summarizeFasta is called before and after running filterFasta

[zhuchcn]

PR description

summarizeFasta is now called before and after running filterFasta. The output directory is like below:

test/output/test-integration-entrypoint-gvf/call-NonCanonicalPeptide-1.0.0/UCLA0001/moPepGen-0.4.0/output/
├── decoy
├── encode
├── split
├── UCLA0001_variant_peptides.fasta
├── UCLA0001_variant_peptides_filtered.fasta
├── UCLA0001_variant_peptides_filtered_PostFilter_summary.txt
└── UCLA0001_variant_peptides_PreFilter_summary.txt

Also fixed the issue that Arriba and FusionCatcher output not input into callVariant

Maybe I don't really need the 'PreFilter' and 'PostFilter', because their filename prefixes are different.

Checklist

• [X] I have read the code review guidelines and the code review best practice on GitHub check-list.

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• [X] I have added my name to the contributors listings in the metadata.yaml and the manifest block in the nextflow.config as part of this pull request, am listed already, or do not wish to be listed. (This acknowledgement is optional.)

• [ ] I have added the changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

• [ ] I have updated the version number in the metadata.yaml and manifest block of the nextflow.config file following semver, or the version number has already been updated. (Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.)

• [X] All test cases have passed.

Closes #31 Closes #34

[lydiayliu]

Maybe just

UCLA0001_variant_peptides_summary.txt
UCLA0001_variant_peptides_filtered_summary.txt

?

[zhuchcn]

Done!

test/output/test-integration-entrypoint-gvf/call-NonCanonicalPeptide-1.0.0/UCLA0001/moPepGen-0.4.0/output/
├── decoy
├── encode
├── split
├── UCLA0001_variant_peptides.fasta
├── UCLA0001_variant_peptides_filtered.fasta
├── UCLA0001_variant_peptides_filtered_summary.txt
└── UCLA0001_variant_peptides_summary.txt