60 lines
1.9 KiB
Plaintext
60 lines
1.9 KiB
Plaintext
import groovy.json.JsonBuilder
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process getParams {
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label "wf_common"
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publishDir "${params.out_dir}", mode: 'copy', pattern: "params.json"
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cache false
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cpus 1
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memory "2 GB"
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output:
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path "params.json"
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script:
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def paramsJSON = new JsonBuilder(params).toPrettyString()
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"""
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# Output nextflow params object to JSON
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echo '$paramsJSON' > params.json
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"""
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}
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process configure_igv {
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publishDir "${params.out_dir}/", mode: 'copy', pattern: 'igv.json', enabled: params.containsKey("igv") && params.igv
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label "wf_common"
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cpus 1
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memory "2 GB"
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input:
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// the python script will work out what to do with all the files based on their
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// extensions
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path "file-names.txt"
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val locus_str
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val aln_extra_opts
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val var_extra_opts
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output: path "igv.json"
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script:
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// the locus argument just makes sure that the initial view in IGV shows something
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// interesting
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String locus_arg = locus_str ? "--locus $locus_str" : ""
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// extra options for alignment tracks
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def aln_opts_json_str = \
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aln_extra_opts ? new JsonBuilder(aln_extra_opts).toPrettyString() : ""
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String aln_extra_opts_arg = \
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aln_extra_opts ? "--extra-alignment-opts extra-aln-opts.json" : ""
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// extra options for variant tracks
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def var_opts_json_str = \
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var_extra_opts ? new JsonBuilder(var_extra_opts).toPrettyString() : ""
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String var_extra_opts_arg = \
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var_extra_opts ? "--extra-vcf-opts extra-var-opts.json" : ""
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"""
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# write out JSON files with extra options for the alignment and variant tracks
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echo '$aln_opts_json_str' > extra-aln-opts.json
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echo '$var_opts_json_str' > extra-var-opts.json
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workflow-glue configure_igv \
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--fofn file-names.txt \
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$locus_arg \
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$aln_extra_opts_arg \
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$var_extra_opts_arg \
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> igv.json
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"""
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}
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