1 authored by Sarah Peter's avatar Sarah Peter

Show status of working dir after the steps

parent 9fe15473
......@@ -253,6 +253,24 @@ s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load
19.1737 0:00:19 262.14 1404.55 258.79 258.94 0.00 0.00 0.00
```
After this step your working directory should contain the following files:
```
.
|-- benchmarks
| `-- mapping
| `-- INPUT-TC1-ST2-D0.12.tsv
|-- bowtie2
| |-- INPUT-TC1-ST2-D0.12.bam
| `-- INPUT-TC1-ST2-D0.12.bam.bai
|-- chip-seq -> /work/projects/ulhpc-tutorials/bio/snakemake/chip-seq
|-- envs -> /work/projects/ulhpc-tutorials/bio/snakemake/envs
|-- logs
| `-- bowtie2_INPUT-TC1-ST2-D0.12.log
|-- reference -> /work/projects/ulhpc-tutorials/bio/snakemake/reference/
|-- Snakefile
```
<a name="peaks"></a>
### Peak calling
......@@ -301,6 +319,37 @@ Let's run this step with:
Note that snakemake will not run the mapping step for `bowtie2/INPUT-TC1-ST2-D0.12.bam` again. It only runs rules for which the output is not present or the input has changed.
After this step your working directory should contain the following files:
```
.
|-- benchmarks
| `-- mapping
| |-- H3K4-TC1-ST2-D0.12.tsv
| `-- INPUT-TC1-ST2-D0.12.tsv
|-- bowtie2
| |-- H3K4-TC1-ST2-D0.12.bam
| |-- H3K4-TC1-ST2-D0.12.bam.bai
| |-- INPUT-TC1-ST2-D0.12.bam
| `-- INPUT-TC1-ST2-D0.12.bam.bai
|-- chip-seq -> /work/projects/ulhpc-tutorials/bio/snakemake/chip-seq
|-- envs -> /work/projects/ulhpc-tutorials/bio/snakemake/envs
|-- logs
| |-- bowtie2_H3K4-TC1-ST2-D0.12.log
| `-- bowtie2_INPUT-TC1-ST2-D0.12.log
|-- macs2
| |-- TC1-ST2-D0.12_control_lambda.bdg
| |-- TC1-ST2-D0.12_model.r
| |-- TC1-ST2-D0.12_peaks.narrowPeak
| |-- TC1-ST2-D0.12_peaks.xls
| |-- TC1-ST2-D0.12_summits.bed
| `-- TC1-ST2-D0.12_treat_pileup.bdg
|-- output
| `-- TC1-ST2-D0.12_peaks.narrowPeak
|-- reference -> /work/projects/ulhpc-tutorials/bio/snakemake/reference/
|-- Snakefile
```
<a name="bigwig"></a>
### Generate bigWig files for visualisation
......@@ -340,6 +389,13 @@ Let's test this step with:
This time snakemake will only run the "bigwig" rule for the one file we specified.
After this step the `output` directory should contain the following files:
```
TC1-ST2-D0.12_peaks.narrowPeak
TC1-ST2-D0.12_treat_pileup.bigwig
```
<a name="summary"></a>
### Summary rule
......@@ -367,6 +423,14 @@ Finally run the workflow again, this time without a specific target file:
(node)$> snakemake --use-conda -pr
```
After this step the `output` directory should contain the following files:
```
TC1-ST2-D0.12_control_lambda.bigwig
TC1-ST2-D0.12_peaks.narrowPeak
TC1-ST2-D0.12_treat_pileup.bigwig
```
Snakemake can visualise the dependency graph of the workflow with the following command:
```bash
......@@ -533,6 +597,8 @@ Let's have a look at the jobs that were submitted:
Check the submit and end time to see which jobs were running at the same time and when snakemake waited for jobs to finish.
After this step you should see a bunch of `slurm-XXXXXX-<rule name>.out` and `slurm-XXXXXX-<rule name>.err` files in your working directory, which contain the (error) logs of the different snakemake rules.
<a name="igv"></a>
## Inspect results in IGV
......
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