PREREQUISITES: 
The pipeline is configured to run on a SLURM based cluster with modules. The pipeline is built in nextflow (nextflow.io). It has been tested using nextflow/0.30.2. Earlier versions of nextflow will not work.
This pipeline should run on other system architectures, but will require some customization.

Modules / Software versions:
R/3.5.2
bamtools/2.5.1
bedtools/2.27.1
deeptools/3.0.1
kallisto/0.45.0
macs/2.1.2
meme/5.0.1
nextflow/0.30.2
picard/2.17.11
picard/2.9.2
samtools/1.8
samtools/1.9
sratoolkit/2.9.2
ucsc/373

R packages:
corrplot
data.table
dplyr
extrafont
factoextra
ggcorrplot
ggfortify
ggplot2
ggpmisc
ggpubr
ggrepel
grid
gridExtra
leaps
lsr
numform
pROC
plyr
png
preprocessCore
purrr
reshape2
scales
tictoc
ShortRead

SYSTEM REQUIREMENTS:
~1Tb free space; Pipe will generate generate up to 1 Tb of temp files. 
Other requirements are encoded in nextflow processes. 

REQUIRED FILES:
This folder contains the accessory data required to run the pipeline.

In addition to these files, the pipeline requires aligned BAM files (tested only with BWA 0.7.12 alignment) as follows:

Nomenclature for aligned BAM files:
SS.RN.MMMMMM.anything.bam
SS = stage (LE,ZY,EP,LP,DI)
RN = round (R1, R2)
MMMMMM = histone modification name (must be exactly as below (case sensitive))
* Note: the names should be retained from the fastq.gz files in the GEO record (GSM121760)

Aligned bam files should be located in the following folders:
/data/timeCourse
** These files should be aligned to the mm10 genome with K-MetStat panel sequences included.
** This genome can be obtained using the genomeFiles/getGenomeFiles.sh script
DI.R1.H3K4me3.ChIPSeq.mm10_KmetStat.bam
DI.R1.H3K9Ac.ChIPSeq.mm10_KmetStat.bam
DI.R1.input.ChIPSeq.mm10_KmetStat.bam
DI.R2.H3K4me3.ChIPSeq.mm10_KmetStat.bam
DI.R2.H3K9Ac.ChIPSeq.mm10_KmetStat.bam
DI.R2.abK4me.ChIPSeq.mm10_KmetStat.bam
DI.R2.input.ChIPSeq.mm10_KmetStat.bam
EP.R1.H3K4me3.ChIPSeq.mm10_KmetStat.bam
EP.R1.H3K9Ac.ChIPSeq.mm10_KmetStat.bam
EP.R1.input.ChIPSeq.mm10_KmetStat.bam
EP.R2.H3K4me3.ChIPSeq.mm10_KmetStat.bam
EP.R2.H3K9Ac.ChIPSeq.mm10_KmetStat.bam
EP.R2.abK4me.ChIPSeq.mm10_KmetStat.bam
EP.R2.input.ChIPSeq.mm10_KmetStat.bam
LE.R1.H3K4me3.ChIPSeq.mm10_KmetStat.bam
LE.R1.H3K9Ac.ChIPSeq.mm10_KmetStat.bam
LE.R1.input.ChIPSeq.mm10_KmetStat.bam
LE.R2.H3K4me3.ChIPSeq.mm10_KmetStat.bam
LE.R2.H3K9Ac.ChIPSeq.mm10_KmetStat.bam
LE.R2.abK4me.ChIPSeq.mm10_KmetStat.bam
LE.R2.input.ChIPSeq.mm10_KmetStat.bam
LP.R1.H3K4me3.ChIPSeq.mm10_KmetStat.bam
LP.R1.H3K9Ac.ChIPSeq.mm10_KmetStat.bam
LP.R1.input.ChIPSeq.mm10_KmetStat.bam
LP.R2.H3K4me3.ChIPSeq.mm10_KmetStat.bam
LP.R2.H3K9Ac.ChIPSeq.mm10_KmetStat.bam
LP.R2.abK4me.ChIPSeq.mm10_KmetStat.bam
LP.R2.input.ChIPSeq.mm10_KmetStat.bam
ZY.R1.H3K4me3.ChIPSeq.mm10_KmetStat.bam
ZY.R1.H3K9Ac.ChIPSeq.mm10_KmetStat.bam
ZY.R1.input.ChIPSeq.mm10_KmetStat.bam
ZY.R2.H3K4me3.ChIPSeq.mm10_KmetStat.bam
ZY.R2.H3K9Ac.ChIPSeq.mm10_KmetStat.bam
ZY.R2.abK4me.ChIPSeq.mm10_KmetStat.bam
ZY.R2.input.ChIPSeq.mm10_KmetStat.bam

/data/histmods:
H3K27ac_SCP3pos_H1Tneg.bam
H3K27me1_SCP3pos_H1Tneg.bam
H3K27me3_SCP3pos_H1Tneg.bam
H3K36me3_SCP3pos_H1Tneg.bam
H3K4ac_SCP3pos_H1Tneg.bam
H3K4me1_SCP3pos_H1Tneg.bam
H3K4me2_SCP3pos_H1Tneg.bam
H3K79me1_SCP3pos_H1Tneg.bam
H3K79me3_SCP3pos_H1Tneg.bam
H3K9ac_SCP3pos_H1Tneg.bam
H3K9me2_SCP3pos_H1Tneg.bam
H3K9me3_SCP3pos_H1Tneg.bam
H3_SCP3pos_H1Tneg.bam
H4K12ac_SCP3pos_H1Tneg.bam
H4K20me3_SCP3pos_H1Tneg.bam
H4K8ac_SCP3pos_H1Tneg.bam
H4ac5_SCP3pos_H1Tneg.bam
IgG_SCP3pos_H1Tneg.bam
Input_SCP3pos_H1Tneg.bam
abK4me_SCP3pos_H1Tneg.bam
*NOTE: H3K4me3_SCP3pos_H1Tneg.bam will be built from ZY.R1.H3K4me3 bam file

Genome files: 
The pipeline requires the following files in the accessoryFiles/genomeFiles folder:
mm10_genome.fa
mm10_genome.fa.fai
mm10_KmetStat_genome.fa
mm10_KmetStat_genome.fa.fai

These files can be generated using the following script: 
accessoryFiles/genomeFiles/getGenomeFiles.sh

----------------------------------------------------------------------------------------------
RUNNING THE PIPELINE:
----------------------------------------------------------------------------------------------
nextflow run -with-timeline
             -with-trace
             -with-report
             -c {accessoryFilesFolder}/nextflowConfig/nextflow.config
             {accessoryFilesFolder}/scripts/analyticPipe_LamEtAl_NatComm2019.groovy
             --projectdir    {project folder <<FULL PATH>>}
             --outdir        {output folder  <<FULL PATH>>}
             --timecoursedir {timecourse BAM folder <<FULL PATH>>}
             --allHMdir      {SCP3pos H1tneg histone modifications BAM folder <<FULL PATH>>}

{accessoryFilesFolder}      : downloaded folder with accessory files (location of this README)
{project folder}            : parent folder of {accessoryFilesFolder}
{output folder}             : location for output files
{timeCourse BAM folder}     : location of all aligned BAM files from experiments in 5 MPI populations (see above)
{SCP3pos H1tneg BAM folder} : location of all aligned BAM files from experiments in SCP3pos H1tneg nuclei (see above)