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Pierre Lindenbaum lindenb

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View cromwell.log
$ 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
lindenb / .gitignore
Last active Nov 20, 2020
a basic GWAK extension generating the reverse complement of a DNA sequence
View .gitignore
*.o
*.so
*~
gawk-*
View test.html
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Sequence Braiding</title>
<meta name="description" content="">
<meta name="author" content="">
@lindenb
lindenb / Makefile
Last active Oct 6, 2020
test nextflow dsl2.
View Makefile
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
lindenb / Usage.md
Created Sep 10, 2020
Question: is there any way to filter NCBI datasets by sample type?
View Usage.md
$ 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
View biostar441624.txt
http://www.ebi.ac.uk/efo/EFO_0003898 ankylosing spondylitis
http://www.ebi.ac.uk/efo/EFO_0000783 myositis
http://www.ebi.ac.uk/efo/EFO_1001806 macrophage activation syndrome
http://www.ebi.ac.uk/efo/EFO_1001807 malacoplakia
http://www.ebi.ac.uk/efo/EFO_1000719 juvenile dermatitis herpetiformis
http://www.orpha.net/ORDO/Orphanet_602 Distal myopathy, Nonaka type
http://www.orpha.net/ORDO/Orphanet_2841 Familial benign chronic pemphigus
http://www.ebi.ac.uk/efo/EFO_0005676 Autoimmune Hepatitis
http://www.ebi.ac.uk/efo/EFO_0009313 Linear IgA Dermatosis
http://www.ebi.ac.uk/efo/EFO_0000540 immune system disease
@lindenb
lindenb / finddups.nf
Created Mar 4, 2020
workflow nextflow finding duplicated files and creating a bash script to replace the duplicate with a symbolic link
View finddups.nf
params.directories="."
params.headsize=100000
params.extensions="bam bai"
params.help=false
params.extrafind=""
params.lines = 1000
params.publishDir="."
def helpMessage() {
log.info"""
@lindenb
lindenb / bam2cram.nf
Created Mar 4, 2020
BAM to CRAM workflow . bam cram reference fasta nextflow nf
View bam2cram.nf
params.directories="."
params.help=false
params.references=""
params.prefix=""
params.publishDir="."
params.extrafind=""
references = file(params.references)
def helpMessage() {
@lindenb
lindenb / fastq2ucram.nf
Last active Feb 29, 2020
fastq2ucram fastq to ucram nextflow cram bam fastq
View fastq2ucram.nf
params.directories="."
params.help=false
params.center="Nantes"
params.reference=""
params.prefix=""
params.publishDir="."
def helpMessage() {
log.info"""
@lindenb
lindenb / roh.nf
Created Jan 23, 2020
nextflow workflow for 'bcftools roh' . bioinformatics autozygosity vcf cnv
View roh.nf
params.prefix="output."
params.vcf=""
params.help=false
params.rohopts=" --rec-rate 100 --skip-indels "
params.pedigree = "NO_PED"
def helpMessage() {
log.info"""
=========================================