lindenb

sampleAndBam

returns an array (sample,bam) from a bam or a file.

it gets the SAM header from a BAM or a CRAM and extracts the identifier from the sam read groups https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMReadGroupRecord.html

Would be the equivalent of:

find "${params.bamdir}" -type f -name "*.bam" | while read F

lindenb

bedIn = file( params.bed )
reference = file( params.reference )

bamChannel = Channel.fromPath( params.bams ).
		splitCsv(header: false,sep:',',strip:true).
		map{T->T[0]}

String jvarkit(String tool) {
	return "/path/to/jvarkit-git/dist/"+tool+".jar";
	}

lindenb

  
reference=file("${params.reference}")
bams=file("${params.bams}")

process getChromosomes {
	tag "get chromosomes from ${ref}"
	executor 'local'
	input:
		file ref from reference
	output:

lindenb

/**
https://www.biostars.org/p/379454/#379505

Code golf: detecting homopolymers of length N in the (human) genome

Author: Pierre Lindenbaum

compilation:

 gcc -O3 -Wall -o biostar379454 biostar379454.c

lindenb

wget -O - -q "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=gb&retmode=xml&id=NZ_AOLM01000025"   | xsltproc --novalid biostar378467.xsl - > out.tsv

lindenb

import java.net.*;
import java.util.*;
import java.io.*;
import org.w3c.dom.*;
import javax.xml.xpath.*;
import javax.xml.parsers.*;
public class Biostar376339 {
public static void main(final String args[]) {
try {
String urlstr="https://www.uniprot.org/uniprot/P0AD86.xml";

lindenb

url:  http://hgdownload.soe.ucsc.edu/hubs/gtexAnalysis/hg19/gtexAwgAseCombined.bb
description: Allele-Specific Expression Combined Sites from GTEx Analysis
name: GTExASCombined

lindenb

/**
Author: Pierre Lindenbaum PhD. 2019

This tools calculate the mean depth of a bam (ignoring the non-covered bases)
and output a BED file of the regions covered more than mean-depth*FACTOR

compilation: gcc -o a.out -O3 -Wall -I../htslib highcov.c -L../htslib  -lm -lpthread -lhts -lz -llzma -lbz2

 */
 

lindenb

process mergeFastq {
tag "merging ${sample}"

input:
	set sample,fastqs from Channel.fromPath(params.input).splitCsv(header:false,sep:'\t',skip:1).groupTuple(by:0)
output:
	file("${sample}.fastq")
script:

"""

lindenb

/**
Pierre Lindenbaum, 2019

gcc -o a.out -O3 -Wall -Isamtools/include discordant.c  -Lsamtools/lib -lhts

*/
#include <stdio.h>
#include <stdlib.h>
#include <errno.h>
#include <string.h>