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chien-chi
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update inputs.json example
1 parent 0711741 commit 573fdf6

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‎automation_inputs.json‎

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{
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"nmdc_mags.contig_file": "https://data.microbiomedata.org/data/nmdc:omprc-11-9mvz7z22/nmdc:wfmgas-11-rcs4bt79.1/nmdc_wfmgas-11-rcs4bt79.1_contigs.fna",
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"nmdc_mags.gff_file": "https://data.microbiomedata.org/data/nmdc:omprc-11-9mvz7z22/nmdc:wfmgan-11-hdaenp36.1/nmdc_wfmgan-11-hdaenp36.1_functional_annotation.gff",
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"nmdc_mags.crispr_file": "https://data.microbiomedata.org/data/nmdc:omprc-11-9mvz7z22/nmdc:wfmgan-11-hdaenp36.1/nmdc_wfmgan-11-hdaenp36.1_crt.crisprs",
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"nmdc_mags.cog_file": "https://data.microbiomedata.org/data/nmdc:omprc-11-9mvz7z22/nmdc:wfmgan-11-hdaenp36.1/nmdc_wfmgan-11-hdaenp36.1_cog.gff",
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"nmdc_mags.pfam_file": "https://data.microbiomedata.org/data/nmdc:omprc-11-9mvz7z22/nmdc:wfmgan-11-hdaenp36.1/nmdc_wfmgan-11-hdaenp36.1_pfam.gff",
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"nmdc_mags.product_names_file": "https://data.microbiomedata.org/data/nmdc:omprc-11-9mvz7z22/nmdc:wfmgan-11-hdaenp36.1/nmdc_wfmgan-11-hdaenp36.1_product_names.tsv",
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"nmdc_mags.tigrfam_file": "https://data.microbiomedata.org/data/nmdc:omprc-11-9mvz7z22/nmdc:wfmgan-11-hdaenp36.1/nmdc_wfmgan-11-hdaenp36.1_tigrfam.gff",
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"nmdc_mags.ec_file": "https://data.microbiomedata.org/data/nmdc:omprc-11-9mvz7z22/nmdc:wfmgan-11-hdaenp36.1/nmdc_wfmgan-11-hdaenp36.1_ec.tsv",
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"nmdc_mags.ko_file": "https://data.microbiomedata.org/data/nmdc:omprc-11-9mvz7z22/nmdc:wfmgan-11-hdaenp36.1/nmdc_wfmgan-11-hdaenp36.1_ko.tsv",
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"nmdc_mags.lineage_file": "https://data.microbiomedata.org/data/nmdc:omprc-11-9mvz7z22/nmdc:wfmgan-11-hdaenp36.1/nmdc_wfmgan-11-hdaenp36.1_scaffold_lineage.tsv",
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"nmdc_mags.sam_file": "https://data.microbiomedata.org/data/nmdc:omprc-11-9mvz7z22/nmdc:wfmgas-11-rcs4bt79.1/nmdc_wfmgas-11-rcs4bt79.1_pairedMapped_sorted.bam",
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"nmdc_mags.proteins_file": "https://data.microbiomedata.org/data/nmdc:omprc-11-9mvz7z22/nmdc:wfmgan-11-hdaenp36.1/nmdc_wfmgan-11-hdaenp36.1_proteins.faa",
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"nmdc_mags.gene_phylogeny_file": "https://data.microbiomedata.org/data/nmdc:omprc-11-9mvz7z22/nmdc:wfmgan-11-hdaenp36.1/nmdc_wfmgan-11-hdaenp36.1_gene_phylogeny.tsv",
