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View GitHub Profile
View revcomplement.dot
digraph "DNA Base Complement Workflow" {
rankdir=LR;
graph [fontname="Arial",fontsize=13,color="#384A52",fontcolor="#384A52"];
node [fontname="Arial",fontsize=11,color="#384A52",fontcolor="#384A52",fillcolor="#EFF2F5",shape=box,style=filled];
edge [fontname="Arial",fontsize=9, color="#384A52",fontcolor="#384A52"];
"Base Complement" [shape=box];
"Make DNA" [shape=box];
"Reverse" [shape=box];
"Base Complement" -> "Reverse" [taillabel="compl", headlabel="in"];
"Make DNA" -> "Base Complement" [taillabel="dna", headlabel="in"];
View resequencing.dot
digraph "resequencing_workflow" {
rankdir=LR;
graph [fontname="Arial",fontsize=13,color="#384A52",fontcolor="#384A52"];
node [fontname="Arial",fontsize=11,color="#384A52",fontcolor="#384A52",fillcolor="#EFF2F5",shape=box,style=filled];
edge [fontname="Arial",fontsize=9, color="#384A52",fontcolor="#384A52"];
"bwa_aln_NA06984_1" [shape=box];
"bwa_aln_NA06984_2" [shape=box];
"bwa_aln_NA12489_1" [shape=box];
"bwa_aln_NA12489_2" [shape=box];
"download_fastq_NA06984_1" [shape=box];
View command_to_parameters_example.go
package main
import (
sp "github.com/scipipe/scipipe"
spc "github.com/scipipe/scipipe/components"
)
func main() {
wf := sp.NewWorkflow("example_workflow", 4)
View show_test_coverage_dotnetcore.sh
#!/bin/bash
# ---------------------------------------------------------------------
# Generate test coverage for .Net core 2 projects.
# ---------------------------------------------------------------------
# Author: Samuel Lampa
#
# This script is supposed to be run in a Windows bash-environment such
# as MSYS2 (See this post for a guide on how to set up one:
# https://bionics.it/posts/linux-like-non-wsl-terminal-env-on-windows)
#
View scipipe_late.go
package main
import (
sp "github.com/scipipe/scipipe"
)
func main() {
wf := sp.NewWorkflow("hello_world", 4)
hello := wf.NewProc("hello", "echo 'Hello ' > {o:out}")
View scipipe_early.go
package main
import (
sp "github.com/samuell/scipipe"
)
func main() {
hello := sp.Sh("echo foo > {o:out}")
hello.OutPathFuncs["out"] = func() string {
return "hello.txt"
View scipipe_proc_init_api.go
// -------------------------
// Option A
// -------------------------
merge := wf.NewProc("merge_"+ind, "bwa sampe {i:ref} {i:sai1} {i:sai2} {i:fq1} {i:fq2} > {o:merged} # {i:refdone} {p:ind}",
merge.InParam("ind").FromStr(ind)
merge.In("ref").From(ungzipRef.Out("out"))
merge.In("refdone").From(indexRef.Out("done"))
merge.In("sai1").From(outs[ind]["1"]["sai"])
merge.In("sai2").From(outs[ind]["2"]["sai"])
merge.In("fq1").From(outs[ind]["1"]["fastq"])
View grandparent_prolog_rule.pro
parent(mark, jim).
parent(sam, mark).
grandparent(Grandparent, Child) :-
parent(Grandparent, Parent),
parent(Parent, Child).
View test.md
SELECT ?s ?p ?o WHERE { ?s ?p ?o }
View drugbank_xml_to_tsv_with_scipipe.go
package main
import (
"encoding/csv"
"encoding/xml"
"io"
"os"
sp "github.com/scipipe/scipipe"
)
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