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bee7e55618
* Added nextflow language * Added main.nf to list of filenames * Fixed duplicate groovy scope * Removed hello-world example * Update grammar submodule * Removed main.nf from filenames * Added nextflow.config example
68 lines
1.9 KiB
Plaintext
68 lines
1.9 KiB
Plaintext
#!/usr/bin/env nextflow
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/*
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* This is free and unencumbered software released into the public domain.
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*
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* Anyone is free to copy, modify, publish, use, compile, sell, or
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* distribute this software, either in source code form or as a compiled
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* binary, for any purpose, commercial or non-commercial, and by any
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* means.
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*
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* In jurisdictions that recognize copyright laws, the author or authors
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* of this software dedicate any and all copyright interest in the
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* software to the public domain. We make this dedication for the benefit
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* of the public at large and to the detriment of our heirs and
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* successors. We intend this dedication to be an overt act of
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* relinquishment in perpetuity of all present and future rights to this
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* software under copyright law.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
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* IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR
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* OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
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* ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*
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* For more information, please refer to <http://unlicense.org/>
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*/
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/*
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* Author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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*/
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params.query = "$HOME/sample.fa"
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params.db = "$HOME/tools/blast-db/pdb/pdb"
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process blast {
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output:
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file top_hits
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"""
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blastp -query ${params.query} -db ${params.db} -outfmt 6 \
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| head -n 10 \
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| cut -f 2 > top_hits
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"""
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}
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process extract {
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input:
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file top_hits
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output:
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file sequences
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"""
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blastdbcmd -db ${params.db} -entry_batch $top_hits > sequences
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"""
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}
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process align {
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input:
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file sequences
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echo true
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"""
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t_coffee $sequences 2>&- | tee align_result
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"""
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}
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