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name: fq_subsample | ||
description: fq subsample outputs a subset of records from single or paired FASTQ files. | ||
keywords: [fastq, subsample, subset] | ||
links: | ||
homepage: https://github.com/stjude-rust-labs/fq/blob/master/README.md | ||
documentation: https://github.com/stjude-rust-labs/fq/blob/master/README.md | ||
repository: https://github.com/stjude-rust-labs/fq | ||
license: MIT | ||
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argument_groups: | ||
- name: "Input" | ||
arguments: | ||
- name: "--input_1" | ||
type: file | ||
required: true | ||
description: First input fastq file to subsample. Accepts both raw and gzipped FASTQ inputs. | ||
- name: "--input_2" | ||
type: file | ||
description: Second input fastq files to subsample. Accepts both raw and gzipped FASTQ inputs. | ||
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- name: "Output" | ||
arguments: | ||
- name: "--output_1" | ||
type: file | ||
direction: output | ||
default: $id.read_1.subsampled.fastq | ||
description: Sampled read 1 fastq files. Output will be gzipped if ends in `.gz`. | ||
- name: "--output_2" | ||
type: file | ||
direction: output | ||
default: $id.read_2.subsampled.fastq | ||
description: Sampled read 2 fastq files. Output will be gzipped if ends in `.gz`. | ||
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- name: "Options" | ||
arguments: | ||
- name: "--probability" | ||
type: double | ||
description: The probability a record is kept, as a percentage (0.0, 1.0). Cannot be used with `record-count` | ||
- name: "--record_count" | ||
type: integer | ||
description: The exact number of records to keep. Cannot be used with `probability` | ||
- name: "--seed" | ||
type: integer | ||
description: Seed to use for the random number generator | ||
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resources: | ||
- type: bash_script | ||
path: script.sh | ||
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test_resources: | ||
- type: bash_script | ||
path: test.sh | ||
- path: test_data | ||
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engines: | ||
- type: docker | ||
image: ubuntu:22.04 | ||
setup: | ||
- type: docker | ||
env: | ||
- TZ Europe/Brussels | ||
run: | | ||
ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && \ | ||
apt-get update && \ | ||
apt-get install -y --no-install-recommends build-essential git-all curl && \ | ||
curl https://sh.rustup.rs -sSf | sh -s -- -y && \ | ||
. "$HOME/.cargo/env" && \ | ||
git clone --depth 1 --branch v0.11.0 https://github.com/stjude-rust-labs/fq.git && \ | ||
mv fq /usr/local/ && cd /usr/local/fq && \ | ||
cargo install --locked --path . && \ | ||
mv /usr/local/fq/target/release/fq /usr/local/bin/ | ||
runners: | ||
- type: executable | ||
- type: nextflow |
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``` | ||
fq subsample -h | ||
``` | ||
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Outputs a subset of records | ||
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Usage: fq subsample [OPTIONS] --r1-dst <R1_DST> <--probability <PROBABILITY>|--record-count <RECORD_COUNT>> <R1_SRC> [R2_SRC] | ||
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Arguments: | ||
<R1_SRC> Read 1 source. Accepts both raw and gzipped FASTQ inputs | ||
[R2_SRC] Read 2 source. Accepts both raw and gzipped FASTQ inputs | ||
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Options: | ||
-p, --probability <PROBABILITY> The probability a record is kept, as a percentage (0.0, 1.0). Cannot be used with `record-count` | ||
-n, --record-count <RECORD_COUNT> The exact number of records to keep. Cannot be used with `probability` | ||
-s, --seed <SEED> Seed to use for the random number generator | ||
--r1-dst <R1_DST> Read 1 destination. Output will be gzipped if ends in `.gz` | ||
--r2-dst <R2_DST> Read 2 destination. Output will be gzipped if ends in `.gz` | ||
-h, --help Print help | ||
-V, --version |
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#!/bin/bash | ||
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## VIASH START | ||
## VIASH END | ||
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set -eo pipefail | ||
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required_args=("-p" "--probability" "-n" "--record_count") | ||
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# exclusive OR for required arguments $par_probability and $par_record_count | ||
if [[ -n $par_probability && -n $par_record_count ]] || [[ -z $par_probability && -z $par_record_count ]]; then | ||
echo "FQ/SUBSAMPLE requires either --probability or --record_count to be specified" | ||
exit 1 | ||
fi | ||
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fq subsample \ | ||
${par_output_1:+--r1-dst "${par_output_1}"} \ | ||
${par_output_2:+--r2-dst "${par_output_2}"} \ | ||
${par_probability:+--probability "${par_probability}"} \ | ||
${par_record_count:+--record-count "${par_record_count}"} \ | ||
${par_seed:+--seed "${par_seed}"} \ | ||
${par_input_1} \ | ||
${par_input_2} | ||
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#!/bin/bash | ||
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echo ">>> Testing $meta_executable" | ||
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echo ">>> Testing for paired-end reads" | ||
"$meta_executable" \ | ||
--input_1 $meta_resources_dir/test_data/a.1.fastq \ | ||
--input_2 $meta_resources_dir/test_data/a.1.fastq \ | ||
--record_count 3 \ | ||
--seed 1 \ | ||
--output_1 a.1.subsampled.fastq \ | ||
--output_2 a.2.subsampled.fastq | ||
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echo ">> Checking if the correct files are present" | ||
[ ! -f "a.1.subsampled.fastq" ] && echo "Subsampled FASTQ file for read 1 is missing!" && exit 1 | ||
[ ! -s "a.1.subsampled.fastq" ] && echo "Subsampled FASTQ file is empty!" && exit 1 | ||
[ ! -f "a.2.subsampled.fastq" ] && echo "Subsampled FASTQ file for read 2 is missing" && exit 1 | ||
[ ! -s "a.2.subsampled.fastq" ] && echo "Subsampled FASTQ file is empty" && exit 1 | ||
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rm a.1.subsampled.fastq a.2.subsampled.fastq | ||
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echo ">>> Testing for single-end reads" | ||
"$meta_executable" \ | ||
--input_1 $meta_resources_dir/test_data/a.1.fastq \ | ||
--input_2 $meta_resources_dir/test_data/a.1.fastq \ | ||
--record_count 3 \ | ||
--seed 1 \ | ||
--output_1 a.1.subsampled.fastq | ||
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echo ">> Checking if the correct files are present" | ||
[ ! -f "a.1.subsampled.fastq" ] && echo "Subsampled FASTQ file is missing" && exit 1 | ||
[ ! -s "a.1.subsampled.fastq" ] && echo "Subsampled FASTQ file is empty" && exit 1 | ||
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echo ">>> Tests finished successfully" | ||
exit 0 | ||
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ACGGCAT | ||
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CATACGG | ||
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GCATACG | ||
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@1 | ||
ACGGCAT | ||
+ | ||
!!!!!!! | ||
@2 | ||
TACGGCA | ||
+ | ||
!!!!!!! | ||
@3 | ||
ATACGGC | ||
+ | ||
!!!!!!! | ||
@4 | ||
CATACGG | ||
+ | ||
!!!!!!! | ||
@5 | ||
GCATACG | ||
+ | ||
!!!!!!! |