new module: RESEQ/RESEQ

[adamrtalbot]

Is there an existing module for this?

• [X] I have searched for the existing module

Is there an open PR for this?

• [X] I have searched for existing PRs

Is there an open issue for this?

• [X] I have searched for existing issues

Are you going to work on this?

• [ ] If I'm planning to work on this module, I added myself to the Assignees to facilitate tracking who is working on the module

[adamrtalbot]

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02265-7

[adamrtalbot]

https://github.com/schmeing/ReSeq

[aperz]

@adamrtalbot could you supply the exact data sets you used to run ReSeq? And the command you used, if that's possible :)

[adamrtalbot]

I'm afraid it was at an old job. It should work with any 'normal' BAM as I remember.

[adamrtalbot]

OK I managed to get it working with the test data files but I had to use the flag --adapterFile TruSeq_single to disable adapters!

[adamrtalbot]

OK, an additional thing I had to add was the coverage (-c). With the homo_sapiens data:

reseq illuminaPE \
    --verbosity 4 \
    -j 4 \
    -r genome.fasta \
    -b test.paired_end.sorted.bam \
    -c 1 \
    --adapterFile TruSeq_single \
    -1 test.1.fastq.gz \
    -2 test.2.fastq.gz

[adamrtalbot]

Nextflow process will look something like this for paired end data:

reseq illuminaPE \\
    ${args} \\
    -j ${task.cpus} \\
    -r ${fasta} \\
    -b ${bam} \\
    -1 ${prefix}.1.fastq.gz \\
    -2 ${prefix}.2.fastq.gz

[adamrtalbot]

Genome: file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) Index: file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) BAM: file(params.modules_testdata_base_path + genomics/homo_sapiens/illumina/bam/test.paired_end.name.sorted.bam, checkIfExists: true)

[aperz]

Awesome, thank you

[aperz]

Trying to solve https://github.com/schmeing/ReSeq/issues/23