ChangeLog.md

Changelog

1.4.1 (2025-2-05)

• Fixed a bug in churros_genPvalwig that required old names of bigWig files.
• Fixed bugs in the scripts in the tutorial directory.
• Corrected several mistakes in the manual.

1.4.0 (2025-1-04)

• Fixed a bug in churros_callpeak that did not use the -f BEDPE option in MACS2 when paired end samples are supplied.
• Fixed an installation of fgsea required by ChIPseeker and clusterProfiler.

1.3.0 (2024-10-29)

• Starting with this version, Churros can accept BAM files as input in samplelist.txt instead of FASTQ files.
• Modified churros to abort when an error occurs in fastqc to detect cases where there are problems with the FASTQ file.

1.2.2 (2024-10-02)

• Updated SAMtools from 1.19.2 to 1.21
• Updated SRA Toolkit from 3.0.10 to v3.1.1
• Added parallel-fastq-dump
• Added Arabidopsis thaliana genome (TAIR10) in download_genomedata.sh.

1.2.1 (2024-9-25)

• Fixed a bug in churros where the last line of the samplelist was not read correctly if there was no newline character at the end.
• Modified churros to allow space-separated samplelist.txt.
• Fixed an issue where several R tools were unusable since v1.2.0.
• Added scripts for DNA methylation analysis in the tutorial directory.

1.2.0 (2024-8-25)

• Fixed a bug in SSP and DROMPAplus that causes a memory error when the input file has long reads (>200 bp).

1.1.2 (2024-8-10)

• Fixed a bug in churros_compare that caused the sample labels in drompa+.macspeak.PCSHARP.100.pdf to be displayed incorrectly if the input samples were not specified in samplepairlist.txt.

1.1.1 (2024-7-18)

• Fixed a bug in churros_compare that had an error when comparing bigWig files.

1.1.0 (2024-7-02)

• Fixed a bug in build-index.sh that did not accept indexing for bismark.
• Added methylKit for RRBS analysis.
• Added MEDIPS for MeDIP-seq analysis.
• Added abismal for WGBS analysis.
• Added MethPipe for WGBS analysis.

1.0.0 (2024-5-19)

• Added churros_mapping_spikein for spike-in normalization.
• Changed Python environment from conda to micromamba (/opt/micromamba)

0.13.2 (2024-4-6)

• Big fix when no input samples are specified in samplepairlist.txt.

0.13.1 (2024-3-29)

• Added to churros the function that checks if the samples shown in samplepairlist.txt are in samplelist.txt.
• Fixed a bug in churros when applying single-end reads with the --fastqtrimming option.

0.13.0 (2024-3-18)

• Modified fastp execution to handle paired-end FASTQ files at a same time
• Added --nofilter, --fastqtrimming and --parse2wigparam options to churros
• Added -N: do not filter PCR duplication and -Q: additional parameter for parse2wig+ options to churros_mapping
• Added -e and -x options to churros_genPvalwig to generate different wig files for visualization.
• Added n: do not filter PCR duplication and -P: other options options to parse2wig+.sh.
• Added mptable.UCSC.T2T.28mer.flen150.txt and mptable.UCSC.T2T.36mer.flen150.txt in SSP/data/mptable.
• Added the ideogram file for the T2T genome in DROMPAplus/data/ideogram.
• Fixed a bug in churros_mapping and churros_callpeak that did not handle the name of the mapfiles correctly when passing additional parameters to bowtie2.sh.
• Fixed a bug in churros_peakcall that did not create macs/samplepairlist.txt correctly when input samples were not specified.
• Updated churros_mapping to show header correctly for paired-end FASTQ files.
• Modified download_genomedata.sh to download the reference file of the T2T genome.
• Added ATACseqQC for quality check of ATAC-seq data
• Added TFBSTools for motif search
• Updated chromap from v0.2.5 to v0.2.6
• Updated SSP and DROMPAplus to modify parsestats4DROMPAplus.pl
• Fixed the warning of xargs in churros_callpeak
• download_genomedata.sh:
  • Updated the version of Ensemble data from 106 to 111.
  • Added Medaka genome.
• Changed churros_visualize to allow ChIP samples even without the input sample when the -G option is specified.
• Added the -n: do not filter PCR duplicate option to churros_genPvalwig.

