├── LICENSE ├── README.md ├── amr_finder ├── .gitignore ├── README.md ├── amr_report.cwl ├── amrfinder ├── amrfinder-prot.sh ├── blastp.cwl ├── blastp_params.yaml ├── blastx.cwl ├── fasta_check.cwl ├── gff_check.cwl ├── hmmsearch.cwl ├── hmmsearch_params.yaml ├── impl_amrfinder.py ├── test_dna.fa ├── test_dna_fail.fa ├── test_prot.fa ├── test_prot.gff ├── test_prot_fail.fa ├── update_docker_version.sh ├── wf_amr_dna.cwl ├── wf_amr_dna_params.yaml ├── wf_amr_prot.cwl ├── wf_amr_prot_params.yaml └── wf_makeblastdb.cwl └── contam_filter ├── blastn.cwl ├── blastn_params.yaml ├── common_fastas.yaml ├── create_blast_list.cwl ├── create_db_list.cwl ├── decompress.cwl ├── decompress_params.yaml ├── default_fastas.yaml ├── euk_fasta.yaml ├── euk_params.yaml ├── flatten.cwl ├── flatten_params.yaml ├── makeblastdb.cwl ├── makeblastdb_params.yaml ├── pa_test.fa.gz ├── params.yaml ├── prok_fasta.yaml ├── prok_params.yaml ├── typedefs.yaml ├── vecscreen.cwl ├── wf_blastit.cwl ├── 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