Pierre Lindenbaum lindenb
😶
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| http://www.ebi.ac.uk/efo/EFO_0003898 ankylosing spondylitis | |
| http://www.ebi.ac.uk/efo/EFO_0000783 myositis | |
| http://www.ebi.ac.uk/efo/EFO_1001806 macrophage activation syndrome | |
| http://www.ebi.ac.uk/efo/EFO_1001807 malacoplakia | |
| http://www.ebi.ac.uk/efo/EFO_1000719 juvenile dermatitis herpetiformis | |
| http://www.orpha.net/ORDO/Orphanet_602 Distal myopathy, Nonaka type | |
| http://www.orpha.net/ORDO/Orphanet_2841 Familial benign chronic pemphigus | |
| http://www.ebi.ac.uk/efo/EFO_0005676 Autoimmune Hepatitis | |
| http://www.ebi.ac.uk/efo/EFO_0009313 Linear IgA Dermatosis | |
| http://www.ebi.ac.uk/efo/EFO_0000540 immune system disease |
lindenb
/ finddups.nf
Created
March 4, 2020 13:51
workflow nextflow finding duplicated files and creating a bash script to replace the duplicate with a symbolic link
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| params.directories="." | |
| params.headsize=100000 | |
| params.extensions="bam bai" | |
| params.help=false | |
| params.extrafind="" | |
| params.lines = 1000 | |
| params.publishDir="." | |
| def helpMessage() { | |
| log.info""" |
lindenb
/ bam2cram.nf
Created
March 4, 2020 08:22
BAM to CRAM workflow . bam cram reference fasta nextflow nf
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| params.directories="." | |
| params.help=false | |
| params.references="" | |
| params.prefix="" | |
| params.publishDir="." | |
| params.extrafind="" | |
| references = file(params.references) | |
| def helpMessage() { |
lindenb
/ fastq2ucram.nf
Last active
February 29, 2020 18:58
fastq2ucram fastq to ucram nextflow cram bam fastq
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| params.directories="." | |
| params.help=false | |
| params.center="Nantes" | |
| params.reference="" | |
| params.prefix="" | |
| params.publishDir="." | |
| def helpMessage() { | |
| log.info""" |
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| params.prefix="output." | |
| params.vcf="" | |
| params.help=false | |
| params.rohopts=" --rec-rate 100 --skip-indels " | |
| params.pedigree = "NO_PED" | |
| def helpMessage() { | |
| log.info""" | |
| ========================================= |
lindenb
/ somalier.nf
Last active
January 17, 2020 07:55
nextflow workflow for somalier #nextflow #workflow #somalier #relatedness #samples #bam
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| params.prefix="output." | |
| params.bamlist="" | |
| params.sites="https://github.com/brentp/somalier/files/3412453/sites.hg19.vcf.gz" | |
| params.help=false | |
| params.pedigree="NO_FILE" | |
| def helpMessage() { | |
| log.info""" | |
| ========================================= |
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| gatk="/home/lindenb/packages/gatk/gatk-4.1.4.1/gatk" | |
| String jvarkit(String tool) { | |
| return "/home/lindenb/src/jvarkit-git/dist/"+tool+".jar"; | |
| } | |
| reference=file(params.reference) | |
| process extractor { | |
| tag "script extracting bounds" | |
| cache 'lenient' |
lindenb
/ merge_pdfs.bash
Created
December 18, 2019 14:22
merging multiple pdfs using ghostview and recursion ( gs recursive recursif pdf)
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| merger() { | |
| echo "merging \$1 and \$2" 1>&2 | |
| ls -lah "\$1" "\$2" 1>&2 | |
| gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -dPDFSETTINGS=/prepress -sOutputFile=jeter.pdf "\$1" "\$2" | |
| mv jeter.pdf "\$1" | |
| rm "\$2" | |
| } | |
lindenb
/ biostar.xslt
Created
September 30, 2019 12:26
https://www.biostars.org/p/2867/ blast xslt xsl
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| <?xml version='1.0' encoding="UTF-8" ?> | |
| <xsl:stylesheet | |
| xmlns:xsl='http://www.w3.org/1999/XSL/Transform' | |
| version='1.0' | |
| > | |
| <xsl:output method="xml" encoding="UTF-8" indent="yes"/> | |
| <xsl:template match="*|text()"> | |
| <xsl:copy> | |
| <xsl:apply-templates select="*|text()"/> |
lindenb
/ bioalcidae.code
Last active
August 13, 2019 19:55
https://www.biostars.org/p/394289/ : Extracting reads mapping to CDS regions but not the first 45bp after ATG gtf cds
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| stream(). | |
| flatMap(G->G.getTranscripts().stream()). | |
| filter(T->T.getCodonStart().isPresent() && T.getCodonStop().isPresent() && T.hasStrand()). | |
| forEach(T->{ | |
| List<Integer> positions = new ArrayList<>(); | |
| for(com.github.lindenb.jvarkit.util.bio.structure.Cds cds : T.getAllCds()) { | |
| for(int x=cds.getStart();x<=cds.getEnd();++x) positions.add(x); | |
| } | |
| if(positions.size() <= 45) return; |