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Pierre Lindenbaum lindenb

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I hate people.
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@lindenb
lindenb / main.nf
Created September 11, 2023 07:01
https://www.biostars.org/p/9574590/ Nextflow - How to pass the yml yaml format input file from an argument to channel as a list
View main.nf
params.samples="NO_FILE"
workflow {
ch = Channel.fromPath(params.samples).
flatMap(F->{
def yaml = new org.yaml.snakeyaml.Yaml();
def map = yaml.load(F);
return map.samples;
});
doIt(ch)
@lindenb
lindenb / bio-anchor.html
Created August 28, 2023 16:20
A first test with WebComponent, extending HTMLElement javascript bioinformatics
View bio-anchor.html
<html>
<head>
</head>
<body>
<bio-anchor build="hg38">rs25</bio-anchor> and
<bio-anchor build="hg38">ENSG00000005108</bio-anchor>
<bio-anchor build="hg38">chr1:1234-1235</bio-anchor>
<bio-anchor build="hg38">xxx</bio-anchor>
</body>
@lindenb
lindenb / Makefile
Created August 3, 2023 12:29
biostars9571322 Mafile based ngs worfklow for tutorial
View Makefile
# input is
# DATA/father.R1.fq.gz
# DATA/father.R2.fq.gz
# DATA/mother.R1.fq.gz
# DATA/mother.R2.fq.gz
# DATA/child.R1.fq.gz
# DATA/child.R2.fq.gz
#
define mapreads
@lindenb
lindenb / Artists.md
Created July 3, 2023 11:46
matériel artistes art artist pen pencil paper
View Artists.md

Boulet

  • carbon pen platinium DP800S
  • aquarelle winsor & newton
  • pinceaux "Raphaël*
  • papier 250g Clairefontaine
@lindenb
lindenb / chatGPT. monopoly.md
Created April 23, 2023 16:37
Génère moi un jeu de plateau inspiré de #Monopoly se situant dans un labo de Recherche en génétique. L'argent est remplacé par des publications.
View chatGPT. monopoly.md

Pas de problème, voici les règles pour un jeu de plateau inspiré de Monopoly, mais situé dans un laboratoire de recherche en génétique, où les joueurs achètent des laboratoires plutôt que des propriétés :

Matériel :

  • Plateau de jeu
  • Cartes "Chercheurs invités"
  • Cartes "Subventions"
  • Pions (molécule d'ADN, microscope, fiole, pipette, gant de laboratoire)
  • Billets de publications scientifiques (au lieu d'argent)
  • Laboratoires (au lieu de propriétés)
@lindenb
lindenb / README.md
Last active February 15, 2023 21:21
Biostar Images vs text carbon planet climate
View README.md

Don't upload images when you can just copy and paste the text.

The following PNG image has a weight of 357,000 bytes

https://www.biostars.org/media/images/8be0316c-0f5a-4e5b-a769-1e4d0afb

while the text containing the very same information is about only 1,109 bytes, hence a much lower carbon footprint.

##sequence-region JAFJXZ010000052.1 1 250
@lindenb
lindenb / biostars9550377.nf
Last active January 6, 2023 18:05
biostars9550377 "speeding up bcftools view"
View biostars9550377.nf
/* author Pierre Lindenbaum */
params.vcfs="NO_FILE"
params.samples="NO_FILE"
workflow {
each_vcf = Channel.fromPath(params.vcfs).splitText().map{it.trim()}
c2vcf = CHROMS_IN_VCF(each_vcf)
View README.md

with include{MyTest}

Cannot find a component with name 'MyTest' in module: .../20230103.nf.class/./class.nf

 -- Check script 'test.nf' at line: 2 or see '.nextflow.log' file for more details

without include{MyTest}

@lindenb
lindenb / Makefile
Created September 22, 2022 19:33
biostar9539326.c proper way to alter bgzf-compressed fastq files using htslib, multithreaded
View Makefile
CC?=gcc
ifeq ($(HTSLIB),)
$(error undefined $$HTSLIB)
endif
CFLAGS= -Wall -O3 -I$(HTSLIB)
LDFLAGS= -L$(HTSLIB) -lz -lhts