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Merge pull request #184 from broadinstitute/dp-clades
add new sarscov2_lineages workflow and travis cleanups
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,103 @@ | ||
| version 1.0 | ||
|
|
||
| task nextclade_one_sample { | ||
| meta { | ||
| description: "Nextclade classification of one sample. Leaving optional inputs unspecified will use SARS-CoV-2 defaults." | ||
| } | ||
| input { | ||
| File genome_fasta | ||
| File? root_sequence | ||
| File? auspice_reference_tree_json | ||
| File? qc_config_json | ||
| File? gene_annotations_json | ||
| File? pcr_primers_csv | ||
| } | ||
| String basename = basename(genome_fasta, ".fasta") | ||
| command { | ||
| set -e | ||
| nextclade.js --version > VERSION | ||
| nextclade.js \ | ||
| --input-fasta "~{genome_fasta}" \ | ||
| ~{"--input-root-seq " + root_sequence} \ | ||
| ~{"--input-tree " + auspice_reference_tree_json} \ | ||
| ~{"--input-qc-config " + qc_config_json} \ | ||
| ~{"--input-gene-map " + gene_annotations_json} \ | ||
| ~{"--input-pcr-primers " + pcr_primers_csv} \ | ||
| --output-json "~{basename}".nextclade.json \ | ||
| --output-tsv "~{basename}".nextclade.tsv \ | ||
| --output-tree "~{basename}".nextclade.auspice.json | ||
| cp "~{basename}".nextclade.tsv input.tsv | ||
| python3 <<CODE | ||
| # transpose table | ||
| with open('input.tsv', 'rt') as inf: | ||
| with open('transposed.tsv', 'wt') as outf: | ||
| for c in zip(*(l.rstrip().split('\t') for l in inf)): | ||
| outf.write('\t'.join(c)+'\n') | ||
| CODE | ||
| } | ||
| runtime { | ||
| docker: "neherlab/nextclade:0.10.0" | ||
| memory: "3 GB" | ||
| cpu: 2 | ||
| disks: "local-disk 50 HDD" | ||
| dx_instance_type: "mem1_ssd1_v2_x2" | ||
| } | ||
| output { | ||
| String nextclade_version = read_string("VERSION") | ||
| File nextclade_json = "~{basename}.nextclade.json" | ||
| File auspice_json = "~{basename}.nextclade.auspice.json" | ||
| File nextclade_tsv = "~{basename}.nextclade.tsv" | ||
| String nextclade_clade = read_map("transposed.tsv")["clade"] | ||
| } | ||
| } | ||
| task pangolin_one_sample { | ||
| meta { | ||
| description: "Pangolin classification of one SARS-CoV-2 sample." | ||
| } | ||
| input { | ||
| File genome_fasta | ||
| Int? min_length | ||
| Float? max_ambig | ||
| Boolean include_putative = true | ||
| } | ||
| String basename = basename(genome_fasta, ".fasta") | ||
| command { | ||
| set -e | ||
| pangolin -v > VERSION_PANGOLIN | ||
| pangolin -lv > VERSION_LINEAGES | ||
| pangolin -pv > VERSION_PANGOLEARN | ||
| pangolin "~{genome_fasta}" \ | ||
| --outfile "~{basename}.pangolin_report.csv" \ | ||
| -t "$(nproc)" \ | ||
| --include-putative \ | ||
| ~{"--min-length " + min_length} \ | ||
| ~{"--max-ambig " + max_ambig} \ | ||
| ~{true="--include-putative" false="" include_putative} \ | ||
| --verbose | ||
| cp "~{basename}.pangolin_report.csv" input.csv | ||
| python3 <<CODE | ||
| # transpose table and convert csv to tsv | ||
| with open('input.csv', 'rt') as inf: | ||
| with open('transposed.tsv', 'wt') as outf: | ||
| for c in zip(*(l.rstrip().split(',') for l in inf)): | ||
| outf.write('\t'.join(c)+'\n') | ||
| CODE | ||
| } | ||
| runtime { | ||
| docker: "staphb/pangolin:2.1.1" | ||
| memory: "3 GB" | ||
| cpu: 2 | ||
| disks: "local-disk 50 HDD" | ||
| dx_instance_type: "mem1_ssd1_v2_x2" | ||
| } | ||
| output { | ||
| String pangolin_version = read_string("VERSION_PANGOLIN") | ||
| String lineages_version = read_string("VERSION_LINEAGES") | ||
| String pangolearn_version = read_string("VERSION_PANGOLEARN") | ||
| File pangolin_csv = "~{basename}.pangolin_report.csv" | ||
| String pangolin_clade = read_map("transposed.tsv")["lineage"] | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| version 1.0 | ||
|
|
||
| import "../tasks/tasks_sarscov2.wdl" as sarscov2 | ||
|
|
||
| workflow sarscov2_lineages { | ||
| meta { | ||
| description: "Call Nextclade and Pangolin lineages on a single SARS-CoV-2 genome" | ||
| } | ||
|
|
||
| input { | ||
| File genome_fasta | ||
| } | ||
|
|
||
| call sarscov2.nextclade_one_sample { | ||
| input: | ||
| genome_fasta = genome_fasta | ||
| } | ||
|
|
||
| call sarscov2.pangolin_one_sample { | ||
| input: | ||
| genome_fasta = genome_fasta | ||
| } | ||
|
|
||
| output { | ||
| String nextclade_clade = nextclade_one_sample.nextclade_clade | ||
| File nextclade_tsv = nextclade_one_sample.nextclade_tsv | ||
| String pangolin_clade = pangolin_one_sample.pangolin_clade | ||
| File pangolin_csv = pangolin_one_sample.pangolin_csv | ||
| } | ||
| } |
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