find path/to/dir -type f -name "S*.vcf.gz" > jeter.list
nextflow run --vcfs ${PWD}/jeter.list biostar9526718.nf
add -C config.cfg toconfigure your cluster config....
Pierre Lindenbaum lindenb
😶
lindenb
/ biostar9528296.c
Last active
June 23, 2022 07:35
https://www.biostars.org/p/9528296/ How to search the human genome for sequences that differ from a given sequence by a set number of mismatches? C
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| #include <stdio.h> | |
| #include <string.h> | |
| #include <stdlib.h> | |
| #include <ctype.h> | |
| #define MAX_SEQ_LENGTH 100 | |
| static char compl(char c) { | |
| switch(c) { | |
| case 'A': return 'T'; |
lindenb
/ Usage.md
Created
June 11, 2022 12:49
https://www.biostars.org/p/9526679/ How to merge 20K single-sample VCFs *without* using plink or plink2? #bcftools #nextflow
lindenb
/ biostar9524046.nf
Created
May 21, 2022 14:26
biostar9524046.nf https://www.biostars.org/p/9524046/ Forum:Compare the samples in a VCF concordance picard
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| nextflow.enable.dsl=2 | |
| params.vcf="" | |
| workflow { | |
| picard = downloadPicard() | |
| samples_ch = vcf2samples(params.vcf).splitCsv(header: false,sep:'\t',strip:true) | |
| pair_ch = samples_ch.combine(samples_ch).filter{T->!T[1].equals(T[3])} | |
| concordances_ch = concordance(picard,pair_ch) |
lindenb
/ biostar9523782.nf
Last active
May 19, 2022 16:28
https://www.biostars.org/p/9523782/ blast biostar nextflow fasta sequence align
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| nextflow.enable.dsl=2 | |
| /* full path to query directory */ | |
| params.qdir="/DIR1" | |
| /* full path to target/database directory */ | |
| params.tdir="/DIR2" | |
| workflow { |
lindenb
/ release.sh
Created
July 1, 2021 10:19
How to create full release from command line, not just a tag? https://git.521000.bestmunity/t/how-to-create-full-release-from-command-line-not-just-a-tag/916/2
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| #!/bin/bash | |
| # https://git.521000.bestmunity/t/how-to-create-full-release-from-command-line-not-just-a-tag/916/2 | |
| if [ "$#" -ne 2 ]; then | |
| echo "Expected: 'version' 'message'" | |
| exit -1 | |
| fi |
lindenb
/ FastGatk.java
Created
June 9, 2021 08:37
Fast GATK: calling a small region for a large number of Bams with GATK HaplotypeCaller
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| /* | |
| The MIT License (MIT) | |
| Copyright (c) 2021 Pierre Lindenbaum | |
| Permission is hereby granted, free of charge, to any person obtaining a copy | |
| of this software and associated documentation files (the "Software"), to deal | |
| in the Software without restriction, including without limitation the rights | |
| to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
| copies of the Software, and to permit persons to whom the Software is |
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| $ time java -jar cromwell-57.jar run jeter.wdl | |
| [2021-02-24 18:43:16,75] [info] Running with database db.url = jdbc:hsqldb:mem:43a7a2b5-d8e7-4129-a9d5-c939dbf31ddf;shutdown=false;hsqldb.tx=mvcc | |
| [2021-02-24 18:45:41,45] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000 | |
| [2021-02-24 18:45:42,04] [info] [RenameWorkflowOptionsInMetadata] 100% | |
| [2021-02-24 18:45:44,94] [info] Running with database db.url = jdbc:hsqldb:mem:f57101ad-0a60-4bc1-947f-efb7610b1497;shutdown=false;hsqldb.tx=mvcc | |
| [2021-02-24 18:45:55,25] [info] Slf4jLogger started | |
| [2021-02-24 18:45:58,25] [info] Workflow heartbeat configuration: | |
| { | |
| "cromwellId" : "cromid-3d07b24", |
lindenb
/ .gitignore
Last active
November 20, 2020 14:15
a basic GWAK extension generating the reverse complement of a DNA sequence
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| *.o | |
| *.so | |
| *~ | |
| gawk-* |
lindenb
/ test.html
Created
October 21, 2020 19:21
braiding test ( https://github.com/VisDunneRight/sequence_braiding )
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| <!DOCTYPE html> | |
| <html lang="en"> | |
| <head> | |
| <meta charset="utf-8"> | |
| <title>Sequence Braiding</title> | |
| <meta name="description" content=""> | |
| <meta name="author" content=""> |
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| PREFIX=20201006.DSL2 | |
| OUTDIR=work | |
| all: main.nf $(OUTDIR)/jeter.fastqs.list | |
| mkdir -p $(OUTDIR) | |
| nextflow run -with-dag workflow.dot -with-report -with-timeline -with-trace -resume \ | |
| -work-dir "$(OUTDIR)" \ | |
| --fastqs $(OUTDIR)/jeter.fastqs.list \ | |
| $< | |
| @echo "output is $(OUTDIR)" |