Pierre Lindenbaum lindenb

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I hate people.

Institut-du-Thorax, Nantes, France.

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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

Usage

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....

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

	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

	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

	#!/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

	/*
	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

lindenb / cromwell.log

Created February 24, 2021 18:01

cromwell wdl

	$ 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

	*.o
	*.so
	*~
	gawk-*

lindenb / test.html

Created October 21, 2020 19:21

braiding test ( https://github.com/VisDunneRight/sequence_braiding )

	<!DOCTYPE html>
	<html lang="en">
	<head>


	<meta charset="utf-8">
	<title>Sequence Braiding</title>
	<meta name="description" content="">
	<meta name="author" content="">

lindenb / Makefile

Last active October 6, 2020 13:31

test nextflow dsl2.

	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)"

lindenb / Usage.md

Created September 10, 2020 12:23

Question: is there any way to filter NCBI datasets by sample type?

$ wget -q -O - "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19826&targ=self&form=xml&view=quick" |\
  xsltproc biostar460606.xsl - | bash
 
GSM495051 !Sample_source_name_ch1 = noncancer tissue
GSM495052 !Sample_source_name_ch1 = gastric cancer tissue
GSM495053 !Sample_source_name_ch1 = noncancer tissue
GSM495054 !Sample_source_name_ch1 = gastric cancer tissue
GSM495055 !Sample_source_name_ch1 = noncancer tissue
GSM495056 !Sample_source_name_ch1 = gastric cancer tissue

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