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"nmdc_mags.contig_file": "https://data.microbiomedata.org/data/nmdc:omprc-13-bs19pv94/nmdc:wfmgan-11-7ma7ty92.1/nmdc_wfmgan-11-7ma7ty92.1_contigs.fna",
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"nmdc_mags.gff_file": "https://data.microbiomedata.org/data/nmdc:omprc-13-bs19pv94/nmdc:wfmgan-11-7ma7ty92.1/nmdc_wfmgan-11-7ma7ty92.1_functional_annotation.gff",
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"nmdc_mags.crispr_file": "https://data.microbiomedata.org/data/nmdc:omprc-13-bs19pv94/nmdc:wfmgan-11-7ma7ty92.1/nmdc_wfmgan-11-7ma7ty92.1_crt.crisprs",
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"nmdc_mags.cog_file": "https://data.microbiomedata.org/data/nmdc:omprc-13-bs19pv94/nmdc:wfmgan-11-7ma7ty92.1/nmdc_wfmgan-11-7ma7ty92.1_cog.gff",
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"nmdc_mags.pfam_file": "https://data.microbiomedata.org/data/nmdc:omprc-13-bs19pv94/nmdc:wfmgan-11-7ma7ty92.1/nmdc_wfmgan-11-7ma7ty92.1_pfam.gff",
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"nmdc_mags.product_names_file": "https://data.microbiomedata.org/data/nmdc:omprc-13-bs19pv94/nmdc:wfmgan-11-7ma7ty92.1/nmdc_wfmgan-11-7ma7ty92.1_product_names.tsv",
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"nmdc_mags.tigrfam_file": "https://data.microbiomedata.org/data/nmdc:omprc-13-bs19pv94/nmdc:wfmgan-11-7ma7ty92.1/nmdc_wfmgan-11-7ma7ty92.1_tigrfam.gff",
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"nmdc_mags.ec_file": "https://data.microbiomedata.org/data/nmdc:omprc-13-bs19pv94/nmdc:wfmgan-11-7ma7ty92.1/nmdc_wfmgan-11-7ma7ty92.1_ec.tsv",
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"nmdc_mags.ko_file": "https://data.microbiomedata.org/data/nmdc:omprc-13-bs19pv94/nmdc:wfmgan-11-7ma7ty92.1/nmdc_wfmgan-11-7ma7ty92.1_ko.tsv",
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"nmdc_mags.lineage_file": "https://data.microbiomedata.org/data/nmdc:omprc-13-bs19pv94/nmdc:wfmgan-11-7ma7ty92.1/nmdc_wfmgan-11-7ma7ty92.1_scaffold_lineage.tsv",
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"nmdc_mags.sam_file": "https://data.microbiomedata.org/data/nmdc:omprc-13-bs19pv94/nmdc:wfmgas-13-02qywk04.1/nmdc_wfmgas-13-02qywk04.1_pairedMapped_sorted.bam",
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"nmdc_mags.proteins_file": "https://data.microbiomedata.org/data/nmdc:omprc-13-bs19pv94/nmdc:wfmgan-11-7ma7ty92.1/nmdc_wfmgan-11-7ma7ty92.1_proteins.faa",
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"nmdc_mags.gene_phylogeny_file": "https://data.microbiomedata.org/data/nmdc:omprc-13-bs19pv94/nmdc:wfmgan-11-7ma7ty92.1/nmdc_wfmgan-11-7ma7ty92.1_gene_phylogeny.tsv",
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"nmdc_mags.map_file": "https://data.microbiomedata.org/data/nmdc:omprc-13-bs19pv94/nmdc:wfmgan-11-7ma7ty92.1/nmdc_wfmgan-11-7ma7ty92.1_contig_names_mapping.tsv",
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"nmdc_mags.proj": "nmdc:wfmag-11-9dgz7m72.1"
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}

