Fix test profiles

[nschcolnicov]

Description of the bug

Test profiles currently contain local paths, i.e test_full.config

The test profiles that need correcting are:
test_full.config
test_panelprep.config
test_sim.config
test.config

Command used and terminal output

No response

Relevant files

No response

System information

dev

[atrigila]

Example of issues: CSVs point to local files and cannot be used for testing: e.g.
/groups/dog/llenezet/test-datasets/data/panel/21/panel_2020-08-05_chr21.phased.vcf.gz

[LouisLeNezet]

Sorry I didn't yet implement a big test as I needed first a reliable datatest set.
We should look at how it is done in other pipeline to know where big files are stored.

[LouisLeNezet]

Hi,
Normally the nextflow run main.nf -profile test,singularity --outdir results should now work without any problem.

[atrigila]

Hi @LouisLeNezet, here are some ideas of full sized datasets. I implemented the 1000G s3 in the quilt pipeline.

• Reference panel CSV: 1000G VCFs in S3 buckets: https://github.com/atrigila/quilt_nextflow/blob/master/assets/samplesheet_reference_full.csv

• Sample: The downsampled versions at https://s3.amazonaws.com/gatk-test-data/gatk-test-data-readme.html.
  or some other options could be:
  vcf s3://giab/release/NA12878_HG0001/latest/GRCh38/HG0001_NA12878_1_22_v4.2.1_benchmark.vcf.gz or bam https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/NA12878/alignment.index.NA12878_TruSeq_Exome_Nebraska_GRCh37_09252015

• Genome fasta: AWS iGenomes

[LouisLeNezet]

For the fasta it is ready, same for reference panel with the #18 PR.
For the sample the NA12878 is easily accessible but the problem reside in the presence of this individual in the reference panel as well as its parents. For a full test it will imply to duplicate the huge files to remove them to not overestimate the performance of the imputation.
The best would be to have a unrelated bam file at high coverage from outside the 1000 Genome Project.
The GATK resources seems interesting but there is only the NA12878 individual available...