rebrand

.github/workflows/cicd.yml

@@ -66,8 +66,8 @@ jobs:
       uses: svenstaro/upload-release-action@v2
       with:
         repo_token: ${{ secrets.GITHUB_TOKEN }}
-        file: target/release/idseq-dedup${{ matrix.os == 'windows-latest' && '.exe' || '' }}
-        asset_name: idseq-dedup-${{ runner.os }}
+        file: target/release/czid-dedup${{ matrix.os == 'windows-latest' && '.exe' || '' }}
+        asset_name: czid-dedup-${{ runner.os }}
         tag: ${{ github.ref }}
         overwrite: true
 

Cargo.toml

@@ -1,5 +1,5 @@
 [package]
-name = "idseq-dedup"
+name = "czid-dedup"
 version = "0.1.0"
 authors = ["morsecodist <todd@morsecodist.io>"]
 description = "Deduplicates reads from FASTA and FASTQ files"

Readme.md

@@ -1,40 +1,40 @@
-# idseq-dedup
+# czid-dedup
 
-![Rust](https://github.com/chanzuckerberg/idseq-dedup/workflows/CICD/badge.svg) [![codecov](https://codecov.io/gh/chanzuckerberg/idseq-dedup/branch/main/graph/badge.svg?token=LMcriTjfuH)](coverage) [![GitHub license](https://img.shields.io/badge/license-MIT-brightgreen.svg)](https://github.com/chanzuckerberg/idseq-web/blob/master/LICENSE) ![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg)
+![Rust](https://github.com/chanzuckerberg/czid-dedup/workflows/CICD/badge.svg) [![codecov](https://codecov.io/gh/chanzuckerberg/czid-dedup/branch/main/graph/badge.svg?token=LMcriTjfuH)](coverage) [![GitHub license](https://img.shields.io/badge/license-MIT-brightgreen.svg)](https://github.com/chanzuckerberg/czid-web/blob/master/LICENSE) ![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg)
 
-idseq-dedup reads single- or paired-end FASTA or FASTQ files and outputs versions of those files with duplicate reads removed. A duplicate read in this case is a read that is either identical to another read or shares a prefix of length `-l` with another read. Paired reads are only considered identical if both reads (or read prefixes, specified by `-l`) are duplicates to both reads in a previous pair.
+czid-dedup reads single- or paired-end FASTA or FASTQ files and outputs versions of those files with duplicate reads removed. A duplicate read in this case is a read that is either identical to another read or shares a prefix of length `-l` with another read. Paired reads are only considered identical if both reads (or read prefixes, specified by `-l`) are duplicates to both reads in a previous pair.
 
-In addition to the de-duplicated FASTA or FASTQ outputs, idseq-dedup also outputs a cluster file which makes it possible to identify clusters of duplicate reads. The file lists the representative cluster read ID for each initial read ID, where the representative cluster read ID is the read ID that makes it into the output file. If a read is found to be a duplicate of a previous read, it will be filtered out of the FASTA/FASTQ output and paired with the read ID of the previous duplicate read in the cluster output file. Representative cluster read IDs are paired with themselves. The order of the input files is preserved. The representative read will always be the first read of its type.
+In addition to the de-duplicated FASTA or FASTQ outputs, czid-dedup also outputs a cluster file which makes it possible to identify clusters of duplicate reads. The file lists the representative cluster read ID for each initial read ID, where the representative cluster read ID is the read ID that makes it into the output file. If a read is found to be a duplicate of a previous read, it will be filtered out of the FASTA/FASTQ output and paired with the read ID of the previous duplicate read in the cluster output file. Representative cluster read IDs are paired with themselves. The order of the input files is preserved. The representative read will always be the first read of its type.
 
 FASTA/FASTQ parsing provided by [rust-bio](https://github.com/rust-bio/rust-bio).
 
 ## Installation
 
 ### Binary
 
-We release binaries for Linux, MacOS, and Windows. To install one, download the appropriate binary for your operating system from one of our [releases](https://github.com/chanzuckerberg/idseq-dedup/releases/).
+We release binaries for Linux, MacOS, and Windows. To install one, download the appropriate binary for your operating system from one of our [releases](https://github.com/chanzuckerberg/czid-dedup/releases/).
 
 ### From Source
 
 1. [Install rust/cargo](https://www.rust-lang.org/tools/install) if you haven't already
-1. `git clone https://github.com/chanzuckerberg/idseq-dedup.git`
-1. `cd idseq-dedup`
+1. `git clone https://github.com/chanzuckerberg/czid-dedup.git`
+1. `cd czid-dedup`
 1. `cargo build --release`
-1. Your executable will be at `idseq-dedup/target/release/idseq-dedup` (with `.exe` if you're on windows)
+1. Your executable will be at `czid-dedup/target/release/czid-dedup` (with `.exe` if you're on windows)
 
 ## Usage
 
 Run:
 
 ```bash
-idseq-dedup --help
+czid-dedup --help
 ```
 
 for usage information:
 
 ```
 USAGE:
-    idseq-dedup [OPTIONS] --deduped-outputs <deduped-outputs>... --inputs <inputs>...
+    czid-dedup [OPTIONS] --deduped-outputs <deduped-outputs>... --inputs <inputs>...
 
 FLAGS:
     -h, --help       Prints help information
@@ -52,19 +52,19 @@ OPTIONS:
 Deduplicate a single-end FASTA:
 
 ```bash
-idseq-dedup -i my-fasta.fasta -o my-deduped-fasta.fasta
+czid-dedup -i my-fasta.fasta -o my-deduped-fasta.fasta
 ```
 
 Deduplicate a single-end FASTQ (same as FASTA)
 
 ```bash
-idseq-dedup -i my-fastq.fastq -o my-deduped-fastq.fastq
+czid-dedup -i my-fastq.fastq -o my-deduped-fastq.fastq
 ```
 
 Deduplicate paired-end reads (note, inputs are paired to outputs by order not name):
 
 ```bash
-idseq-dedup \
+czid-dedup \
 	-i my-fasta-r1.fasta \
 	-i my-fasta-r2.fasta \
 	-o my-deduped-fasta-r1.fasta \
@@ -74,12 +74,12 @@ idseq-dedup \
 Deduplicate only considering a prefix of length `70`:
 
 ```bash
-idseq-dedup -l 70 -i my-fasta.fasta -o my-deduped-fasta.fasta
+czid-dedup -l 70 -i my-fasta.fasta -o my-deduped-fasta.fasta
 ```
 
 Custom cluster file name:
 
 ```bash
-idseq-dedup -i my-fasta.fasta -o my-deduped-fasta.fasta -c custom-cluster.csv
+czid-dedup -i my-fasta.fasta -o my-deduped-fasta.fasta -c custom-cluster.csv
 ```