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{ | ||
"contigs.deplete.bwaDbs": [ | ||
"dx://file-F9k7Bx00Z3ybJjvY3ZVj7Z9P" | ||
], | ||
"contigs.deplete.blastDbs": [ | ||
"dx://file-F8B3B6Q09y3bZg3j1FqK7bJ9", | ||
"dx://file-F8BjgXj09y3gkfZGPPQZbZkK", | ||
"dx://file-F8B3Pp809y3jBpXq7xjxbq94", | ||
"dx://file-F8B3B6809y3kK1JP5X8Pg361" | ||
], | ||
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||
"contigs.spades.trim_clip_db": | ||
"dx://file-BXF0vYQ0QyBF509G9J12g927" | ||
} |
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{ | ||
"spikein.spikein_report.spikein_db": | ||
"dx://file-F6PXkF00Yqp3zVXq14fF98Kz" | ||
} |
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import "interhost.wdl" as interhost | ||
import "ncbi.wdl" as ncbi | ||
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# DX_SKIP_WORKFLOW | ||
workflow align_and_annot { | ||
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File reference_fasta | ||
Array[File]+ assemblies_fasta | ||
Array[File]+ annotations_tbl | ||
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call interhost.multi_align_mafft_ref as mafft { | ||
input: | ||
reference_fasta = reference_fasta, | ||
assemblies_fasta = assemblies_fasta | ||
} | ||
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scatter(by_chr in zip(mafft.alignments_by_chr, annotations_tbl)) { | ||
call ncbi.annot_transfer as annot { | ||
input: | ||
chr_mutli_aln_fasta = by_chr.left, | ||
reference_fasta = reference_fasta, | ||
reference_feature_table = by_chr.right | ||
} | ||
call ncbi.prepare_genbank as genbank { | ||
input: | ||
assemblies_fasta = assemblies_fasta, | ||
annotations_tbl = annot.transferred_feature_tables, | ||
out_prefix = basename(by_chr.right, '.tbl') | ||
} | ||
} | ||
} |
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Original file line number | Diff line number | Diff line change |
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@@ -1,5 +1,5 @@ | ||
import "tasks/assembly.wdl" as assembly | ||
import "assembly.wdl" as assembly | ||
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workflow assemble_refbased { | ||
call assembly.refine_2x_and_plot | ||
} | ||
} |
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import "metagenomics.wdl" as metagenomics | ||
import "taxon_filter.wdl" as taxon_filter | ||
import "assembly.wdl" as assembly | ||
workflow contigs { | ||
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call taxon_filter.deplete_taxa as deplete | ||
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call assembly.assemble as spades { | ||
input: | ||
assembler = "spades", | ||
reads_unmapped_bam = deplete.cleaned_bam | ||
} | ||
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# TO DO: taxonomic classification of contigs | ||
} |
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@@ -1,5 +1,5 @@ | ||
import "tasks/demux.wdl" as tasks_demux | ||
import "demux.wdl" as tasks_demux | ||
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workflow demux_only { | ||
call tasks_demux.illumina_demux | ||
} | ||
} |
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Original file line number | Diff line number | Diff line change |
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@@ -1,5 +1,5 @@ | ||
import "tasks/taxon_filter.wdl" as taxon_filter | ||
import "taxon_filter.wdl" as taxon_filter | ||
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workflow deplete_only { | ||
call taxon_filter.deplete_taxa | ||
} | ||
} |
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import "ncbi.wdl" as ncbi | ||
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workflow fetch_annotations { | ||
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call ncbi.download_annotations as download | ||
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} |
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import "reports.wdl" as reports | ||
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workflow spikein { | ||
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call reports.spikein_report as spikein_report | ||
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} |
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