This repository has been archived by the owner on Feb 24, 2025. It is now read-only.

fixed errors #2

	name: Task1 QC
	on: [push]

	jobs:
	process_raw:
	runs-on: self-hosted
	steps:
	- name: checkout code and return recently uploaded file in data
	uses: actions/checkout@v2
	- name: get most recent file
	run: \|
	git pull origin main
	data=$(ls -t /data/*.txt \| head -n 1)
	echo "Most recent file: $data"

	- name: set up python
	run: \|
	python -m pip install --upgrade pip
	pip install -r requirements.txt

	- name: parse raw
	run: \|
	// add bash to parse raw data filename, split by '_', and save as local variable
	#!/bin/bash
	filename=$(basename $data)
	IFS='_' read -r sub task version <<< "$filename"
	echo "sub=$sub" >> $GITHUB_ENV
	echo "task=$task" >> $GITHUB_ENV
	echo "version=$version" >> $GITHUB_ENV
	echo "Subject: $sub"
	echo "Task: $task"
	echo "Version: $version"

	- name: convert raw
	run: \|
	mkdir data/${sub}/processed
	python code/ConvertBeh.py -submission ${data} -out data/${sub}/processed -sub ${sub} -task ${task} -taskvers ${version}

	run_qc:
	runs-on: self-hosted
	needs: process_raw
	steps:
	- name: run quality control
	run: python AFqC.py -s data/${sub}/processed/${sub}*.csv -o data/${sub}/ -sub ${sub} \| tee data/${sub}/qc.log

	push:
	runs-on: self-hosted
	needs: run_qc
	steps:
	- name: push results
	run: \|
	git config user.email [email protected]
	git config user.name "Zak Gilliam"
	git add -A
	git commit -m "QC results for ${sub}"
	git push origin main

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