Pierre Lindenbaum lindenb

## 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)

## 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>

## 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

## Artists.md

      
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                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


## chatGPT. monopoly.md

      
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                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)


## README.md

      
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                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

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


## 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)

## README.md

      
              3 files
            
          
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                lindenb
                / README.md
            
            
              Created
              January 3, 2023 15:04
            
              
                https://www.biostars.org/p/9549996/ nextflow class java groovy
              
          
      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}

  
## mastodon.md

      
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                lindenb
                / mastodon.md
            
            
              Last active
              November 13, 2022 18:32
            
              
                find scientists (bioinformatics | biostatistics | genetics ) having a mastodon account using SPARQL + wikidata.
              
          
      View mastodon.md
  
      
    find scientists having a mastodon account using wikidata:
https://query.wikidata.org/#SELECT%20DISTINCT%20%3Fperson%20%3FpersonLabel%20%3FworkLabel%20%3Fmastodon%20%0A%0A%20%20WHERE%20%7B%0A%20%20%20%20%3Fperson%20wdt%3AP31%20wd%3AQ5%20.%0A%20%20%20%20%3Fperson%20wdt%3AP101%20%3Fwork%20.%0A%20%20%20%20%3Fperson%20wdt%3AP4033%20%3Fmastodon%20.%0A%20%20%20%20FILTER%20%28%3Fwork%20IN%20%28wd%3AQ128570%20%2C%20wd%3AQ7162%20%2C%20wd%3AQ214746%20%29%20%29%20.%0A%20%20%20%20SERVICE%20wikibase%3Alabel%20%7B%20bd%3AserviceParam%20wikibase%3Alanguage%20%22%5BAUTO_LANGUAGE%5D%2Cen%22.%20%7D%0A%20%20%20%20%20%20%20%20%20%20%20%20%0A%20%20%7D%0A%20%20LIMIT%20100%0A%0A

  
## Makefile
CC?=gcc

ifeq ($(HTSLIB),)
$(error undefined $$HTSLIB)
endif

CFLAGS= -Wall -O3 -I$(HTSLIB)
LDFLAGS=  -L$(HTSLIB) -lz -lhts
	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)
	<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>
	# 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
	/* 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)
	CC?=gcc

	ifeq ($(HTSLIB),)
	$(error undefined $$HTSLIB)
	endif

	CFLAGS= -Wall -O3 -I$(HTSLIB)
	LDFLAGS= -L$(HTSLIB) -lz -lhts