0.12.2 (2024-3-5)

• Fixed a bug in churros that did not output the mapping statistics file correctly.
• Fixed a bug in churros that caused the header line in the stats file to be incorrect for paired-end files.
• churros_genPvalwig: Added the -e and -x options to output different distribution files as well.
• Added csv2xlsx.pl to convert churros.QCstats.tsv to churros.QCstats.xlsx.

0.12.1 (2024-3-3)

• Fixed a bug in download_genomedata.sh that did not download the genome data correctly.
• Install MS core fonts (ttf-mscorefonts-installer)

0.12.0 (2024-2-25)

• Added Cobind for evaluating overlap of peaks
• Fixed a bug in churros_mapping where the -n option was not recognized.

0.11.1 (2024-2-21)

• Install MS core fonts (ttf-mscorefonts-installer)

0.11.0 (2024-2-3)

• Added checkQC.py for checking the quality of the input ChIP-seq samples
  • checkQC.py outputs the warnings in Churros_result/<build>/QCcheck.log if the samples do not meet the quality criteria.
• Installed sudo
• Updated Miniconda from Python 3.9 to Python 3.10
• Updated Bowtie2 from v2.4.5 to v2.5.3
• Updated chromap from v0.2.4 to v0.2.5
• Updated ChromHMM from v1.24 to v1.25
• Updated ChromImpute from v1.0.3 to v1.0.5

0.10.9 (2024-1-30)

• Added STARE for enhancer-promoter analysis
• Updated SAMtools from 1.17 to 1.19.2
• Updated SRAtoolkit from 3.0.2 to 3.0.10

0.10.8 (2024-1-12)

• Added a script generate_samplelist_from_SRA.py that generates the sample list from SraExperimentPackage.xml and SraRunTable.txt.

0.10.7 (2023-12-31)

• Updated SSP (v1.3.0 -> v1.3.1) and DROMPA+ (v1.18.0 -> v1.18.1).
• Update Manual

0.10.6 (2023-12-26)

• Added warning messages in churros when there are the same raws in samplelist.txt.

0.10.5 (2023-12-21)

• Bug fix in gen_samplelist.sh

0.10.4 (2023-12-12)

• Changed the directory of the fastqc and fastp output files from Churros_result/$build to Churros_result/ because they are independent of the genome build.

0.10.3 (2023-11-06)

• Added convert_SraRunTable_to_samplelist.py that makes samplelist.txt from SraRunTable.txt

0.10.2 (2023-10-07)

• Omited the creation of PDF files for WG and p-value distributions when no input sample is provided

0.10.1 (2023-10-01)

• Fixed bug occurring when no input sample is provided

0.10.0 (2023-08-04)

• Added churros_classheat function
• Added HOMER for Motif analysis

0.9.3 (2023-07-06)

• Added Genometable file for S.pombe
• Modified ssp.sh to accept mptable as an argument
• Modified churros_mapping to use mptable in Ddir/mappability_Mosaics_kmer
• Fixed bug in calculate_mappability_mosaics.sh
• Fixed bug in chrros_mapping stats command for paired-end ChIP-seq data

0.9.2 (2023-06-23)

• Updated ChromHMM from v1.23 to v1.24

0.9.1 (2023-05-11)

• Removed /root/.cpanm/work directory to avoid the user id error

0.9.0 (2023-04-25)

• Changed base image from rnakato/database to rnakato/mapping for simplified installation
• Added GenMap for fast genome mappability computation
• Added utility scripts gen_samplelist.sh and gen_samplepairlist.sh for creating sample lists

0.8.0 (2023-02-19)

• Updated gene annotation for T2T genome
• Updated DROMPAplus to v1.17.1
• Fixed bug in calculate_mappability_mosaics.sh

0.7.1 (2023-02-10)

• Fixed bug in macs2.sh

0.7.0 (2023-02-08)

• Changed default value for peak-calling in MACS2 from --nomodel to default settings

0.6.0 (2023-01-30)

• Added TOBIAS for differential ATAC-seq analysis
• Added STITCHIT for link regulatory elements to genes

0.5.0 (2023-01-07)

• Added Bismark and the custom script Bismark.sh for bisulfite sequencing analysis
• Added TrimGalore for adapter and quality trimming of FastQ files
• Added Cutadapt for adapter trimming of FastQ files

0.4.1 (2022-11-24)

• Added this ChangeLog
• Fixed bug: removed a bug duplicate 'row.names' are not allowed in churros_compare
• Updated DROMPAplus to v1.17.0

0.4.0

• Public release
• Updated manual