This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# your link goes here | |
link = "https://github.com/knightlab-analyses/qurro-mackerel-analysis/blob/master/AnalysisOutput/qurro-plot.qzv" | |
# note: this will break if a repo/organization or subfolder is named "blob" -- would be ideal to use a fancy regex | |
# to be more precise here | |
print(link.replace("github.com", "raw.githubusercontent.com").replace("/blob/", "/")) | |
# example output link: | |
# https://raw.githubusercontent.com/knightlab-analyses/qurro-mackerel-analysis/master/AnalysisOutput/qurro-plot.qzv |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/bin/bash | |
# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress] | |
# | |
# Deinterleaves a FASTQ file of paired reads into two FASTQ | |
# files specified on the command line. Optionally GZip compresses the output | |
# FASTQ files using pigz if the 3rd command line argument is the word "compress" | |
# | |
# Can deinterleave 100 million paired reads (200 million total | |
# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s) | |
# |