# nf-core tutorial

# setup
* log into eddie
* qlogin into node
* `qlogin -pe interactivemem 2 -l h_vmem=3G`
* Move to scratch directory
* `cd /exports/eddie/scratch/$USER`

* Make semplelab folder and move into it
~~~
mkdir nfcore_tut
cd nfcore_tut
~~~
* load singularity, anaconda and nextflow modules
~~~
module load roslin/singularity/3.5.3
module load igmm/apps/nextflow/20.12.0-edge
~~~
* set conda cache directory
~~~
export NXF_CONDA_CACHEDIR="/exports/igmm/eddie/public/semplelab/conda"
~~~
* load conda enviroment (you will need conda setup)
* `conda activate /exports/igmm/eddie/public/semplelab/.env`
* run
~~~
nf-core --version
~~~

You should get output

~~~

,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'

nf-core/tools version 1.13
There is a new version of nf-core/tools available! (1.13.1)

nf-core, version 1.13
~~~

# List nf-core pipelines

~~~
nf-core list --help
~~~

~~~
nf-core list
~~~

### Filter pipelines

~~~
nf-core list rnaseq
~~~

### Sort

~~~
nf-core list rnaseq -s stars
~~~

# Run test hlatyping pipeline

## Pull latest hlatyping pipeline

~~~
nextflow pull nf-core/hlatyping -r 1.2
~~~

## Configuration

1. create the file `custom.config`
2. add the following

~~~
params.email=`myemail`
~~~

## Run locally

This will run the pipeline on the current node using the test profile and singularity

~~~
nextflow run nf-core/hlatyping -r 1.2 -profile test,singularity -c custom.config
~~~

It will fail with an error message

~~~
Error executing process > 'remap_to_hla (1)'

Caused by:
Process requirement exceed available CPUs -- req: 2; avail: 1

Command executed:

samtools view -@ 2 -h -f 0x40 example_pe.bam > output_1.bam
samtools view -@ 2 -h -f 0x80 example_pe.bam > output_2.bam
samtools bam2fq output_1.bam > output_1.fastq
samtools bam2fq output_2.bam > output_2.fastq
yara_mapper -e 3 -t 2 -f bam yara/hla_reference_dna output_1.fastq output_2.fastq > output.bam
samtools view -@ 2 -h -F 4 -f 0x40 -b1 output.bam > mapped_1.bam
samtools view -@ 2 -h -F 4 -f 0x80 -b1 output.bam > mapped_2.bam

Command exit status:
-

Command output:
(empty)

Work dir:
/exports/eddie/scratch/ggrimes2/semplelab/work/d6/bb3f7e53f1f464b0184d804266c4d3

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
~~~

Use

`Ctrl+C` to exit nextflow run

The nextflow run failed as it was requesting 2 CPUS and only 1 avialable.

Re_run using the `-resume option` using the param max_cpus set to 1 `--max_cpus 1`

~~~
nextflow run nf-core/rnaseq -r 3.0 -profile test,singularity -c custom.config --max_cpus 1 -resume
~~~

## Results

By default the results will be placed in a results directory

## Submit to HPC

You can use intitutional configs to submit nextflow to you HPC.

~~~

nextflow run nf-core/hlatyping -r 1.2 -profile eddie,test,singularity -resume

~~~