‎input.json‎

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{
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"nmdc_mags.proj_name": "nmdc_wfmgan-xx-xxxxxxxx",
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"nmdc_mags.contig_file": "/path/to/Assembly/nmdc_wfmgas-xx-xxxxxxx_contigs.fna",
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"nmdc_mags.contig_file": "/path/to/Assembly/nmdc_wfmgan-xx-xxxxxxx_contigs.fna",
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"nmdc_mags.sam_file": "/path/to/Assembly/nmdc_wfmgas-xx-xxxxxxx_pairedMapped_sorted.bam",
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"nmdc_mags.gff_file": "/path/to/Annotation/nmdc_wfmgas-xx-xxxxxxx_functional_annotation.gff",
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"nmdc_mags.proteins_file": "/path/to/Annotation/nmdc_wfmgas-xx-xxxxxxx_proteins.faa",
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"nmdc_mags.cog_file": "/path/to/Annotation/nmdc_wfmgas-xx-xxxxxxx_cog.gff",
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"nmdc_mags.ec_file": "/path/to/Annotation/nmdc_wfmgas-xx-xxxxxxx_ec.tsv",
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"nmdc_mags.ko_file": "/path/to/Annotation/nmdc_wfmgas-xx-xxxxxxx_ko.tsv",
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"nmdc_mags.pfam_file": "/path/to/Annotation/nmdc_wfmgas-xx-xxxxxxx_pfam.gff",
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"nmdc_mags.tigrfam_file": "/path/to/Annotation/nmdc_wfmgas-xx-xxxxxxxtigrfam.gff",
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"nmdc_mags.crispr_file": "/path/to/Annotation/nmdc_wfmgas-xx-xxxxxxx_crt.crisprs",
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"nmdc_mags.product_names_file": "/path/to/Annotation/nmdc_wfmgas-xx-xxxxxxx_product_names.tsv",
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"nmdc_mags.gene_phylogeny_file": "/path/to/Annotation/nmdc_wfmgas-xx-xxxxxxx_gene_phylogeny.tsv",
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"nmdc_mags.lineage_file": "/path/to/Annotation/nmdc_wfmgas-xx-xxxxxxx_scaffold_lineage.tsv",
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"nmdc_mags.gff_file": "/path/to/Annotation/nmdc_wfmgan-xx-xxxxxxx_functional_annotation.gff",
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"nmdc_mags.proteins_file": "/path/to/Annotation/nmdc_wfmgan-xx-xxxxxxx_proteins.faa",
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"nmdc_mags.cog_file": "/path/to/Annotation/nmdc_wfmgan-xx-xxxxxxx_cog.gff",
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"nmdc_mags.ec_file": "/path/to/Annotation/nmdc_wfmgan-xx-xxxxxxx_ec.tsv",
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"nmdc_mags.ko_file": "/path/to/Annotation/nmdc_wfmgan-xx-xxxxxxx_ko.tsv",
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"nmdc_mags.pfam_file": "/path/to/Annotation/nmdc_wfmgan-xx-xxxxxxx_pfam.gff",
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"nmdc_mags.tigrfam_file": "/path/to/Annotation/nmdc_wfmgan-xx-xxxxxxxtigrfam.gff",
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"nmdc_mags.crispr_file": "/path/to/Annotation/nmdc_wfmgan-xx-xxxxxxx_crt.crisprs",
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"nmdc_mags.product_names_file": "/path/to/Annotation/nmdc_wfmgan-xx-xxxxxxx_product_names.tsv",
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"nmdc_mags.gene_phylogeny_file": "/path/to/Annotation/nmdc_wfmgan-xx-xxxxxxx_gene_phylogeny.tsv",
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"nmdc_mags.lineage_file": "/path/to/Annotation/nmdc_wfmgan-xx-xxxxxxx_scaffold_lineage.tsv",
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"nmdc_mags.map_file":"/path/to/Annotation/nmdc_wfmgan-xx-xxxxxxx_contig_names_mapping.tsv",
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"nmdc_mags.gtdbtk_db": "refdata/GTDBTK_DB",
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"nmdc_mags.checkm_db": "refdata/CheckM_DB",
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"nmdc_mags.eukcc2_db": "refdata/EUKCC2_DB/eukcc2_db_ver_1.2",
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"nmdc_mags.threads": 32,
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"nmdc_mags.pthreads": 1
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}

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