<commit_before>#!/bin/bash

# Check whether the md5 signature matches the original one
./001_md5.sh rawdata > out.001

# TODO Control quality of the raw reads
./002_fastqc.sh rawdata '*.fastq.gz' fastqc 12 > out.002

# TODO Collate the output of FastQC in a friendly CSV file
./003_fastqc_summarisation.sh rawdata > out.003

# Merge all paired Fastq files
./004_merge_fastq.sh rawdata rawdata/Merged 12 > out.004

# TODO Control quality of the merged raw reads
#005

# TODO Collate the output of FastQC in a friendly CSV file
#006

# TODO Trim adapter and low-quality bases
./007_trimgalore.sh

# TODO Control quality of the trimmed reads
#008

# TODO Collate the output of FastQC in a friendly CSV file
#009

# TODO Collate trimming statistics
./010_trimgalore_summarisation.sh trimgalore > out.010

# TODO Align trimmed reads of bisulfite libraries
./011_bismark.sh bostaurus trimgalore bismark 4 tmp_bismark > out.011<commit_msg>Updated master script<commit_after>#!/bin/bash

# Check whether the md5 signature matches the original one
./001_md5.sh rawdata > out.001

# TODO Control quality of the raw reads
./002_fastqc.sh rawdata '*.fastq.gz' fastqc 12 > out.002

# TODO Collate the output of FastQC in a friendly CSV file
./003_fastqc_summarisation.sh rawdata > out.003

# Merge all paired Fastq files
./004_merge_fastq.sh rawdata rawdata/Merged 12 > out.004

# TODO Control quality of the merged raw reads
#005

# TODO Collate the output of FastQC in a friendly CSV file
#006

# Trim adapter and low-quality bases
./007_trimgalore.sh trimgalore 12 rawdata/Merged > out.007

# TODO Control quality of the trimmed reads
#008

# TODO Collate the output of FastQC in a friendly CSV file
#009

# Collate trimming statistics
./010_trimgalore_summarisation.sh trimgalore > out.010

# TODO Align trimmed reads of bisulfite libraries
./011_bismark.sh bostaurus trimgalore bismark 4 tmp_bismark > out.011

# TODO Control quality of the aligned reads
#012

# TODO Collate the output of FastQC in a friendly CSV file
#013

# Collate alignment statistics
./014_bismark_summarisation.sh bismark > out.014

# Deduplicate aligned reads / pairs
./015_deduplicate.sh bismark 8 > out.015

# TODO Control quality of the deduplicated reads
#016

# TODO Collate the output of FastQC in a friendly CSV file
#017

# Extract methylation calls from deduplicated aligned reads / pairs
./018_extractor.sh bismark extract 8 > out.018








{'fraction_non_alphanumeric': 0.06407606448945845, 'fraction_numerical': 0.06324927656056221, 'mean_word_length': 4.105485232067511, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 19, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2599783', 'n_tokens_mistral': 913, 'n_tokens_neox': 758, 'n_words': 308}