Add recipe for sccmec

[rpetit3]

sccmec is a simple tool for typing SCCmec cassettes in assemblies

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[rpetit3]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
noarch	sccmec-1.0.0-hdfd78af_0.tar.bz2	LinuxArtifacts.zip	Azure	show You may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>

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Docker image(s) built:

Package	Tag	CI	Install with docker
sccmec	1.0.0--hdfd78af_0	Azure	show Images for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/sccmec:1.0.0--hdfd78af_0.tar.gz | docker load

[rpetit3]

Testing

Conda

mamba create -n sccmec -c conda-forge -c bioconda camlhmp
conda activate sccmec
conda install LinuxArtifacts/packages/noarch/sccmec-1.0.0-hdfd78af_0.tar.bz2
sccmec --input type-III-AB037671.fasta.gz --force
Running camlhmp with following parameters:
    --input type-III-AB037671.fasta.gz
    --yaml /home/robert_petit/miniconda3/envs/sccmec/bin/../share/sccmec/sccmec.yaml
    --targets /home/robert_petit/miniconda3/envs/sccmec/bin/../share/sccmec/sccmec.fasta
    --outdir ./
    --prefix camlhmp
    --min-pident 95
    --min-coverage 95

Starting camlhmp for SCCmec Typing...
Running blastn...
Processing hits...
Final Results...
                                              SCCmec Typing
┏━━━━━━━━━┳━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┓
┃ sample  ┃ type ┃ targets                                                 ┃ schema ┃ version ┃ comment ┃
┡━━━━━━━━━╇━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━┩
│ camlhmp │ III  │ ccrA3,ccrB3,ccrC1,IS431,IS431_1,IS431_2,mecA,mecI,mecR1 │ sccmec │ 1.0.0   │         │
└─────────┴──────┴─────────────────────────────────────────────────────────┴────────┴─────────┴─────────┘
Writing outputs...
Final predicted type written to ./camlhmp.tsv
Results against each type written to ./camlhmp.details.tsv
blastn results written to ./camlhmp.blastn.tsv

Docker

docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data quay.io/biocontainers/sccmec:1.0.0--hdfd78af_0 sccmec --input /data/type-III-AB037671.fasta.gz --outdir /data/ --force
Running camlhmp with following parameters:
    --input /data/type-III-AB037671.fasta.gz
    --yaml /usr/local/bin/../share/sccmec/sccmec.yaml
    --targets /usr/local/bin/../share/sccmec/sccmec.fasta
    --outdir /data/
    --prefix camlhmp
    --min-pident 95
    --min-coverage 95

Starting camlhmp for SCCmec Typing...
Running blastn...
Processing hits...
Final Results...
                                 SCCmec Typing
┏━━━━━━━━━┳━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┓
┃ sample  ┃ type ┃ targets                        ┃ schema ┃ version ┃ comment ┃
┡━━━━━━━━━╇━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━┩
│ camlhmp │ III  │ ccrA3,ccrB3,ccrC1,IS431,IS431… │ sccmec │ 1.0.0   │         │
└─────────┴──────┴────────────────────────────────┴────────┴─────────┴─────────┘
Writing outputs...
Final predicted type written to /data/camlhmp.tsv
Results against each type written to /data/camlhmp.details.tsv
blastn results written to /data/camlhmp.blastn.tsv

I think we are good!

[rpetit3]

@BiocondaBot please add label

[lskatz]

LGTM