Pierre Lindenbaum lindenb

## 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
            
          
              0 forks
            
          
              0 comments
            
          
              0 stars
            
          
                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

      
              2 files
            
          
              0 forks
            
          
              0 comments
            
          
              0 stars
            
          
                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


## Biostar9532375.java
import java.io.*;
import java.util.*;
public class Biostar9532375 {
private static class Sequence {
	String name;
	StringBuilder seq=new StringBuilder();
	boolean same(char c1,char c2) {
		if(c1==c2) return true;
		if(c1=='N' || c2=='N') return true;
		return false;

## biostar9528296.c
#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';

## Usage.md

      
              2 files
            
          
              0 forks
            
          
              0 comments
            
          
              0 stars
            
          
                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
              
          
      View Usage.md
  
      
    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....

  
## biostar9524046.nf
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)

## biostar9523782.nf
nextflow.enable.dsl=2

/* full path to query directory */
params.qdir="/DIR1"

/* full path to target/database directory */
params.tdir="/DIR2"


workflow {

## release.sh
#!/bin/bash

# https://github.community/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
	/* 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
	import java.io.*;
	import java.util.*;
	public class Biostar9532375 {
	private static class Sequence {
	String name;
	StringBuilder seq=new StringBuilder();
	boolean same(char c1,char c2) {
	if(c1==c2) return true;
	if(c1=='N' \|\| c2=='N') return true;
	return false;
	#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';
	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)
	nextflow.enable.dsl=2

	/* full path to query directory */
	params.qdir="/DIR1"

	/* full path to target/database directory */
	params.tdir="/DIR2"


	workflow {
	#!/bin/bash

	# https://github.community/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