Add Ignite executor to run salmon quant

[manu-lifebit]

Overview

The main purpose of this PR is to adapt the nf-core RNAseq pipeline to run with ignite executor and produce read count files through the salmon quantification process.

Purpose

To achieve that we modified some pipeline configuration options to allow it to run on CloudOS and create the salmon quantification files.

Changes

• Adds local.config and standard config files
• Refactor salmon_quant process in main.nf
• Change memory requirements in main.nf
• Adds executor in nextflow.config

Testing

In order to run the script locally:

• Clone the repository:

  git clone https://github.com/lifebit-ai/nf-rnaseq-salmon.git
  cd nf-rnaseq-salmon
  git checkout manu_add_ignite

• Execute the nextflow pipeline

  NXF_VER=20.04.1 nextflow run . --input s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/*_[1,2].fastq.gz --fasta https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa --gtf https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf --gff https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gff --transcript_fasta https://github.com/nf-core/test-datasets/raw/rnaseq/reference/transcriptome.fasta --additional_fasta s3://manu-data-public/rnaseq_files/gfp.fa --umitools_bc_pattern NNNN --pseudo_aligner salmon --genome GRCh38 --skip_alignment

  Results: The pipeline will generate the read count files in the results folder

CloudOS test run: https://cloudos.lifebit.ai/public/jobs/61dd84f38c574a01e8d6c9cd